WorldWideScience

Sample records for surface science molecular

  1. Molecular surface science of heterogeneous catalysis. History and perspective

    International Nuclear Information System (INIS)

    Somorjai, G.A.

    1983-08-01

    A personal account is given of how the author became involved with modern surface science and how it was employed for studies of the chemistry of surfaces and heterogeneous catalysis. New techniques were developed for studying the properties of the surface monolayers: Auger electron spectroscopy, LEED, XPS, molecular beam surface scattering, etc. An apparatus was developed and used to study hydrocarbon conversion reactions on Pt, CO hydrogenation on Rh and Fe, and NH 3 synthesis on Fe. A model has been developed for the working Pt reforming catalyst. The three molecular ingredients that control catalytic properties are atomic surface structure, an active carbonaceous deposit, and the proper oxidation state of surface atoms. 40 references, 21 figures

  2. Molecular surface science of heterogeneous catalysis. History and perspective

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.

    1983-08-01

    A personal account is given of how the author became involved with modern surface science and how it was employed for studies of the chemistry of surfaces and heterogeneous catalysis. New techniques were developed for studying the properties of the surface monolayers: Auger electron spectroscopy, LEED, XPS, molecular beam surface scattering, etc. An apparatus was developed and used to study hydrocarbon conversion reactions on Pt, CO hydrogenation on Rh and Fe, and NH/sub 3/ synthesis on Fe. A model has been developed for the working Pt reforming catalyst. The three molecular ingredients that control catalytic properties are atomic surface structure, an active carbonaceous deposit, and the proper oxidation state of surface atoms. 40 references, 21 figures. (DLC)

  3. Molecular metal catalysts on supports: organometallic chemistry meets surface science.

    Science.gov (United States)

    Serna, Pedro; Gates, Bruce C

    2014-08-19

    -support bonding and structure, which identify the supports as ligands with electron-donor properties that influence reactivity and catalysis. Each of the catalyst design variables has been varied independently, illustrated by mononuclear and tetranuclear iridium on zeolite HY and on MgO and by isostructural rhodium and iridium (diethylene or dicarbonyl) complexes on these supports. The data provide examples resolving the roles of the catalyst design variables and place the catalysis science on a firm foundation of organometallic chemistry linked with surface science. Supported molecular catalysts offer the advantages of characterization in the absence of solvents and with surface-science methods that do not require ultrahigh vacuum. Families of supported metal complexes have been made by replacement of ligands with others from the gas phase. Spectroscopically identified catalytic reaction intermediates help to elucidate catalyst performance and guide design. The methods are illustrated for supported complexes and clusters of rhodium, iridium, osmium, and gold used to catalyze reactions of small molecules that facilitate identification of the ligands present during catalysis: alkene dimerization and hydrogenation, H-D exchange in the reaction of H2 with D2, and CO oxidation. The approach is illustrated with the discovery of a highly active and selective MgO-supported rhodium carbonyl dimer catalyst for hydrogenation of 1,3-butadiene to give butenes.

  4. Molecular sciences

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    The research in molecular sciences summarized includes photochemistry, radiation chemistry, geophysics, electromechanics, heavy-element oxidizers , heavy element chemistry collisions, atoms, organic solids. A list of publications is included

  5. A molecular surface science study of the structure of adsorbates on surfaces: Importance to lubrication

    International Nuclear Information System (INIS)

    Mate, C.M.

    1986-09-01

    The interaction and bonding of atoms and molecules on metal surfaces is explored under ultra-high vacuum conditions using a variety of surface science techniques: high resolution electron energy loss spectroscopy (HREELS), low energy electron diffraction (LEED), thermal desorption spectroscopy (TDS), Auger electron spectroscopy (AES), work function measurements, and second harmonic generation (SHG). 164 refs., 51 figs., 3 tabs

  6. Surface and catalysis science in the Materials and Molecular Research Division

    International Nuclear Information System (INIS)

    1980-01-01

    Surface science studies at Lawrence Berkeley Laboratory are detailed. Subject areas include: structure of surfaces and adsorbed monolayers; reduction and oxidation of surfaces; catalytic chemistry; and structure of interfaces and thin films

  7. Ethers on Si(001): A prime example for the common ground between surface science and molecular organic chemistry

    KAUST Repository

    Pecher, Lisa

    2017-09-15

    Using computational chemistry, we show that the adsorption of ether molecules on Si(001) under ultra-high vacuum conditions can be understood with textbook organic chemistry. The two-step reaction mechanism of (1) dative bond formation between the ether oxygen and a Lewis acidic surface atom and (2) a nucleophilic attack of a nearby Lewis basic surface atom is analysed in detail and found to mirror the acid-catalysed ether cleavage in solution. The O-Si dative bond is found to be the strongest of its kind and reactivity from this state defies the Bell-Evans-Polanyi principle. Electron rearrangement during the C-O bond cleavage is visualized using a newly developed bonding analysis method, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular chemistry SN2 reactions. Our findings thus illustrate how the fields of surface science and molecular chemistry can mutually benefit and unexpected insight can be gained.

  8. Ethers on Si(001): A prime example for the common ground between surface science and molecular organic chemistry

    KAUST Repository

    Pecher, Lisa; Laref, Slimane; Raupach, Marc; Tonner, Ralf Ewald

    2017-01-01

    Using computational chemistry, we show that the adsorption of ether molecules on Si(001) under ultra-high vacuum conditions can be understood with textbook organic chemistry. The two-step reaction mechanism of (1) dative bond formation between the ether oxygen and a Lewis acidic surface atom and (2) a nucleophilic attack of a nearby Lewis basic surface atom is analysed in detail and found to mirror the acid-catalysed ether cleavage in solution. The O-Si dative bond is found to be the strongest of its kind and reactivity from this state defies the Bell-Evans-Polanyi principle. Electron rearrangement during the C-O bond cleavage is visualized using a newly developed bonding analysis method, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular chemistry SN2 reactions. Our findings thus illustrate how the fields of surface science and molecular chemistry can mutually benefit and unexpected insight can be gained.

  9. Surface science an introduction

    CERN Document Server

    Hudson, John

    1991-01-01

    The whole field of surface science is covered in this work. Starting with a description of the structure and thermodynamics of clean surfaces, the book goes on to discuss kinetic theory of gases and molecular beam formation. This is followed by a largesection on gas-surface interactions, and another major section on energetic particle-surface interactions. The final chapter provides the background to crystal nucleation and growth. The approach adopted is interdisciplinary and slanted towards theexperimental side, with practical analytical techniques being used to illustrate general princi

  10. Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry.

    Science.gov (United States)

    Pecher, Lisa; Laref, Slimane; Raupach, Marc; Tonner, Ralf

    2017-11-20

    By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two-step reaction mechanism-1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom-shows that it mirrors acid-catalyzed ether cleavage in solution. The O-Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell-Evans-Polanyi principle. Electron rearrangement during C-O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular S N 2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Towards a Molecular Scale Understanding of Surface Chemistry and Photocatalysis on Metal Oxides: Surface Science Experiments and First Principles Theory

    Energy Technology Data Exchange (ETDEWEB)

    Diebold, Ulrike [Tulane Univ., New Orleans, LA (United States)

    2015-01-29

    This project has provided an increased understanding of molecular processes and structure-activity relationships in photocatalytic systems. This could ultimately lead to guidelines on how to make TiO2-based photocatalytic systems more efficient. This directly relates to the Program’s mission to develop a mechanistic understanding of chemical reactions that pertain to environmental remediation and pollution control; energy production (photoelectrochemical and production of hydrogen); and novel materials synthesis.

  12. Interfacial and Surface Science | Materials Science | NREL

    Science.gov (United States)

    Science group within the Material Science Center. He oversees research studies of surfaces and interfaces Interfacial and Surface Science Interfacial and Surface Science Image of irregular-outlined, light address a broad range of fundamental and applied issues in surface and interfacial science that are

  13. Modern techniques of surface science

    CERN Document Server

    Woodruff, D Phil

    2016-01-01

    This fully revised, updated and reorganised third edition provides a thorough introduction to the characterisation techniques used in surface science and nanoscience today. Each chapter brings together and compares the different techniques used to address a particular research question, including how to determine the surface composition, surface structure, surface electronic structure, surface microstructure at different length scales (down to sub-molecular), and the molecular character of adsorbates and their adsorption or reaction properties. Readers will easily understand the relative strengths and limitations of the techniques available to them and, ultimately, will be able to select the most suitable techniques for their own particular research purposes. This is an essential resource for researchers and practitioners performing materials analysis, and for senior undergraduate students looking to gain a clear understanding of the underlying principles and applications of the different characterisation tec...

  14. Biomaterials surface science

    CERN Document Server

    Taubert, Andreas; Rodriguez-Cabello, José Carlos

    2013-01-01

    The book provides an overview of the highly interdisciplinary field of surface science in the context of biological and biomedical applications. The covered topics range from micro- and nanostructuring for imparting functionality in a top-down manner to the bottom-up fabrication of gradient surfaces by self-assembly, from interfaces between biomaterials and living matter to smart, stimuli-responsive surfaces, and from cell and surface mechanics to the elucidation of cell-chip interactions in biomedical devices.

  15. Surface science and catalysis

    International Nuclear Information System (INIS)

    Somorjai, G.A.

    1985-02-01

    Modern surface science studies have explored a large number of metal catalyst systems. Three classes of catalytic reactions can be identified: (1) those that occur over the metal surface; (2) reactions that take place on top of a strongly adsorbed overlayer and (3) reactions that occur on co-adsorbate modified surfaces. Case histories for each class are presented. 44 refs., 13 figs., 3 tabs

  16. Exploring the science of thinking independently together: Faraday Discussion Volume 204 - Complex Molecular Surfaces and Interfaces, Sheffield, UK, July 2017.

    Science.gov (United States)

    Samperi, M; Hirsch, B E; Diaz Fernandez, Y A

    2017-11-23

    The 2017 Faraday Discussion on Complex Molecular Surfaces and Interfaces brought together theoreticians and experimentalists from both physical and chemical backgrounds to discuss the relevant applied and fundamental research topics within the broader field of chemical surface analysis and characterization. Main discussion topics from the meeting included the importance of "disordered" two-dimensional (2D) molecular structures and the utility of kinetically trapped states. An emerging need for new experimental tools to address dynamics and kinetic pathways involved in self-assembled systems, as well as the future prospects and current limitations of in silico studies were also discussed. The following article provides a brief overview of the work presented and the challenges discussed during the meeting.

  17. Surface science techniques

    CERN Document Server

    Walls, JM

    2013-01-01

    This volume provides a comprehensive and up to the minute review of the techniques used to determine the nature and composition of surfaces. Originally published as a special issue of the Pergamon journal Vacuum, it comprises a carefully edited collection of chapters written by specialists in each of the techniques and includes coverage of the electron and ion spectroscopies, as well as the atom-imaging methods such as the atom probe field ion microscope and the scanning tunnelling microscope. Surface science is an important area of study since the outermost surface layers play a crucial role

  18. Computer representation of molecular surfaces

    International Nuclear Information System (INIS)

    Max, N.L.

    1981-01-01

    This review article surveys recent work on computer representation of molecular surfaces. Several different algorithms are discussed for producing vector or raster drawings of space-filling models formed as the union of spheres. Other smoother surfaces are also considered

  19. Surface science techniques

    CERN Document Server

    Bracco, Gianangelo

    2013-01-01

    The book describes the experimental techniques employed to study surfaces and interfaces. The emphasis is on the experimental method. Therefore all chapters start with an introduction of the scientific problem, the theory necessary to understand how the technique works and how to understand the results. Descriptions of real experimental setups, experimental results at different systems are given to show both the strength and the limits of the technique. In a final part the new developments and possible extensions of the techniques are presented. The included techniques provide microscopic as well as macroscopic information. They cover most of the techniques used in surface science.

  20. Molecular Science Computing: 2010 Greenbook

    Energy Technology Data Exchange (ETDEWEB)

    De Jong, Wibe A.; Cowley, David E.; Dunning, Thom H.; Vorpagel, Erich R.

    2010-04-02

    This 2010 Greenbook outlines the science drivers for performing integrated computational environmental molecular research at EMSL and defines the next-generation HPC capabilities that must be developed at the MSC to address this critical research. The EMSL MSC Science Panel used EMSL’s vision and science focus and white papers from current and potential future EMSL scientific user communities to define the scientific direction and resulting HPC resource requirements presented in this 2010 Greenbook.

  1. Atomic and molecular sciences

    International Nuclear Information System (INIS)

    Lane, N.F.

    1989-01-01

    The theoretical atomic and molecular physics program at Rice University addresses basic questions about the collision dynamics of electrons, atoms, ions and molecules, emphasizing processes related to possible new energy technologies and other applications. The program focuses on inelastic collision processes that are important in understanding energy and ionization balance in disturbed gases and plasmas. Emphasis is placed on systems and processes where some experimental information is available or where theoretical results may be expected to stimulate new measurements. Examples of current projects include: excitation and charge-transfer processes; orientation and alignment of excited states following collisions; Rydberg atom collisions with atoms and molecules; Penning ionization and ion-pair formation in atom-atom collisions; electron-impact ionization in dense, high-temperature plasmas; electron-molecule collisions; and related topics

  2. EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

    Science.gov (United States)

    Weinelt, Martin; von Oppen, Felix

    2012-10-01

    In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on

  3. Versatile piezoelectric pulsed molecular beam source for gaseous compounds and organic molecules with femtomole accuracy for UHV and surface science applications

    International Nuclear Information System (INIS)

    Schiesser, Alexander; Schaefer, Rolf

    2009-01-01

    This note describes the construction of a piezoelectric pulsed molecular beam source based upon a design presented in an earlier work [D. Proch and T. Trickl, Rev. Sci. Instrum. 60, 713 (1988)]. The design features significant modifications that permit the determination of the number of molecules in a beam pulse with an accuracy of 1x10 11 molecules per pulse. The 21 cm long plunger-nozzle setup allows the molecules to be brought to any point of the UHV chamber with very high intensity. Furthermore, besides typical gaseous compounds, also smaller organic molecules with a vapor pressure higher than 0.1 mbar at room temperature may serve as feed material. This makes the new design suitable for various applications in chemical and surface science studies.

  4. Progress in surface and membrane science

    CERN Document Server

    Danielli, J F; Cadenhead, D A

    1973-01-01

    Progress in Surface and Membrane Science, Volume 7 covers the developments in the study of surface and membrane science. The book discusses the theoretical and experimental aspects of the van der Waals forces; the electric double layer on the semiconductor-electrolyte interface; and the long-range and short-range order in adsorbed films. The text also describes the hydrodynamical theory of surface shear viscosity; the structure and properties of monolayers of synthetic polypeptides at the air-water interface; and the structure and molecular dynamics of water. The role of glycoproteins in cell

  5. Molecular tailoring of solid surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Evenson, Simon Alan

    1997-07-01

    The overall performance of a material can be dramatically improved by tailoring its surface at the molecular level. The aim of this project was to develop a universal technique for attaching dendrimers (well-defined, nanoscale, functional polymers) and Jeffamines (high molecular weight polymer chains) to the surface of any shaped solid substrate. This desire for controlled functionalization is ultimately driven by the need to improve material compatibility in various biomedical applications. Atomic force microscopy (AFM) was used initially to study the packing and structure of Langmuir-Blodgett films on surfaces, and subsequently resulted in the first visualization of individual, spherically shaped, nanoscopic polyamidoamine dendrimers. The next goal was to develop a methodology for attaching such macromolecules to inert surfaces. Thin copolymer films were deposited onto solid substrates to produce materials with a fixed concentration of surface anhydride groups. Vapor-phase functionalization reactions were then carried out with trifluorinated amines to confirm the viability of this technique to bond molecules to surfaces. Finally, pulsed plasma polymerization of maleic anhydride took this approach one stage further, by forming well-adhered polymer films containing a predetermined concentration of reactive anhydride groups. Subsequent functionalization reactions led to the secure attachment of dendrimers and Jeffamines at any desired packing density. An alternative route to biocompatibilization used 1,2-ethanedithiol to yield thiolated surfaces containing very high polymeric sulfur : carbon ratios. (author)

  6. Molecular tailoring of solid surfaces

    International Nuclear Information System (INIS)

    Evenson, Simon Alan

    1997-01-01

    The overall performance of a material can be dramatically improved by tailoring its surface at the molecular level. The aim of this project was to develop a universal technique for attaching dendrimers (well-defined, nanoscale, functional polymers) and Jeffamines (high molecular weight polymer chains) to the surface of any shaped solid substrate. This desire for controlled functionalization is ultimately driven by the need to improve material compatibility in various biomedical applications. Atomic force microscopy (AFM) was used initially to study the packing and structure of Langmuir-Blodgett films on surfaces, and subsequently resulted in the first visualization of individual, spherically shaped, nanoscopic polyamidoamine dendrimers. The next goal was to develop a methodology for attaching such macromolecules to inert surfaces. Thin copolymer films were deposited onto solid substrates to produce materials with a fixed concentration of surface anhydride groups. Vapor-phase functionalization reactions were then carried out with trifluorinated amines to confirm the viability of this technique to bond molecules to surfaces. Finally, pulsed plasma polymerization of maleic anhydride took this approach one stage further, by forming well-adhered polymer films containing a predetermined concentration of reactive anhydride groups. Subsequent functionalization reactions led to the secure attachment of dendrimers and Jeffamines at any desired packing density. An alternative route to biocompatibilization used 1,2-ethanedithiol to yield thiolated surfaces containing very high polymeric sulfur : carbon ratios. (author)

  7. Solvay Conference on Surface Science

    CERN Document Server

    1988-01-01

    The articles collected in this volume give a broad overview of the current state of surface science. Pioneers in the field and researchers met together at this Solvay Conference to discuss important new developments in surface science, with an emphasis on the common area between solid state physics and physical chemistry. The contributions deal with the following subjects: structure of surfaces, surface science and catalysis, two-dimensional physics and phase transitions, scanning tunneling microscopy, surface scattering and surface dynamics, chemical reactions at surfaces, solid-solid interfaces and superlattices, and surface studies with synchrotron radiation. On each of these subjects an introductory review talk and a number of short research contributions are followed by extensive discussions, which appear in full in the text. This nineteenth Solvay Conference commemorates the 75th anniversary of the Solvay Institutes.

  8. Atomic and molecular science: progress and opportunities

    International Nuclear Information System (INIS)

    Mathur, D.

    2000-01-01

    In the contemporary scenario, atomic, molecular and optical (AMO) science focuses on the physical and chemical properties of the common building blocks of matter - atoms, molecules and light. The main characteristic of AMO science is that it is both an intellectually stimulating fundamental science and a powerful enabling science that supports an increasing number of other important areas of science and technology. In brief, the fundamental interests in atoms, molecules and clusters (as well as their ions) include studies of their structure and properties, their optical interactions, collisional properties, including quantum state-resolved studies, and interactions with external fields, solids and surfaces. Fundamental aspects of present-day optical sciences include studies of laser spectroscopy, nonlinear optics, quantum optics, optical interactions with condensed matter, ultrafast optics and coherent light sources. The enabling aspect of AMO science derives from efforts to control atoms, molecules, clusters, charged particles and light more precisely, to accurately to determine, experimentally and theoretically, their properties, and to invent new, methods of generating light with tailor-made properties

  9. Molecular science for drug development and biomedicine.

    Science.gov (United States)

    Zhong, Wei-Zhu; Zhou, Shu-Feng

    2014-11-04

    With the avalanche of biological sequences generated in the postgenomic age, molecular science is facing an unprecedented challenge, i.e., how to timely utilize the huge amount of data to benefit human beings. Stimulated by such a challenge, a rapid development has taken place in molecular science, particularly in the areas associated with drug development and biomedicine, both experimental and theoretical. The current thematic issue was launched with the focus on the topic of "Molecular Science for Drug Development and Biomedicine", in hopes to further stimulate more useful techniques and findings from various approaches of molecular science for drug development and biomedicine.[...].

  10. Molecular science solving global problems

    International Nuclear Information System (INIS)

    Dunning, T.H. Jr.; Stults, B.R.

    1995-01-01

    From the late 1940s to the late 1980s, the Department of Energy (DOE) had a critical role in the Cold War. Many sites were built to contribute to the nation's nuclear weapons effort. However, not enough attention was paid to how the waste generated at these facilities should be handled. As a result, a number of sites fouled the soil around them or dumped low-level radioactive waste into nearby rivers. A DOE laboratory is under construction with a charter to help. Called the Environmental Molecular Sciences Laboratory (EMSL), this national user facility will be located at DOE's Pacific Northwest Laboratory (PNL) in Richland, WA. This laboratory has been funded by DOE and Congress to play a major role as the nation confronts the enormous challenge of reducing environmental and human risks from hundreds of government and industrial waste sites in an economically viable manner. The original proposal for the EMSL took a number of twists and turns on its way to its present form, but one thing remained constant: the belief that safe, permanent, cost-effective solutions to many of the country's environmental problems could be achieved only by multidisciplinary teams working to understand and control molecular processes. The processes of most concern are those that govern the transport and transformation of contaminants, the treatment and storage of high-level mixed wastes, and the risks those contaminants ultimately pose to workers and the public

  11. Surface science and heterogeneous catalysis

    International Nuclear Information System (INIS)

    Somorjai, G.A.

    1980-05-01

    The catalytic reactions studied include hydrocarbon conversion over platinum, the transition metal-catalyzed hydrogenation of carbon monoxide, and the photocatalyzed dissociation of water over oxide surfaces. The method of combined surface science and catalytic studies is similar to those used in synthetic organic chemistry. The single-crystal models for the working catalyst are compared with real catalysts by comparing the rates of cyclopropane ring opening on platinum and the hydrogenation of carbon monoxide on rhodium single crystal surface with those on practical commercial catalyst systems. Excellent agreement was obtained for these reactions. This document reviews what was learned about heterogeneous catalysis from these surface science approaches over the past 15 years and present models of the active catalyst surface

  12. The surface science of enzymes

    DEFF Research Database (Denmark)

    Rod, Thomas Holm; Nørskov, Jens Kehlet

    2002-01-01

    One of the largest challenges to science in the coming years is to find the relation between enzyme structure and function. Can we predict which reactions an enzyme catalyzes from knowledge of its structure-or from its amino acid sequence? Can we use that knowledge to modify enzyme function......? To solve these problems we must understand in some detail how enzymes interact with reactants from its surroundings. These interactions take place at the surface of the enzyme and the question of enzyme function can be viewed as the surface science of enzymes. In this article we discuss how to describe...... catalysis by enzymes, and in particular the analogies between enzyme catalyzed reactions and surface catalyzed reactions. We do this by discussing two concrete examples of reactions catalyzed both in nature (by enzymes) and in industrial reactors (by inorganic materials), and show that although analogies...

  13. Molecularization in nutritional science: a view from philosophy of science.

    Science.gov (United States)

    Ströhle, Alexander; Döring, Frank

    2010-10-01

    Over the past decade, a trend toward molecularization, which could be observed in almost all bioscientific disciplines, now appears to have also developed in nutritional science. However, molecular nutrition research gives birth to a series of questions. Therefore, we take a look at the epistemological foundation of (molecular) nutritional science. We (i) analyze the scientific status of (molecular) nutritional science and its position in the canon of other scientific disciplines, (ii) focus on the cognitive aims of nutritional science in general and (iii) on the chances and limits of molecular nutrition research in particular. By taking up the thoughts of an earlier work, we are analyzing (molecular) nutritional science from a strictly realist and emergentist-naturalist perspective. Methodologically, molecular nutrition research is bound to a microreductive research approach. We emphasize, however, that it need not be a radical microreductionism whose scientific reputation is not the best. Instead we favor moderate microreductionism, which combines reduction with integration. As mechanismic explanations are one of the primary aims of factual sciences, we consider it as the task of molecular nutrition research to find profound, i.e. molecular-mechanismic, explanations for the conditions, characteristics and changes of organisms related to the organism-nutrition environment interaction.

  14. Molecular Science Research Center annual report

    Energy Technology Data Exchange (ETDEWEB)

    Knotek, M.L.

    1991-01-01

    The Chemical Structure and Dynamics group is studying chemical kinetics and reactions dynamics of terrestrial and atmospheric processes as well as the chemistry of complex waste forms and waste storage media. Staff are using new laser systems and surface-mapping techniques in combination with molecular clusters that mimic adsorbate/surface interactions. The Macromolecular Structure and Dynamics group is determining biomolecular structure/function relationships for processes the control the biological transformation of contaminants and the health effects of toxic substances. The Materials and Interfaces program is generating information needed to design and synthesize advanced materials for the analysis and separation of mixed chemical waste, the long-term storage of concentrated hazardous materials, and the development of chemical sensors for environmental monitoring of various organic and inorganic species. The Theory, Modeling, and Simulation group is developing detailed molecular-level descriptions of the chemical, physical, and biological processes in natural and contaminated systems. Researchers are using the full spectrum of computational techniques. The Computer and Information Sciences group is developing new approaches to handle vast amounts of data and to perform calculations for complex natural systems. The EMSL will contain a high-performance computing facility, ancillary computing laboratories, and high-speed data acquisition systems for all major research instruments.

  15. How old is surface science?

    International Nuclear Information System (INIS)

    Paparazzo, E.

    2004-01-01

    Philosophical and literary testimonies from the Classical World (5th century B.C. to 3rd century A.D.) involving solid surfaces are reviewed. Plato thought the surface to be a real entity, whereas Aristotle considered it to possess an unqualified existence, i.e. not to be a substance, but just an accidental entity. The Old Stoics asserted that surfaces do not possess any physical existence, although the Stoic philosopher Posidonius--apparently the only exception in his school--held them to exist both in thought and reality. While both the Atomists and the Epicureans were very little interested in them, the Sceptic philosopher Sextus Empiricus considered surfaces to be the limits of a body, although he maintained that both the view that they are corporeal or the view that they are incorporeal present unsurmountable difficulties. Among Roman authors, the testimony from Pliny the Elder is mostly concerned with metallic surfaces, chemical change occurring there, and surface treatments used in antiquity. Besides the philosophical motivations, the implications of the testimonies are discussed in the light of surface science. The purely geometrical surface of Plato is found to compare favorably to single-crystal surface, Posidonius' 'corporeal' surface is best likened to an air-oxidized, or otherwise ambient-modified surface, and ancient accounts on mixture are compared to XPS results obtained in adhesion studies of enameled steels. I argue that the long-standing dominance of Aristotle's view from antiquity onwards may have had a part in delaying theoretical speculation into solid surfaces

  16. Influence of polymer additive molecular weight on surface and ...

    Indian Academy of Sciences (India)

    2, April 2011, pp. 347–356. c Indian Academy of Sciences. Influence of polymer additive molecular weight on surface and microstructural characteristics of electrodeposited copper. R MANU. ∗ and SOBHA JAYAKRISHNAN. Electroplating and Metal Finishing Technology Division, Central Electrochemical Research Institute,.

  17. Molecular Science Research Center 1992 annual report

    Energy Technology Data Exchange (ETDEWEB)

    Knotek, M.L.

    1994-01-01

    The Molecular Science Research Center is a designated national user facility, available to scientists from universities, industry, and other national laboratories. After an opening section, which includes conferences hosted, appointments, and projects, this document presents progress in the following fields: chemical structure and dynamics; environmental dynamics and simulation; macromolecular structure and dynamics; materials and interfaces; theory, modeling, and simulation; and computing and information sciences. Appendices are included: MSRC staff and associates, 1992 publications and presentations, activities, and acronyms and abbreviations.

  18. Molecular Imprinting Applications in Forensic Science.

    Science.gov (United States)

    Yılmaz, Erkut; Garipcan, Bora; Patra, Hirak K; Uzun, Lokman

    2017-03-28

    Producing molecular imprinting-based materials has received increasing attention due to recognition selectivity, stability, cast effectiveness, and ease of production in various forms for a wide range of applications. The molecular imprinting technique has a variety of applications in the areas of the food industry, environmental monitoring, and medicine for diverse purposes like sample pretreatment, sensing, and separation/purification. A versatile usage, stability and recognition capabilities also make them perfect candidates for use in forensic sciences. Forensic science is a demanding area and there is a growing interest in molecularly imprinted polymers (MIPs) in this field. In this review, recent molecular imprinting applications in the related areas of forensic sciences are discussed while considering the literature of last two decades. Not only direct forensic applications but also studies of possible forensic value were taken into account like illicit drugs, banned sport drugs, effective toxins and chemical warfare agents in a review of over 100 articles. The literature was classified according to targets, material shapes, production strategies, detection method, and instrumentation. We aimed to summarize the current applications of MIPs in forensic science and put forth a projection of their potential uses as promising alternatives for benchmark competitors.

  19. Solid surface vs. liquid surface: nanoarchitectonics, molecular machines, and DNA origami.

    Science.gov (United States)

    Ariga, Katsuhiko; Mori, Taizo; Nakanishi, Waka; Hill, Jonathan P

    2017-09-13

    The investigation of molecules and materials at interfaces is critical for the accumulation of new scientific insights and technological advances in the chemical and physical sciences. Immobilization on solid surfaces permits the investigation of different properties of functional molecules or materials with high sensitivity and high spatial resolution. Liquid surfaces also present important media for physicochemical innovation and insight based on their great flexibility and dynamicity, rapid diffusion of molecular components for mixing and rearrangements, as well as drastic spatial variation in the prevailing dielectric environment. Therefore, a comparative discussion of the relative merits of the properties of materials when positioned at solid or liquid surfaces would be informative regarding present-to-future developments of surface-based technologies. In this perspective article, recent research examples of nanoarchitectonics, molecular machines, DNA nanotechnology, and DNA origami are compared with respect to the type of surface used, i.e. solid surfaces vs. liquid surfaces, for future perspectives of interfacial physics and chemistry.

  20. Progress in surface and membrane science

    CERN Document Server

    Danielli, J F; Cadenhead, D A

    1973-01-01

    Progress in Surface and Membrane Science, Volume 6 covers the developments in the study of surface and membrane science. The book discusses the progress in surface and membrane science; the solid state chemistry of the silver halide surface; and the experimental and theoretical aspects of the double layer at the mercury-solution interface. The text also describes contact-angle hysteresis; ion binding and ion transport produced by neutral lipid-soluble molecules; and the biophysical interactions of blood proteins with polymeric and artificial surfaces. Physical chemists, biophysicists, and phys

  1. Progress in surface and membrane science

    CERN Document Server

    Cadenhead, D A

    1977-01-01

    Progress in Surface and Membrane Science, Volume 11 covers the advances in the study of surface and membrane science. The book discusses the quantum theory of surface phenomena; some fundamental aspects of electrocrystallization; and exoelectric emission. The text also describes the surface of titanium dioxide; and the prospects for atomic resolution electron microscopy in membranology. Chemists, physicists, and people involved in the electrochemical power laboratory will find the book useful.

  2. Deep Generative Models for Molecular Science

    DEFF Research Database (Denmark)

    Jørgensen, Peter Bjørn; Schmidt, Mikkel Nørgaard; Winther, Ole

    2018-01-01

    Generative deep machine learning models now rival traditional quantum-mechanical computations in predicting properties of new structures, and they come with a significantly lower computational cost, opening new avenues in computational molecular science. In the last few years, a variety of deep...... generative models have been proposed for modeling molecules, which differ in both their model structure and choice of input features. We review these recent advances within deep generative models for predicting molecular properties, with particular focus on models based on the probabilistic autoencoder (or...

  3. Surface Science Foundations of Catalysis and Nanoscience

    CERN Document Server

    Kolasinski, Kurt K

    2012-01-01

    Surface science has evolved beyond being a sub-field of chemistry or physics and has now become an underpinning science. The Third Edition of this book incorporates extensive worked solutions, as well as details on how problem solving relevant to surface science should be performed. It contextualizes the exercises and their solutions to further explicate the methods of problem solving, application of scientific principles and to deliver a deeper understanding of the field of surface science. Solutions will be accompanied by figures and/or graphs of data, as appropriate.

  4. Molecular Science Research Center, 1991 annual report

    Energy Technology Data Exchange (ETDEWEB)

    Knotek, M.L.

    1992-03-01

    During 1991, the Molecular Science Research Center (MSRC) experienced solid growth and accomplishment and the Environmental, and Molecular Sciences Laboratory (EMSL) construction project moved forward. We began with strong programs in chemical structure and dynamics and theory, modeling, and simulation, and both these programs continued to thrive. We also made significant advances in the development of programs in materials and interfaces and macromolecular structure and dynamics, largely as a result of the key staff recruited to lead these efforts. If there was one pervasive activity for the past year, however, it was to strengthen the role of the EMSL in the overall environmental restoration and waste management (ER/WM) mission at Hanford. These extended activities involved not only MSRC and EMSL staff but all PNL scientific and technical staff engaged in ER/WM programs.

  5. Surface Science Foundations of Catalysis and Nanoscience

    CERN Document Server

    Kolasinski, Kurt K

    2012-01-01

    Surface science has evolved from being a sub-field of chemistry or physics, and has now established itself as an interdisciplinary topic. Knowledge has developed sufficiently that we can now understand catalysis from a surface science perspective. No-where is the underpinning nature of surface science better illustrated than with nanoscience. Now in its third edition, this successful textbook aims to provide students with an understanding of chemical transformations and the formation of structures at surfaces. The chapters build from simple to more advanced principles with each featuring exerc

  6. Progress in surface and membrane science

    CERN Document Server

    Danielli, J F; Cadenhead, D A

    1972-01-01

    Progress in Surface and Membrane Science, Volume 5 covers the developments in the study of surface and membrane science. The book discusses the Mössbauer effect in surface science; the surface functional groups on carbon and silica; and the wetting phenomena pertaining to adhesion. The text also describes the physical state of phospholipids and cholesterol in monolayers, bilayers, and membranes; the characteristics of heterocoagulation; and the effects of calcium on excitable membranes and neurotransmitter action. Chemists, physiologists, biophysicists, and civil engineers will find the book i

  7. International Journal of Molecular Science 2017 Best Paper Award.

    Science.gov (United States)

    2017-11-02

    The Editors of the International Journal of Molecular Sciences have established the Best Paper Award to recognize the most outstanding articles published in the areas of molecular biology, molecular physics and chemistry that have been published in the International Journal of Molecular Sciences. The prizes have been awarded annually since 2012 [...].

  8. Progress in surface and membrane science

    CERN Document Server

    Cadenhead, D A

    1979-01-01

    Progress in Surface and Membrane Science, Volume 12 covers the advances in the study of surface and membrane science. The book discusses the topographical differentiation of the cell surface; the NMR studies of model biological membrane system; and an irreversible thermodynamic approach to energy coupling in mitochondria and chloroplasts. The text also describes water at surfaces; the nature of microemulsions; and the energy principle in the stability of interfaces. Biochemists, physicists, chemical engineers, and people involved in surface and coatings research will find the book invaluable.

  9. Progress in surface and membrane science

    CERN Document Server

    Danielli, J F; Cadenhead, D A

    1971-01-01

    Progress in Surface and Membrane Science, Volume 4 covers the developments in the study of surface and membrane science. The book discusses waves at interfaces; recent investigations on the thickness of surface layers; and surface analysis by low-energy electron diffraction and Auger electron spectroscopy. The text also describes the anode electrolyte interface; the interactions of adsorbed proteins and polypeptides at interfaces; and peptide-induced ion transport in synthetic and biological membranes. The monolayer adsorption on crystalline surfaces is also considered. Chemists and metallurgi

  10. Learning surface molecular structures via machine vision

    Science.gov (United States)

    Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

    2017-08-01

    Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

  11. Surface Science at the Solid Liquid Interface

    Science.gov (United States)

    1993-10-06

    prominent experimental avenue, developed originally by Hubbard et al,_ involves emersing monocrystalline elec- As for metal surfaces in ultrahigh vacuum...reliable means of both preparing and dosateizn ordered monocrystalline metal surfaces in UHV has led to ing appropriate molecular components of...surface atoms in place of bottom panel of Fig. 2, equal intensity contours are shown 23 underlying surface atoms, the compression is 24/23 - I in the

  12. Molecular environmental science and synchrotron radiation sources

    Energy Technology Data Exchange (ETDEWEB)

    Brown, G.E. Jr. [Stanford Univ., CA (United States)

    1995-12-31

    Molecular environmental science is a relatively new field but focuses on the chemical and physical forms of toxic and/or radioactive contaminants in soils, sediments, man-made waste forms, natural waters, and the atmosphere; their possible reactions with inorganic and organic compounds, plants, and organisms in the environment; and the molecular-level factors that control their toxicity, bioavailability, and transport. The chemical speciation of a contaminant is a major factor in determining its behavior in the environment, and synchrotron-based X-ray absorption fine structure (XAFS) spectroscopy is one of the spectroscopies of choice to quantitatively determine speciation of heavy metal contaminants in situ without selective extraction or other sample treatment. The use of high-flux insertion device beam lines at synchrotron sources and multi-element array detectors has permitted XAFS studies of metals such as Se and As in natural soils at concentration levels as low as 50 ppm. The X-ray absorption near edge structure of these metals is particularly useful in determining their oxidation state. Examples of such studies will be presented, and new insertion device beam lines under development at SSRL and the Advanced Photon Source for molecular environmental science applications will be discussed.

  13. Progress in surface and membrane science

    CERN Document Server

    Cadenhead, D A; Rosenberg, M D

    1974-01-01

    Progress in Surface and Membrane Science, Volume 8 covers the developments in the study of surface and membrane science. The book discusses the applications of statistical mechanics to physical adsorption; the impact of electron spectroscopy and cognate techniques on the study of solid surfaces; and the ellipsometric studies of thin films. The text also describes the interfacial photochemistry of bilayer lipid membranes; cell junctions and their development; and the composition and function of the inner mitochondrial membrane. The role of the cell surface in contact inhibition of cell division

  14. Recent progress in surface science v.2

    CERN Document Server

    Danielli, J F; Riddiford, A C

    1964-01-01

    Recent Progress in Surface Science, Volume 2 is a 10-chapter text that covers the significant advances in some aspects of surface science, including in catalysis, genetic control of cell surface, and cell membrane. The opening chapter deals with the major factors affecting adsorption at the gas-solid interface. The subsequent chapters explore the advances in understanding of heterogeneous catalysis in terms of fundamental surface processes, as well as the concept of dynamic contact angles. These topics are followed by discussions on emulsions, flotation, and the extraordinary complexity of cel

  15. Current trends of surface science and catalysis

    CERN Document Server

    Park, Jeong Young

    2014-01-01

    Including detail on applying surface science in renewable energy conversion, this book covers the latest results on model catalysts including single crystals, bridging "materials and pressure gaps", and hot electron flows in heterogeneous catalysis.

  16. Report of the surface science workshop

    International Nuclear Information System (INIS)

    Somorjai, G.A.; Yates, J.T. Jr.; Clinton, W.

    1977-03-01

    A three-day workshop was held to review the various areas of energy development and technology in which surface science plays major roles and makes major contributions, and to identify the major surface-science-related problem areas in the fields with ERDA's mission in the fossil, nuclear, fusion, geothermal, and solar energy technologies and in the field of environmental control. The workshop activities are summarized

  17. Report of the surface science workshop

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.; Yates, J.T. Jr.; Clinton, W.

    1977-03-01

    A three-day workshop was held to review the various areas of energy development and technology in which surface science plays major roles and makes major contributions, and to identify the major surface-science-related problem areas in the fields with ERDA's mission in the fossil, nuclear, fusion, geothermal, and solar energy technologies and in the field of environmental control. The workshop activities are summarized. (GHT)

  18. Progress in surface and membrane science

    CERN Document Server

    Cadenhead, D A; Rosenberg, M D

    1975-01-01

    Progress in Surface and Membrane Science, Volume 9 covers the developments in surface and membrane science. The book discusses the physical adsorption of gases and vapors in micropores; the chemisorption theory; and the role of radioisotopes in the studies of chemisorption and catalysis. The text also describes the interaction of ions with monolayers; and the isolation and characterization of mycoplasma membranes. Chemists, physical chemists, and microbiologists will find the book useful.

  19. Surface science tools for nanomaterials characterization

    CERN Document Server

    2015-01-01

    Fourth volume of a 40volume series on nano science and nanotechnology, edited by the renowned scientist Challa S.S.R. Kumar. This handbook gives a comprehensive overview about Surface Science Tools for Nanomaterials Characterization. Modern applications and state-of-the-art techniques are covered and make this volume an essential reading for research scientists in academia and industry.

  20. Environmental Molecular Sciences Laboratory 2004 Annual Report

    Energy Technology Data Exchange (ETDEWEB)

    White, Julia C.

    2005-04-17

    This 2004 Annual Report describes the research and accomplishments of staff and users of the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), located in Richland, Washington. EMSL is a multidisciplinary, national scientific user facility and research organization, operated by Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy's Office of Biological and Environmental Research. The resources and opportunities within the facility are an outgrowth of the U.S. Department of Energy's (DOE) commitment to fundamental research for understanding and resolving environmental and other critical scientific issues.

  1. Progress in surface and membrane science

    CERN Document Server

    Cadenhead, D A

    1976-01-01

    Progress in Surface and Membrane Science, Volume 10 covers the advances in surface and membrane science. The book discusses the selective changes of cellular particles influencing sedimentation properties; and the rotating disk and ring-disk electrodes in investigations of surface phenomena at the metal-electrolyte interface. The text also describes the membrane potential of phospholipid bilayer and biological membranes; the adsorption of surfactant monolayers at gas/liquid and liquid/liquid interfaces; and the enzymes immobilized on glass. Chemists and people involved in electrochemistry will

  2. Progress in surface and membrane science

    CERN Document Server

    Cadenhead, D A

    1981-01-01

    Progress in Surface and Membrane Science, Volume 14 covers the advances in the study of surface and membrane science. The book discusses statistical thermodynamics of monolayer adsorption from gas and liquid mixtures on homogeneous and heterogeneous solid surfaces; and the structure of the boundary layers of liquids and its influence on the mass transfer in fine pores. The text then describes the coupling of ionic and non-electrolyte fluxes in ion selective membranes; the electrocatalytic properties of matalloporphins at the interface; and the adsorption from binary gas and liquid phases. Phas

  3. Technical activities, 1990: Surface Science Division

    International Nuclear Information System (INIS)

    Powell, C.J.

    1991-05-01

    The report summarizes technical activities and accomplishments of the NIST Surface Science Division during Fiscal Year 1990. Overviews are presented of the Division and of its three constituent groups: Surface Dynamical Processes, Thin Films and Interfaces, and Surface Spectroscopies and Standards. These overviews are followed by reports of selected technical accomplishments during the year. A summary is given of Division outputs and interactions that includes lists of publications, talks, committee assignments, seminars (including both Division seminars and Interface Science seminars arranged through the Division), conferences organized, and a standard reference material certified. Finally, lists are given of Division staff and of guest scientists who have worked in the Division during the past year

  4. Marine molecular biology: An emerging field of biological sciences

    Digital Repository Service at National Institute of Oceanography (India)

    Thakur, N.L.; Jain, R.; Natalio, F.; Hamer, B.; Thakur, A.N.; Muller, W.E.G.

    An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies...

  5. Interlocking Molecular Gear Chains Built on Surfaces.

    Science.gov (United States)

    Zhao, Rundong; Qi, Fei; Zhao, Yan-Ling; Hermann, Klaus E; Zhang, Rui-Qin; Van Hove, Michel A

    2018-05-17

    Periodic chains of molecular gears in which molecules couple with each other and rotate on surfaces have been previously explored by us theoretically using ab initio simulation tools. On the basis of the knowledge and experience gained about the interactions between neighboring molecular gears, we here explore the transmission of rotational motion and energy over larger distances, namely, through a longer chain of gear-like passive "slave" molecules. Such microscopic gears exhibit quite different behaviors compared to rigid cogwheels in the macroscopic world due to their structural flexibility affecting intermolecular interaction. Here, we investigate the capabilities of such gear chains and reveal the mechanisms of the transmission process in terms of both quantum-level density functional theory (DFT) and simple classical mechanics. We find that the transmission of rotation along gear chains depends strongly on the gear-gear distance: short distances can cause tilting of gears and even irregular "creep-then-jump" (or "stick-slip") motion or expulsion of gears; long gear-gear distances cause weak coupling between gears, slipping and skipping. More importantly, for transmission of rotation at intermediate gear-gear distances, our modeling clearly exhibits the relative roles of several important factors: flexibility of gear arms, axles, and supports, as well as resulting rotational delays, slippages, and thermal and other effects. These studies therefore allow better informed design of future molecular machine components involving motors, gears, axles, etc.

  6. Molecular thermodynamics for food science and engineering.

    Science.gov (United States)

    Nguyen, Phuong-Mai; Guiga, Wafa; Vitrac, Olivier

    2016-10-01

    We argue that thanks to molecular modeling approaches, many thermodynamic properties required in Food Science and Food Engineering will be calculable within a few hours from first principles in a near future. These new possibilities will enable to bridge via multiscale modeling composition, process and storage effects to reach global optimization, innovative concepts for food or its packaging. An outlook of techniques and a series of examples are given in this perspective. We emphasize solute chemical potentials in polymers, liquids and their mixtures as they cannot be understood and estimated without theory. The presented atomistic and coarse-grained methods offer a natural framework to their conceptualization in polynary systems, entangled or crosslinked homo- or heteropolymers. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Surface analysis methods in materials science

    CERN Document Server

    Sexton, Brett; Smart, Roger

    1992-01-01

    The idea for this book stemmed from a remark by Philip Jennings of Murdoch University in a discussion session following a regular meeting of the Australian Surface Science group. He observed that a text on surface analysis and applica­ tions to materials suitable for final year undergraduate and postgraduate science students was not currently available. Furthermore, the members of the Australian Surface Science group had the research experience and range of coverage of sur­ face analytical techniques and applications to provide a text for this purpose. A of techniques and applications to be included was agreed at that meeting. The list intended readership of the book has been broadened since the early discussions, particularly to encompass industrial users, but there has been no significant alter­ ation in content. The editors, in consultation with the contributors, have agreed that the book should be prepared for four major groups of readers: - senior undergraduate students in chemistry, physics, metallur...

  8. Molecular forensic science of nuclear materials

    International Nuclear Information System (INIS)

    Wilkerson, Marianne Perry

    2010-01-01

    We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO 2 (An: U, Pu) to form non-stoichiometric species described as AnO 2+x . Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxides materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, process history, or transport of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science required to characterize actinide oxide molecular structures for forensics science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

  9. Practical guide to surface science and spectroscopy

    CERN Document Server

    Chung, Yip-Wah

    2001-01-01

    Practical Guide to Surface Science and Spectroscopy provides a practical introduction to surface science as well as describes the basic analytical techniques that researchers use to understand what occurs at the surfaces of materials and at their interfaces. These techniques include auger electron spectroscopy, photoelectron spectroscopy, inelastic scattering of electrons and ions, low energy electron diffraction, scanning probe microscopy, and interfacial segregation. Understanding the behavior of materials at their surfaces is essential for materials scientists and engineers as they design and fabricate microelectronics and semiconductor devices. The book gives over 100 examples, discussion questions and problems with varying levels of difficulty. Included with this book is a CD-ROM, which not only contains the same information, but also provides many elements of animation and interaction that are not easily emulated on paper. In diverse subject matters ranging from the operation of ion pumps, computer-...

  10. Surface science principles and current applications

    CERN Document Server

    Taglauer, E; Wandelt, K

    1996-01-01

    Modern technologies increasingly rely on low-dimensional physics at interfaces and in thin-films and nano-structures. Surface science holds a key position in providing the experimental methods and theoretical models for a basic understanding of these effects. This book includes case studies and status reports about research topics such as: surface structure determination by tensor-LEED and surface X-ray diffraction; the preparation and detection of low-dimensional electronic surface states; quantitative surface compositional analysis; the dynamics of adsorption and reaction of adsorbates, e.g. kinetic oscillations; the characterization and control of thin-film and multilayer growth including the influence of surfactants; a critical assessment of the surface physics approach to heterogeneous catalysis.

  11. Manipulation and control of a single molecular rotor on Au (111) surface

    International Nuclear Information System (INIS)

    Hai-Gang, Zhang; Jin-Hai, Mao; Qi, Liu; Nan, Jiang; Hai-Tao, Zhou; Hai-Ming, Guo; Dong-Xia, Shi; Hong-Jun, Gao

    2010-01-01

    Three different methods are used to manipulate and control phthalocyanine based single molecular rotors on Au (111) surface: (1) changing the molecular structure to alter the rotation potential; (2) using the tunnelling current of the scanning tunnelling microscope (STM) to change the thermal equilibrium of the molecular rotor; (3) artificial manipulation of the molecular rotor to switch the rotation on or off by an STM tip. Furthermore, a molecular 'gear wheel' is successfully achieved with two neighbouring molecules. (cross-disciplinary physics and related areas of science and technology)

  12. Scientific data management in the environmental molecular sciences laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, P.R.; Keller, T.L.

    1995-09-01

    The Environmental Molecular Sciences Laboratory (EMSL) is currently under construction at Pacific Northwest Laboratory (PNL) for the U.S. Department of Energy (DOE). This laboratory will be used for molecular and environmental sciences research to identify comprehensive solutions to DOE`s environmental problems. Major facilities within the EMSL include the Molecular Sciences Computing Facility (MSCF), a laser-surface dynamics laboratory, a high-field nuclear magnetic resonance (NMR) laboratory, and a mass spectrometry laboratory. The EMSL is scheduled to open early in 1997 and will house about 260 resident and visiting scientists. It is anticipated that at least six (6) terabytes of data will be archived in the first year of operation. An object-oriented database management system (OODBMS) and a mass storage system will be integrated to provide an intelligent, automated mechanism to manage data. The resulting system, called the DataBase Computer System (DBCS), will provide total scientific data management capabilities to EMSL users. A prototype mass storage system based on the National Storage Laboratory`s (NSL) UniTree has been procured and is in limited use. This system consists of two independent hierarchies of storage devices. One hierarchy of lower capacity, slower speed devices provides support for smaller files transferred over the Fiber Distributed Data Interface (FDDI) network. Also part of the system is a second hierarchy of higher capacity, higher speed devices that will be used to support high performance clients (e.g., a large scale parallel processor). The ObjectStore OODBMS will be used to manage metadata for archived datasets, maintain relationships between archived datasets, and -hold small, duplicate subsets of archived datasets (i.e., derivative data). The interim system is called DBCS, Phase 0 (DBCS-0). The production system for the EMSL, DBCS Phase 1 (DBCS-1), will be procured and installed in the summer of 1996.

  13. Surface-Enhanced Raman Scattering in Molecular Junctions.

    Science.gov (United States)

    Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

    2017-08-18

    Surface-enhanced Raman scattering (SERS) is a surface-sensitive vibrational spectroscopy that allows Raman spectroscopy on a single molecular scale. Here, we present a review of SERS from molecular junctions, in which a single molecule or molecules are made to have contact from the top to the bottom of metal surfaces. The molecular junctions are nice platforms for SERS as well as transport measurement. Electronic characterization based on the transport measurements of molecular junctions has been extensively studied for the development of miniaturized electronic devices. Simultaneous SERS and transport measurement of the molecular junctions allow both structural (geometrical) and electronic information on the single molecule scale. The improvement of SERS measurement on molecular junctions open the door toward new nanoscience and nanotechnology in molecular electronics.

  14. Environmental Molecular Sciences Laboratory Annual Report: Fiscal Year 2006

    Energy Technology Data Exchange (ETDEWEB)

    Foster, Nancy S.; Showalter, Mary Ann

    2007-03-23

    This report describes the activities and research performed at the Environmental Molecular Sciences Laboratory, a Department of Energy national scientific user facility at Pacific Northwest National Laboratory, during Fiscal Year 2006.

  15. Marine molecular biology: an emerging field of biological sciences.

    Science.gov (United States)

    Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G

    2008-01-01

    An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

  16. Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

    Science.gov (United States)

    Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

    2017-06-12

    Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

  17. Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

    Science.gov (United States)

    Bartlett, Rebecca S.; Jette, Marie E.; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

    2012-01-01

    Purpose: This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Method: Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has…

  18. Recent progress in surface science 3

    CERN Document Server

    Danielli, J F; Rosenberg, M D

    2013-01-01

    Recent Progress in Surface Science, Volume 3 covers topics on the structure and mechanisms of the cell membranes. The book discusses the incorporation of chemisorbed species; the recent developments in the study of epitaxy; and the ""diffusion"" or ""hydride"" component of overpotential at cathodes of the ""platinum metals"". The text also describes the mechanism of hydrogen exchange in proteins; the nuclear magnetic resonance studies of lipids, lipoproteins, and cell membranes; and the monolayers of synthetic phospholipids. The formation, electrical properties, transport, and excitability cha

  19. Life Sciences Implications of Lunar Surface Operations

    Science.gov (United States)

    Chappell, Steven P.; Norcross, Jason R.; Abercromby, Andrew F.; Gernhardt, Michael L.

    2010-01-01

    The purpose of this report is to document preliminary, predicted, life sciences implications of expected operational concepts for lunar surface extravehicular activity (EVA). Algorithms developed through simulation and testing in lunar analog environments were used to predict crew metabolic rates and ground reaction forces experienced during lunar EVA. Subsequently, the total metabolic energy consumption, the daily bone load stimulus, total oxygen needed, and other variables were calculated and provided to Human Research Program and Exploration Systems Mission Directorate stakeholders. To provide context to the modeling, the report includes an overview of some scenarios that have been considered. Concise descriptions of the analog testing and development of the algorithms are also provided. This document may be updated to remain current with evolving lunar or other planetary surface operations, assumptions and concepts, and to provide additional data and analyses collected during the ongoing analog research program.

  20. Molecular biology of the Chlamydia pneumoniae surface

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Østergaard, Lars; Birkelund, Svend

    1997-01-01

    surface differs from that of Chlamydia trachomatis. In order to study the surface of C. pneumoniae we generated monoclonal antibodies (MAbs) against C. pneumoniae strain VR-1310 and selected 14 MAbs that reacted with the surface of C. pneumoniae. All MAbs reacted in immunoelectron microscopy...... with the surface of both whole C. pneumoniae VR-1310 elementary bodies and with purified sarcosyl extracted outer membrane complexes. However, only 2 of the MAbs reacted in immunoblotting with C. pneumoniae proteins and only with antigen that had not been heat treated in SDS-sample buffer. This indicates...

  1. Atomic and molecular science with synchrotron radiation

    International Nuclear Information System (INIS)

    1989-01-01

    This paper discusses the following topics: electron correlation in atoms; atomic innershell excitation and decay mechanisms; timing experiments; x-ray scattering; properties of ionized species; electronic properties of actinide atoms; total photon-interaction cross sections; and molecular physics. 66 refs

  2. Molecular Science Computing Facility Scientific Challenges: Linking Across Scales

    Energy Technology Data Exchange (ETDEWEB)

    De Jong, Wibe A.; Windus, Theresa L.

    2005-07-01

    The purpose of this document is to define the evolving science drivers for performing environmental molecular research at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and to provide guidance associated with the next-generation high-performance computing center that must be developed at EMSL's Molecular Science Computing Facility (MSCF) in order to address this critical research. The MSCF is the pre-eminent computing facility?supported by the U.S. Department of Energy's (DOE's) Office of Biological and Environmental Research (BER)?tailored to provide the fastest time-to-solution for current computational challenges in chemistry and biology, as well as providing the means for broad research in the molecular and environmental sciences. The MSCF provides integral resources and expertise to emerging EMSL Scientific Grand Challenges and Collaborative Access Teams that are designed to leverage the multiple integrated research capabilities of EMSL, thereby creating a synergy between computation and experiment to address environmental molecular science challenges critical to DOE and the nation.

  3. Demystifying computer science for molecular ecologists.

    Science.gov (United States)

    Belcaid, Mahdi; Toonen, Robert J

    2015-06-01

    In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373-389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated. © 2015 John Wiley & Sons Ltd.

  4. Committee on Atomic, Molecular, and Optical Sciences (CAMOS)

    International Nuclear Information System (INIS)

    1992-01-01

    The Committee on Atomic, Molecular, and Optical Sciences is a standing committee under the auspices of the Board on Physics and Astronomy, Commission on Physical Sciences, Mathematics, and Applications of the National Academy of Sciences -- National Research Council. The atomic, molecular, and optical (AMO) sciences represent a broad and diverse field in which much of the research is carried out by small groups. These groups generally have not operated in concert with each other and, prior to the establishment of CAMOS, there was no single committee or organization that accepted the responsibility of monitoring the continuing development and assessing the general public health of the field as a whole. CAMOS has accepted this responsibility and currently provides a focus for the AMO community that is unique and essential. The membership of CAMOS is drawn from research laboratories in universities, industry, and government. Areas of expertise on the committee include atomic physics, molecular science, and optics. A special effort has been made to include a balanced representation from the three subfields. (A roster is attached.) CAMOS has conducted a number of studies related to the health of atomic and molecular science and is well prepared to response to requests for studies on specific issues. This report brief reviews the committee work of progress

  5. Probing gas-surface interactions with a molecular beam

    International Nuclear Information System (INIS)

    Spruit, M.E.M.

    1988-01-01

    The dynamics of direct scattering, trapping and sticking in molecular beam scattering is probed. The O 2 /Ag interaction was chosen, using the close-packed (111) plane of Ag as target surface. 170 refs.; 22 figs.; 3 tabs

  6. Supersonic molecular beam experiments on surface chemical reactions.

    Science.gov (United States)

    Okada, Michio

    2014-10-01

    The interaction of a molecule and a surface is important in various fields, and in particular in complex systems like biomaterials and their related chemistry. However, the detailed understanding of the elementary steps in the surface chemistry, for example, stereodynamics, is still insufficient even for simple model systems. In this Personal Account, I review our recent studies of chemical reactions on single-crystalline Cu and Si surfaces induced by hyperthermal oxygen molecular beams and by oriented molecular beams, respectively. Studies of oxide formation on Cu induced by hyperthermal molecular beams demonstrate a significant role of the translational energy of the incident molecules. The use of hyperthermal molecular beams enables us to open up new chemical reaction paths specific for the hyperthermal energy region, and to develop new methods for the fabrication of thin films. On the other hand, oriented molecular beams also demonstrate the possibility of understanding surface chemical reactions in detail by varying the orientation of the incident molecules. The steric effects found on Si surfaces hint at new ways of material fabrication on Si surfaces. Controlling the initial conditions of incoming molecules is a powerful tool for finely monitoring the elementary step of the surface chemical reactions and creating new materials on surfaces. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Committee on Atomic, Molecular, and Optical Sciences (CAMOS)

    International Nuclear Information System (INIS)

    1992-01-01

    The Committee on Atomic, Molecular and Optical Sciences (CAMOS) of the National Research Council (NRC) is charged with monitoring the health of the field of atomic, molecular, and optical (AMO) science in the United States. Accordingly, the Committee identifies and examines both broad and specific issues affecting the field. Regular meetings, teleconferences, briefings from agencies and the scientific community, the formation of study panels to prepare reports, and special symposia are among the mechanisms used by the CAMOS to meet its charge. This progress report presents a review of CAMOS activities from February 1, 1992 to January 31, 1993. This report also includes the status of activities associated with the CAMOS study on the field that is being conducted by the Panel on the Future of Atomic, Molecular, and Optical Sciences (FAMOS)

  8. Molecular surface mesh generation by filtering electron density map.

    Science.gov (United States)

    Giard, Joachim; Macq, Benoît

    2010-01-01

    Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

  9. Molecular Surface Mesh Generation by Filtering Electron Density Map

    Directory of Open Access Journals (Sweden)

    Joachim Giard

    2010-01-01

    Full Text Available Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

  10. Patterned gallium surfaces as molecular mirrors.

    Science.gov (United States)

    Bossi, Alessandra; Rivetti, Claudio; Mangiarotti, Laura; Whitcombe, Michael J; Turner, Anthony P F; Piletsky, Sergey A

    2007-09-30

    An entirely new means of printing molecular information on a planar film, involving casting nanoscale impressions of the template protein molecules in molten gallium, is presented here for the first time. The metallic imprints not only replicate the shape and size of the proteins used as template. They also show specific binding for the template species. Such a simple approach to the creation of antibody-like properties in metallic mirrors can lead to applications in separations, microfluidic devices, and the development of new optical and electronic sensors, and will be of interest to chemists, materials scientists, analytical specialists, and electronic engineers.

  11. Precambrian Surface Temperatures and Molecular Phylogeny

    Science.gov (United States)

    Schwartzman, David; Lineweaver, Charles H.

    2004-06-01

    The timing of emergence of major organismal groups is consistent with the climatic temperature being equal to their upper temperature limit of growth (T_{max}), implying a temperature constraint on the evolution of each group, with the climatic temperature inferred from the oxygen isotope record of marine cherts. Support for this constraint comes from the correlation of T_{max} with the rRNA molecular phylogenetic distance from the last common ancestor (LCA) for both thermophilic Archaea and Bacteria. In particular, this correlation for hyperthermophilic Archaea suggests a climatic temperature of about 120°C at the time of the LCA, likely in the Hadean.

  12. Femtochemistry and femtobiology ultrafast dynamics in molecular science

    CERN Document Server

    Douhal, Abderrazzak

    2002-01-01

    This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

  13. Wetting Properties of Molecularly Rough Surfaces

    Czech Academy of Sciences Publication Activity Database

    Svoboda, Martin; Malijevský, Alexandr; Lísal, Martin

    2015-01-01

    Roč. 143, č. 10 (2015), s. 104701 ISSN 0021-9606 R&D Projects: GA ČR GA13-09914S; GA MŠk LH12020 Institutional support: RVO:67985858 Keywords : contant-angle * solid-surface * dynamics Subject RIV: BJ - Thermodynamics Impact factor: 2.894, year: 2015

  14. EDITORIAL: Focus on Advances in Surface and Interface Science 2008 FOCUS ON ADVANCES IN SURFACE AND INTERFACE SCIENCE 2008

    Science.gov (United States)

    Scheffler, Matthias; Schneider, Wolf-Dieter

    2008-12-01

    Basic research in surface and interface science is highly interdisciplinary, covering the fields of physics, chemistry, biophysics, geo-, atmospheric and environmental sciences, material science, chemical engineering, and more. The various phenomena are interesting by themselves, and they are most important in nearly all modern technologies, as for example electronic, magnetic, and optical devices, sensors, catalysts, lubricants, hard and thermal-barrier coatings, protection against corrosion and crack formation under harsh environments. In fact, detailed understanding of the elementary processes at surfaces is necessary to support and to advance the high technology that very much founds the prosperity and lifestyle of our society. Current state-of-the-art experimental studies of elementary processes at surfaces, of surface properties and functions employ a variety of sophisticated tools. Some are capable of revealing the location and motion of individual atoms. Others measure excitations (electronic, magnetic and vibronic), employing, for example, special light sources such as synchrotrons, high magnetic fields, or free electron lasers. The surprising variety of intriguing physical phenomena at surfaces, interfaces, and nanostructures also pose a persistent challenge for the development of theoretical descriptions, methods, and even basic physical concepts. This second focus issue on the topic of 'Advances in Surface and Interface Science' in New Journal of Physics, following on from last year's successful collection, provides an exciting synoptic view on the latest pertinent developments in the field. Focus on Advances in Surface and Interface Science 2008 Contents Organic layers at metal/electrolyte interfaces: molecular structure and reactivity of viologen monolayers Stephan Breuer, Duc T Pham, Sascha Huemann, Knud Gentz, Caroline Zoerlein, Ralf Hunger, Klaus Wandelt and Peter Broekmann Spin polarized d surface resonance state of fcc Co/Cu(001) K Miyamoto, K

  15. Tuning the deposition of molecular graphene nanoribbons by surface functionalization

    Science.gov (United States)

    Konnerth, R.; Cervetti, C.; Narita, A.; Feng, X.; Müllen, K.; Hoyer, A.; Burghard, M.; Kern, K.; Dressel, M.; Bogani, L.

    2015-07-01

    We show that individual, isolated graphene nanoribbons, created with a molecular synthetic approach, can be assembled on functionalised wafer surfaces treated with silanes. The use of surface groups with different hydrophobicities allows tuning the density of the ribbons and assessing the products of the polymerisation process.

  16. Adsorption of molecular hydrogen on nanostructered surfaces

    International Nuclear Information System (INIS)

    Uranga Piña, Llinersy; Martínez Mesa, Aliezer; Seifert, Gotthard

    2015-01-01

    Were investigated the effect of the structural characteristics of model nanoporous environments on the adsorption of molecular hydrogen. The adsorption properties of the target nanostructures (graphene and ZnO sheets, carbon foams, metal-organic frameworks) are evaluated in a broad range of thermodynamic conditions. The study is carried out within the density functional theory for quantum fluids at finite temperature (QLDFT), which allows to account for the many-body and quantum delocalization effects in a single theoretical framework. The exchange-correlation (excess) functional is derived from the empirical equation of state of the homogeneous system. We focus on the evaluation of hydrogen storage capacities of the substrates and on the emergence of quantum effects triggered by the confinement imposed by the host structure. The approach provides accurate estimates of the hydrogen storage capacities for realistic adsorptive media. The relation between the microscopic structure of the hydrogen fluid and the calculated adsorption properties is also addressed. (full text)

  17. Environmental and Molecular Science Laboratory Arrow

    Energy Technology Data Exchange (ETDEWEB)

    2016-06-24

    Arrows is a software package that combines NWChem, SQL and NOSQL databases, email, and social networks (e.g. Twitter, Tumblr) that simplifies molecular and materials modeling and makes these modeling capabilities accessible to all scientists and engineers. EMSL Arrows is very simple to use. The user just emails chemical reactions to arrows@emsl.pnnl.gov and then an email is sent back with thermodynamic, reaction pathway (kinetic), spectroscopy, and other results. EMSL Arrows parses the email and then searches the database for the compounds in the reactions. If a compound isn't there, an NWChem calculation is setup and submitted to calculate it. Once the calculation is finished the results are entered into the database and then results are emailed back.

  18. Van der Waals and Molecular Science

    International Nuclear Information System (INIS)

    Kox, A J

    1997-01-01

    For many years it has been a source of amazement to scientists and historians of science that no serious scientific biography of J D van der Waals existed. When, more than ten years ago, I became engaged in a correspondence with the Russian historian of science B E Yavelow on the topic of van der Waals, whose biography he was writing, I was both pleased and a bit puzzled. It was clear that Yavelow had not done any archival research in the Netherlands himself, yet he was intimately familiar with many obscure facts from the life of van der Waals. Naturally, I was very curious to see the end result, which appeared in 1985, but although the Amsterdam University Library obtained a copy, my limited knowledge of Russian kept me from forming a judgement on the book. Finally, after more than ten years, an English edition has appeared. The two original Russian authors have joined forces with the well known scientist J S Rowlinson (who earlier edited an English translation of van der Waals's dissertation) to produce a revised and enlarged English version of the Russian original. Now that I have finally been able to study this work, I must admit to being much impressed. Both the life and the work of van der Waals are dealt with in an exemplary way: the authors' command of primary and secondary sources is impressive, as is their understanding of the Dutch social and educational circumstances in the last century. Teaching and research at the newly-founded University of Amsterdam, as well as activities in the Academy of Sciences, are discussed in great and interesting detail. Van der Waals's education and rise from a simple teacher to one of the foremost theoretical physicists in Europe teaches us much about his personality as well as about the opportunities offered by the Dutch educational system. In their discussion of the development of van der Waals's ideas and their impact (including an interesting chapter on the reception in Russia) the authors are not afraid to go into

  19. Effect of polar surfaces on organic molecular crystals

    Science.gov (United States)

    Sharia, Onise; Tsyshevskiy, Roman; Kuklja, Maija; University of Maryland College Park Team

    Polar oxide materials reveal intriguing opportunities in the field of electronics, superconductivity and nanotechnology. While behavior of polar surfaces has been widely studied on oxide materials and oxide-oxide interfaces, manifestations and properties of polar surfaces in molecular crystals are still poorly understood. Here we discover that the polar catastrophe phenomenon, known on oxides, also takes place in molecular materials as illustrated with an example of cyclotetramethylene tetranitramine (HMX) crystals. We show that the surface charge separation is a feasible compensation mechanism to counterbalance the macroscopic dipole moment and remove the electrostatic instability. We discuss the role of surface charge on degradation of polar surfaces, electrical conductivity, optical band-gap closure and surface metallization. Research is supported by the US ONR (Grants N00014-16-1-2069 and N00014-16-1-2346) and NSF. We used NERSC, XSEDE and MARCC computational resources.

  20. CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE.

    Science.gov (United States)

    Mikucki, Michael; Zhou, Y C

    2017-01-01

    This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization.

  1. Autonomous molecular cascades for evaluation of cell surfaces

    Science.gov (United States)

    Rudchenko, Maria; Taylor, Steven; Pallavi, Payal; Dechkovskaia, Alesia; Khan, Safana; Butler, Vincent P., Jr.; Rudchenko, Sergei; Stojanovic, Milan N.

    2013-08-01

    Molecular automata are mixtures of molecules that undergo precisely defined structural changes in response to sequential interactions with inputs. Previously studied nucleic acid-based automata include game-playing molecular devices (MAYA automata) and finite-state automata for the analysis of nucleic acids, with the latter inspiring circuits for the analysis of RNA species inside cells. Here, we describe automata based on strand-displacement cascades directed by antibodies that can analyse cells by using their surface markers as inputs. The final output of a molecular automaton that successfully completes its analysis is the presence of a unique molecular tag on the cell surface of a specific subpopulation of lymphocytes within human blood cells.

  2. Advances in Molecular Rotational Spectroscopy for Applied Science

    Science.gov (United States)

    Harris, Brent; Fields, Shelby S.; Pulliam, Robin; Muckle, Matt; Neill, Justin L.

    2017-06-01

    Advances in chemical sensitivity and robust, solid-state designs for microwave/millimeter-wave instrumentation compel the expansion of molecular rotational spectroscopy as research tool into applied science. It is familiar to consider molecular rotational spectroscopy for air analysis. Those techniques for molecular rotational spectroscopy are included in our presentation of a more broad application space for materials analysis using Fourier Transform Molecular Rotational Resonance (FT-MRR) spectrometers. There are potentially transformative advantages for direct gas analysis of complex mixtures, determination of unknown evolved gases with parts per trillion detection limits in solid materials, and unambiguous chiral determination. The introduction of FT-MRR as an alternative detection principle for analytical chemistry has created a ripe research space for the development of new analytical methods and sampling equipment to fully enable FT-MRR. We present the current state of purpose-built FT-MRR instrumentation and the latest application measurements that make use of new sampling methods.

  3. Molecular dynamics simulation of annealed ZnO surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Min, Tjun Kit; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

    2015-04-24

    The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.

  4. Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics

    Science.gov (United States)

    Dai, Hai-Lung

    2002-03-01

    Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

  5. EDITORIAL: From reciprocal space to real space in surface science From reciprocal space to real space in surface science

    Science.gov (United States)

    Bartels, Ludwig; Ernst, Karl-Heinz

    2012-09-01

    Triest.let's finish—aus basta Some move atoms around to hear how they sound.Karl-Heinz Rieder, Erice, 6 April 1998 From reciprocal space to real space in surface science contents From reciprocal space to real space in surface scienceLudwig Bartels and Karl-Heinz Ernst Karl-Heinz Reider: the quiet pioneerGiorgio Benedek Scattering of CO and N2 molecules by a graphite surfaceJunepyo Oh, Takahiro Kondo, Keitaro Arakawa, Yoshihiko Saito, Junji Nakamura, W W Hayes and J R Manson Helium, neon and argon diffraction from Ru(0001)M Minniti, C Díaz, J L Fernández Cuñado, A Politano, D Maccariello, F Martín, D Farías and R Miranda Enhanced charge transfer in a monolayer of the organic charge transfer complex TTF-TNAP on Au(111)T R Umbach, I Fernandez-Torrente, J N Ladenthin, J I Pascual and K J Franke Extended pattern recognition scheme for self-learning kinetic Monte Carlo simulationsSyed Islamuddin Shah, Giridhar Nandipati, Abdelkader Kara and Talat S Rahman Acetylene on Cu(111): imaging a molecular surface arrangement with a constantly rearranging tipYeming Zhu, Jonathan Wyrick, Kamelia D Cohen, Katie Marie Magnone, Connor Holzke, Daniel Salib, Quan Ma, Dezheng Sun and Ludwig Bartels Coulomb attraction during the carpet growth mode of NaClFriederike Matthaei, Sarah Heidorn, Konrad Boom, Cord Bertram, Ali Safiei, Jörg Henzl and Karina Morgenstern Molecular self-assembly on an insulating surface: interplay between substrate templating and intermolecular interactionsMarkus Kittelmann, Philipp Rahe and Angelika Kühnle Vertical manipulation of native adatoms on the InAs(111)A surfaceJ Yang, C Nacci, J Martínez-Blanco, K Kanisawa and S Fölsch Charge transfer between isomer domains on n+-doped Si(111)-2 × 1: energetic stabilizationR M Feenstra, G Bussetti, B Bonanni, A Violante, C Goletti, P Chiaradia, M G Betti and C Mariani Probing the properties of metal-oxide interfaces: silica films on Mo and Ru supportsLeonid Lichtenstein, Markus Heyde, Stefan Ulrich, Niklas Nilius

  6. Immobilized enzymes: understanding enzyme - surface interactions at the molecular level.

    Science.gov (United States)

    Hoarau, Marie; Badieyan, Somayesadat; Marsh, E Neil G

    2017-11-22

    Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity. An appreciation of the molecular interactions between enzyme and surface support has allowed the surface chemistry and method of enzyme attachement to be fine-tuned such that activity and stability can be greatly enhanced. These advances suggest that a much wider variety of enzymes may eventually be amenable to immobilization as green catalysts.

  7. Thermochemical Surface Engineering: A Playground for Science and Innovation

    DEFF Research Database (Denmark)

    Christiansen, Thomas Lundin; Dahl, Kristian Vinter; Jellesen, Morten Stendahl

    2017-01-01

    Surface engineering by thermochemical processing is the intentional change of the composition of a material at elevated temperature with the purpose to improve materials performance. In thermochemical processing components from the starting material are essential in the development of the phases...... at the surface. Current research and innovation activities are used to exemplify thermochemical surface engineering and the interplay of science and innovation. The examples given encompass aspects of the synthesis of extremely porous materials, low temperature surface hardening of stainless steel, surface...

  8. Spin polarized electrons in surface science

    International Nuclear Information System (INIS)

    Siegmann, H.C.

    1983-01-01

    The potentialities of spin-polarised electron beams as a probe of surface magnetic properties are outlined. Elastic as well as inelastic scattering of electrons from solid surfaces are considered. (G.Q.)

  9. Molecular Environmental Science and Synchrotron Radiation Facilities An Update of the 1995 DOE-Airlie Report on Molecular Environmental Science

    Energy Technology Data Exchange (ETDEWEB)

    Bargar, John R

    1999-05-07

    This workshop was requested by Dr. Robert Marianelli, Director of the DOE-BES Chemical Sciences Division, to update the findings of the Workshop on Molecular Environmental Sciences (MES) held at Airlie, VA, in July 1995. The Airlie Workshop Report defined the new interdisciplinary field referred to as Molecular Environmental Science (MES), reviewed the synchrotron radiation methods used in MES research, assessed the adequacy of synchrotron radiation facilities for research in this field, and summarized the beam time requirements of MES users based on a national MES user survey. The objectives of MES research are to provide information on the chemical and physical forms (speciation), spatial distribution, and reactivity of contaminants in natural materials and man-made waste forms, and to develop a fundamental understanding of the complex molecular-scale environmental processes, both chemical and biological, that affect the stability, transformations, mobility, and toxicity of contaminant species. These objectives require parallel studies of ''real'' environmental samples, which are complicated multi-phase mixtures with chemical and physical heterogeneities, and of simplified model systems in which variables can be controlled and fundamental processes can be examined. Only by this combination of approaches can a basic understanding of environmental processes at the molecular-scale be achieved.

  10. Molecular Environmental Science and Synchrotron Radiation Facilities An Update of the 1995 DOE-Airlie Report on Molecular Environmental Science

    International Nuclear Information System (INIS)

    Bargar, John R

    1999-01-01

    This workshop was requested by Dr. Robert Marianelli, Director of the DOE-BES Chemical Sciences Division, to update the findings of the Workshop on Molecular Environmental Sciences (MES) held at Airlie, VA, in July 1995. The Airlie Workshop Report defined the new interdisciplinary field referred to as Molecular Environmental Science (MES), reviewed the synchrotron radiation methods used in MES research, assessed the adequacy of synchrotron radiation facilities for research in this field, and summarized the beam time requirements of MES users based on a national MES user survey. The objectives of MES research are to provide information on the chemical and physical forms (speciation), spatial distribution, and reactivity of contaminants in natural materials and man-made waste forms, and to develop a fundamental understanding of the complex molecular-scale environmental processes, both chemical and biological, that affect the stability, transformations, mobility, and toxicity of contaminant species. These objectives require parallel studies of ''real'' environmental samples, which are complicated multi-phase mixtures with chemical and physical heterogeneities, and of simplified model systems in which variables can be controlled and fundamental processes can be examined. Only by this combination of approaches can a basic understanding of environmental processes at the molecular-scale be achieved

  11. Ti and Zr surfaces studied by molecular dynamics

    International Nuclear Information System (INIS)

    Pascuet, Maria I.; Passianot, Roberto C.; Monti, Ana M.

    2003-01-01

    The interaction between point defects technique and the (0001), (1-210), (10-10) surfaces in Ti and Zr is studied by the molecular dynamics technique. Both of metals are in the hexagonal structure and within a temperature range of 100 to 900 K. The atomic interactions are modeled by EAM-type many-body potentials, that were used previously in static simulations. New migration mechanisms are unraveled and others are verified with respect to those already proposed in the static studies. Also included is an analysis of the vacancy stability in the sub-surface layers of the prismatic surfaces. (author)

  12. Molecularly engineered graphene surfaces for sensing applications: A review

    International Nuclear Information System (INIS)

    Liu, Jingquan; Liu, Zhen; Barrow, Colin J.; Yang, Wenrong

    2015-01-01

    Highlights: • The importance of surface chemistry of graphene materials is clearly described. • We discuss molecularly engineered graphene surfaces for sensing applications. • We describe the latest developments of these materials for sensing technology. - Abstract: Graphene is scientifically and commercially important because of its unique molecular structure which is monoatomic in thickness, rigorously two-dimensional and highly conjugated. Consequently, graphene exhibits exceptional electrical, optical, thermal and mechanical properties. Herein, we critically discuss the surface modification of graphene, the specific advantages that graphene-based materials can provide over other materials in sensor research and their related chemical and electrochemical properties. Furthermore, we describe the latest developments in the use of these materials for sensing technology, including chemical sensors and biosensors and their applications in security, environmental safety and diseases detection and diagnosis

  13. Molecularly engineered graphene surfaces for sensing applications: A review

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jingquan, E-mail: jliu@qdu.edu.cn [College of Chemical Science and Engineering, Laboratory of Fiber Materials and Modern Textile, The Growing Base for State Key Laboratory, Qingdao University, Qingdao (China); Liu, Zhen; Barrow, Colin J. [Centre for Chemistry and Biotechnology, Deakin University, Geelong, VIC 3217 (Australia); Yang, Wenrong, E-mail: wenrong.yang@deakin.edu.au [Centre for Chemistry and Biotechnology, Deakin University, Geelong, VIC 3217 (Australia)

    2015-02-15

    Highlights: • The importance of surface chemistry of graphene materials is clearly described. • We discuss molecularly engineered graphene surfaces for sensing applications. • We describe the latest developments of these materials for sensing technology. - Abstract: Graphene is scientifically and commercially important because of its unique molecular structure which is monoatomic in thickness, rigorously two-dimensional and highly conjugated. Consequently, graphene exhibits exceptional electrical, optical, thermal and mechanical properties. Herein, we critically discuss the surface modification of graphene, the specific advantages that graphene-based materials can provide over other materials in sensor research and their related chemical and electrochemical properties. Furthermore, we describe the latest developments in the use of these materials for sensing technology, including chemical sensors and biosensors and their applications in security, environmental safety and diseases detection and diagnosis.

  14. Workshop on surface and interface science at the ESRF

    Energy Technology Data Exchange (ETDEWEB)

    Norris, C.; Stierle, A.; Kasper, N.; Dosch, H.; Schmidt, S.; Hufner, S.; Moritz, W.; Fedley, Ch.S.; Rossi, G.; Durr Hermann, A.; Rohlsberger, R.; Dalmas, J.; Oughaddou, H.; Leandri, Ch.; Gay, J.M.; Treglia, G.; Le Lay, G.; Aufray, B.; Bunk, O.; Johnson, R.L.; Frenken, J.W.M.; Lucas, C.A.; Bauer, G.; Zhong, Z.; Springholz, G.; Lechner, R.; Stang, J.; Schulli, T.; Metzger, T.H.; Holy, V.; Woodruff, D.P.; Dellera, C.; Zegenhagen, J.; Robinson, I.; Malachias, A.; Schulli, T.U.; Magalhaes-Paniago, R.; Stoffel, M.; Schmidt, O.G.; Boragno, C.; Buatier de Mongeot, F.; Valbusa, U.; Felici, R.; Yacoby, Y.; Bedzyk, M.J.; Van der Veen, J.F

    2004-07-01

    The main aim of the workshop is to reflect the future of surface and interface research at the high brilliance synchrotron radiation source ESRF taking into account experimental facilities which are becoming available at new synchrotron radiation facilities in Europe. 6 sessions have been organized: 1) surface and interface research and synchrotron radiation - today and tomorrow -, 2) aspects of surface and interface research, 3) real surfaces and interfaces, 4) synchrotron techniques in surface and interface research, 5) new directions in surface and interface research, and 6) surface and interface science at ESRF. This document gathers the abstracts of the presentations.

  15. Workshop on surface and interface science at the ESRF

    International Nuclear Information System (INIS)

    Norris, C.; Stierle, A.; Kasper, N.; Dosch, H.; Schmidt, S.; Hufner, S.; Moritz, W.; Fedley, Ch.S.; Rossi, G.; Durr Hermann, A.; Rohlsberger, R.; Dalmas, J.; Oughaddou, H.; Leandri, Ch.; Gay, J.M.; Treglia, G.; Le Lay, G.; Aufray, B.; Bunk, O.; Johnson, R.L.; Frenken, J.W.M.; Lucas, C.A.; Bauer, G.; Zhong, Z.; Springholz, G.; Lechner, R.; Stang, J.; Schulli, T.; Metzger, T.H.; Holy, V.; Woodruff, D.P.; Dellera, C.; Zegenhagen, J.; Robinson, I.; Malachias, A.; Schulli, T.U.; Magalhaes-Paniago, R.; Stoffel, M.; Schmidt, O.G.; Boragno, C.; Buatier de Mongeot, F.; Valbusa, U.; Felici, R.; Yacoby, Y.; Bedzyk, M.J.; Van der Veen, J.F.

    2004-01-01

    The main aim of the workshop is to reflect the future of surface and interface research at the high brilliance synchrotron radiation source ESRF taking into account experimental facilities which are becoming available at new synchrotron radiation facilities in Europe. 6 sessions have been organized: 1) surface and interface research and synchrotron radiation - today and tomorrow -, 2) aspects of surface and interface research, 3) real surfaces and interfaces, 4) synchrotron techniques in surface and interface research, 5) new directions in surface and interface research, and 6) surface and interface science at ESRF. This document gathers the abstracts of the presentations

  16. Molecular Dynamics Simulation and Analysis of Interfacial Water at Selected Sulfide Mineral Surfaces under Anaerobic Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.

    2014-04-10

    In this paper, we report on a molecular dynamics simulation (MDS) study of the behavior of interfacial water at selected sulfide mineral surfaces under anaerobic conditions. The study revealed the interfacial water structure and wetting characteristics of the pyrite (100) surface, galena (100) surface, chalcopyrite (012) surface, sphalerite (110) surface, and molybdenite surfaces (i.e., the face, armchair-edge, and zigzag-edge surfaces), including simulated contact angles, relative number density profiles, water dipole orientations, hydrogen-bonding, and residence times. For force fields of the metal and sulfur atoms in selected sulfide minerals used in the MDS, we used the universal force field (UFF) and another set of force fields optimized by quantum chemical calculations for interactions with interfacial water molecules at selected sulfide mineral surfaces. Simulation results for the structural and dynamic properties of interfacial water molecules indicate the natural hydrophobic character for the selected sulfide mineral surfaces under anaerobic conditions as well as the relatively weak hydrophobicity for the sphalerite (110) surface and two molybdenite edge surfaces. Part of the financial support for this study was provided by the U.S. Department of Energy (DOE) under Basic Science Grant No. DE-FG-03-93ER14315. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE, funded work performed by Liem X. Dang. Battelle operates Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES. The authors are grateful to Professor Tsun-Mei Chang for valuable discussions.

  17. Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

    Science.gov (United States)

    Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

    2017-08-22

    A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

  18. Atomic and molecular layer deposition for surface modification

    Energy Technology Data Exchange (ETDEWEB)

    Vähä-Nissi, Mika, E-mail: mika.vaha-nissi@vtt.fi [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland); Sievänen, Jenni; Salo, Erkki; Heikkilä, Pirjo; Kenttä, Eija [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland); Johansson, Leena-Sisko, E-mail: leena-sisko.johansson@aalto.fi [Aalto University, School of Chemical Technology, Department of Forest Products Technology, PO Box 16100, FI‐00076 AALTO (Finland); Koskinen, Jorma T.; Harlin, Ali [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland)

    2014-06-01

    Atomic and molecular layer deposition (ALD and MLD, respectively) techniques are based on repeated cycles of gas–solid surface reactions. A partial monolayer of atoms or molecules is deposited to the surface during a single deposition cycle, enabling tailored film composition in principle down to molecular resolution on ideal surfaces. Typically ALD/MLD has been used for applications where uniform and pinhole free thin film is a necessity even on 3D surfaces. However, thin – even non-uniform – atomic and molecular deposited layers can also be used to tailor the surface characteristics of different non-ideal substrates. For example, print quality of inkjet printing on polymer films and penetration of water into porous nonwovens can be adjusted with low-temperature deposited metal oxide. In addition, adhesion of extrusion coated biopolymer to inorganic oxides can be improved with a hybrid layer based on lactic acid. - Graphical abstract: Print quality of a polylactide film surface modified with atomic layer deposition prior to inkjet printing (360 dpi) with an aqueous ink. Number of printed dots illustrated as a function of 0, 5, 15 and 25 deposition cycles of trimethylaluminum and water. - Highlights: • ALD/MLD can be used to adjust surface characteristics of films and fiber materials. • Hydrophobicity after few deposition cycles of Al{sub 2}O{sub 3} due to e.g. complex formation. • Same effect on cellulosic fabrics observed with low temperature deposited TiO{sub 2}. • Different film growth and oxidation potential with different precursors. • Hybrid layer on inorganic layer can be used to improve adhesion of polymer melt.

  19. Waves on the surface of the Orion molecular cloud.

    Science.gov (United States)

    Berné, Olivier; Marcelino, Núria; Cernicharo, José

    2010-08-19

    Massive stars influence their parental molecular cloud, and it has long been suspected that the development of hydrodynamical instabilities can compress or fragment the cloud. Identifying such instabilities has proved difficult. It has been suggested that elongated structures (such as the 'pillars of creation') and other shapes arise because of instabilities, but alternative explanations are available. One key signature of an instability is a wave-like structure in the gas, which has hitherto not been seen. Here we report the presence of 'waves' at the surface of the Orion molecular cloud near where massive stars are forming. The waves seem to be a Kelvin-Helmholtz instability that arises during the expansion of the nebula as gas heated and ionized by massive stars is blown over pre-existing molecular gas.

  20. Machine learning and pattern recognition from surface molecular architectures.

    Science.gov (United States)

    Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Sumpter, Bobby; Kalinin, Sergei

    The ability to utilize molecular assemblies as data storage devices requires capability to identify individual molecular states on a scale of thousands of molecules. We present a novel method of applying machine learning techniques for extraction of positional and rotational information from ultra-high vacuum scanning tunneling microscopy (STM) images and apply it to self-assembled monolayer of π-bowl sumanene molecules on gold. From density functional theory (DFT) simulations, we assume existence of distinct polar and multiple azimuthal rotational states. We use DFT-generated templates in conjunction with Markov Chain Monte Carlo (MCMC) sampler and noise modeling to create synthetic images representative of our model. We extract positional information of each molecule and use nearest neighbor criteria to construct a graph input to Markov Random Field (MRF) model to identify polar rotational states. We train a convolutional Neural Network (cNN) on a synthetic dataset and combine it with MRF model to classify molecules based on their azimuthal rotational state. We demonstrate effectiveness of such approach compared to other methods. Finally, we apply our approach to experimental images and achieve complete rotational class information extraction. This research was sponsored by the Division of Materials Sciences and Engineering, Office of Science, Basic Energy Sciences, US DOE.

  1. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.

    1996-01-01

    of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

  2. Molecular cartography of the human skin surface in 3D

    Science.gov (United States)

    Bouslimani, Amina; Porto, Carla; Rath, Christopher M.; Wang, Mingxun; Guo, Yurong; Gonzalez, Antonio; Berg-Lyon, Donna; Ackermann, Gail; Moeller Christensen, Gitte Julie; Nakatsuji, Teruaki; Zhang, Lingjuan; Borkowski, Andrew W.; Meehan, Michael J.; Dorrestein, Kathleen; Gallo, Richard L.; Bandeira, Nuno; Knight, Rob; Alexandrov, Theodore; Dorrestein, Pieter C.

    2015-01-01

    The human skin is an organ with a surface area of 1.5–2 m2 that provides our interface with the environment. The molecular composition of this organ is derived from host cells, microbiota, and external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance the technologies needed to explore the topographical distribution of skin molecules, using 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal that the molecular composition of skin has diverse distributions and that the composition is defined not only by skin cells and microbes but also by our daily routines, including the application of hygiene products. The technological development of these maps lays a foundation for studying the spatial relationships of human skin with hygiene, the microbiota, and environment, with potential for developing predictive models of skin phenotypes tailored to individual health. PMID:25825778

  3. Protein signatures using electrostatic molecular surfaces in harmonic space

    Directory of Open Access Journals (Sweden)

    C. Sofia Carvalho

    2013-10-01

    Full Text Available We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the molecular electrostatic potential, whose three-dimensional coordinates have been either experimentally or theoretically determined. Thus we achieve a reduction of the initial three-dimensional information on the molecular surface to the one-dimensional information on pairs of points at a fixed scale apart. Consequently, the similarity search in our method is computationally less demanding and significantly faster than shape comparison methods. As proof of principle, we applied our method to a training set of viral proteins that are involved in major diseases such as Hepatitis C, Dengue fever, Yellow fever, Bovine viral diarrhea and West Nile fever. The training set contains proteins of four different protein families, as well as a mammalian representative enzyme. We found that the power spectrum successfully assigns a unique signature to each protein included in our training set, thus providing a direct probe of functional similarity among proteins. The results agree with established biological data from conventional structural biochemistry analyses.

  4. Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

    Science.gov (United States)

    Poloni, Laura N.

    The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L

  5. Surface tension and contact angles: Molecular origins and associated microstructure

    Science.gov (United States)

    Davis, H. T.

    1982-01-01

    Gradient theory converts the molecular theory of inhomogeneous fluid into nonlinear boundary value problems for density and stress distributions in fluid interfaces, contact line regions, nuclei and microdroplets, and other fluid microstructures. The relationship between the basic patterns of fluid phase behavior and the occurrence and stability of fluid microstructures was clearly established by the theory. All the inputs of the theory have molecular expressions which are computable from simple models. On another level, the theory becomes a phenomenological framework in which the equation of state of homogeneous fluid and sets of influence parameters of inhomogeneous fluids are the inputs and the structures, stress tensions and contact angles of menisci are the outputs. These outputs, which find applications in the science and technology of drops and bubbles, are discussed.

  6. Surface science models of CoMoS hydrodesulfurisation catalysts

    NARCIS (Netherlands)

    Jong, de A.M.; Beer, de V.H.J.; Veen, van J.A.R.; Niemantsverdriet, J.W.; Froment, G.F.; Delmon, B.; Grange, P.

    1997-01-01

    Characterization of supported catalysts with surface spectroscopic techniques is often limited due to restraints imposed by the support material. The use of flat conducting substrates as a model support offers a way to apply these techniques to their full potential. Such surface science models of

  7. Interdisciplinary research center devoted to molecular environmental science opens

    Science.gov (United States)

    Vaughan, David J.

    In October, a new research center opened at the University of Manchester in the United Kingdom. The center is the product of over a decade of ground-breaking interdisciplinary research in the Earth and related biological and chemical sciences at the university The center also responds to the British governments policy of investing in research infrastructure at key universities.The Williamson Research Centre, the first of its kind in Britain and among the first worldwide, is devoted to the emerging field of molecular environmental science. This field also aims to bring about a revolution in understanding of our environment. Though it may be a less violent revolution than some, perhaps, its potential is high for developments that could affect us all.

  8. Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006

  9. Multiresolution molecular mechanics: Surface effects in nanoscale materials

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Qingcheng, E-mail: qiy9@pitt.edu; To, Albert C., E-mail: albertto@pitt.edu

    2017-05-01

    Surface effects have been observed to contribute significantly to the mechanical response of nanoscale structures. The newly proposed energy-based coarse-grained atomistic method Multiresolution Molecular Mechanics (MMM) (Yang, To (2015), ) is applied to capture surface effect for nanosized structures by designing a surface summation rule SR{sup S} within the framework of MMM. Combined with previously proposed bulk summation rule SR{sup B}, the MMM summation rule SR{sup MMM} is completed. SR{sup S} and SR{sup B} are consistently formed within SR{sup MMM} for general finite element shape functions. Analogous to quadrature rules in finite element method (FEM), the key idea to the good performance of SR{sup MMM} lies in that the order or distribution of energy for coarse-grained atomistic model is mathematically derived such that the number, position and weight of quadrature-type (sampling) atoms can be determined. Mathematically, the derived energy distribution of surface area is different from that of bulk region. Physically, the difference is due to the fact that surface atoms lack neighboring bonding. As such, SR{sup S} and SR{sup B} are employed for surface and bulk domains, respectively. Two- and three-dimensional numerical examples using the respective 4-node bilinear quadrilateral, 8-node quadratic quadrilateral and 8-node hexahedral meshes are employed to verify and validate the proposed approach. It is shown that MMM with SR{sup MMM} accurately captures corner, edge and surface effects with less 0.3% degrees of freedom of the original atomistic system, compared against full atomistic simulation. The effectiveness of SR{sup MMM} with respect to high order element is also demonstrated by employing the 8-node quadratic quadrilateral to solve a beam bending problem considering surface effect. In addition, the introduced sampling error with SR{sup MMM} that is analogous to numerical integration error with quadrature rule in FEM is very small. - Highlights:

  10. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwagi, H [Institute for Molecular Science, Okazaki, Aichi (Japan)

    1982-06-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience.

  11. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    International Nuclear Information System (INIS)

    Kashiwagi, H.

    1982-01-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience. (orig.)

  12. Molecular recognition on a cavitand-functionalized silicon surface.

    Science.gov (United States)

    Biavardi, Elisa; Favazza, Maria; Motta, Alessandro; Fragalà, Ignazio L; Massera, Chiara; Prodi, Luca; Montalti, Marco; Melegari, Monica; Condorelli, Guglielmo G; Dalcanale, Enrico

    2009-06-03

    A Si(100) surface featuring molecular recognition properties was obtained by covalent functionalization with a tetraphosphonate cavitand (Tiiii), able to complex positively charged species. Tiiii cavitand was grafted onto the Si by photochemical hydrosilylation together with 1-octene as a spatial spectator. The recognition properties of the Si-Tiiii surface were demonstrated through two independent analytical techniques, namely XPS and fluorescence spectroscopy, during the course of reversible complexation-guest exchange-decomplexation cycles with specifically designed ammonium and pyridinium salts. Control experiments employing a Si(100) surface functionalized with a structurally similar, but complexation inactive, tetrathiophosphonate cavitand (TSiiii) demonstrated no recognition events. This provides evidence for the complexation properties of the Si-Tiiii surface, ruling out the possibility of nonspecific interactions between the substrate and the guests. The residual Si-O(-) terminations on the surface replace the guests' original counterions, thus stabilizing the complex ion pairs. These results represent a further step toward the control of self-assembly of complex supramolecular architectures on surfaces.

  13. Forces on nuclei moving on autoionizing molecular potential energy surfaces.

    Science.gov (United States)

    Moiseyev, Nimrod

    2017-01-14

    Autoionization of molecular systems occurs in diatomic molecules and in small biochemical systems. Quantum chemistry packages enable calculation of complex potential energy surfaces (CPESs). The imaginary part of the CPES is associated with the autoionization decay rate, which is a function of the molecular structure. Molecular dynamics simulations, within the framework of the Born-Oppenheimer approximation, require the definition of a force field. The ability to calculate the forces on the nuclei in bio-systems when autoionization takes place seems to rely on an understanding of radiative damages in RNA and DNA arising from the release of slow moving electrons which have long de Broglie wavelengths. This work addresses calculation of the real forces on the nuclei moving on the CPES. By using the transformation of the time-dependent Schrödinger equation, previously used by Madelung, we proved that the classical forces on nuclei moving on the CPES correlated with the gradient of the real part of the CPES. It was proved that the force on the nuclei of the metastable molecules is time independent although the probability to detect metastable molecules exponentially decays. The classical force is obtained from the transformed Schrödinger equation when ℏ=0 and the Schrödinger equation is reduced to the classical (Newtonian) equations of motion. The forces on the nuclei regardless on what potential energy surface they move (parent CPES or product real PESs) vary in time due to the autoionization process.

  14. Building a Collaboratory in Environmental and Molecular Science

    Energy Technology Data Exchange (ETDEWEB)

    Kouzes, R.T.; Myers, J.D.; Devaney, D.M.; Dunning, T.H.; Wise, J.A.

    1994-03-01

    A Collaboratory is a meta-laboratory that spans multiple geographical areas with collaborators interacting via electronic means. Collaboratories are designed to enable close ties between scientists in a given research area, promote collaborations involving scientists in diverse areas, accelerate the development and dissemination of basic knowledge, and minimize the time-lag between discovery and application. PNL is developing the concept of an Environmental and Molecular Sciences Collaboratory (EMSC) as a natural evolution of the EMSL project. The goal of the EMSC is to increase the efficiency of research and reduce the time required to implement new environmental remediation and preservation technologies. The EMSC will leverage the resources (intellectual and physical) of the EMSL by making them more accessible to remote collaborators as well as by making the resources of remote sites available to local researchers. It will provide a common set of computer hardware and software tools to support remote collaboration, a key step in establishing a collaborative culture for scientists in the theoretical, computational, and experimental molecular sciences across the nation. In short, the EMSC will establish and support an `electronic community of scientists researching and developing innovative environmental preservation and restoration technologies.

  15. Building a Collaboratory in Environmental and Molecular Science

    International Nuclear Information System (INIS)

    Kouzes, R.T.; Myers, J.D.; Devaney, D.M.; Dunning, T.H.; Wise, J.A.

    1994-03-01

    A Collaboratory is a meta-laboratory that spans multiple geographical areas with collaborators interacting via electronic means. Collaboratories are designed to enable close ties between scientists in a given research area, promote collaborations involving scientists in diverse areas, accelerate the development and dissemination of basic knowledge, and minimize the time-lag between discovery and application. PNL is developing the concept of an Environmental and Molecular Sciences Collaboratory (EMSC) as a natural evolution of the EMSL project. The goal of the EMSC is to increase the efficiency of research and reduce the time required to implement new environmental remediation and preservation technologies. The EMSC will leverage the resources (intellectual and physical) of the EMSL by making them more accessible to remote collaborators as well as by making the resources of remote sites available to local researchers. It will provide a common set of computer hardware and software tools to support remote collaboration, a key step in establishing a collaborative culture for scientists in the theoretical, computational, and experimental molecular sciences across the nation. In short, the EMSC will establish and support an 'electronic community of scientists researching and developing innovative environmental preservation and restoration technologies

  16. Implementation of surface hopping molecular dynamics using semiempirical methods

    International Nuclear Information System (INIS)

    Fabiano, E.; Keal, T.W.; Thiel, W.

    2008-01-01

    A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

  17. Molecular beam scattering from clean surfaces of alkali halides

    International Nuclear Information System (INIS)

    Meyers, J.A.

    1975-01-01

    Molecular beam scattering of light gases from in situ cleaved alkali halide surfaces has been studied as a means of developing molecular beam scattering as a surface characterization tool and as a means of obtaining information about the gas atom-solid surface potential interaction. For 4 He scattering from LiF carried out under improved resolution the main results are: (1) there are four bound states in the surface potential well, as energies of -5.8, -2.2, -0.6 and -0.1 MeV. (2) Most of the structure designated as ''fine structure'' is due either to transitions to these four levels via various small reciprocal lattice vectors or to the opening of diffraction channels. (3) The transitions involving the (01) and (0 anti 1) reciprocal lattice vectors (i.e., the ones nearly perpendicular to the incident wavevector) are strong; as much as 85 percent of the specular intensity may be removed. Transitions via the other small reciprocal lattice vectors are much weaker. (4) The widths of the lines are consistent with the velocity distribution, which has a half-width of about 2 percent. (5) The observed energies agree fairly well with those calculated for a zeta-function potential, but are not consistent with a Morse potential. The preliminary results for 4 He/NaF scattering are that there are three bound-states in the surface potential well and are quite similar to the LiF results. These energies are -5.0, -1.9, and -0.5 MeV. 4 He/NaF selective adsorption also shows ''fine structure'' and a more detailed analysis is called for here

  18. Surface confined assemblies and polymers for sensing and molecular logic

    Science.gov (United States)

    de Ruiter, Graham; Altman, Marc; Motiei, Leila; Lahav, Michal; van der Boom, Milko E.

    2013-05-01

    Since the development of molecule-based sensors and the introduction of molecules mimicking the behavior of the AND gate in solution by de Silva in 1993, molecular (Boolean) Logic and Computing (MBLC) has become increasingly popular. The molecular approach toward Boolean logic resulted in intriguing proofs of concepts in solution including logic gates, half-adders, multiplexers, and flip-flop logic circuits. Molecular assemblies can perform diverse logic tasks by reconfiguring their inputs. Our recent research activities focus on MBLC with electrochromic polymers and immobilized polypyridyl complexes on solid support. We have designed a series of coordination-based thin films that are formed linearly by stepwise wet-chemical deposition or by self-propagating molecular assembly. The electrochromic properties of these films can be used for (i) detecting various analytes in solution and in the air, (ii) MBLC, (iii) electron-transfer studies, and (iv) interlayers for efficient inverted bulk-heterojunction solar cells. Our concept toward MBLC with functionalized surfaces is applicable to electrochemical and chemical inputs coupled with optical readout. Using this approach, we demonstrated various logic architectures with redox-active functionalized surfaces. Electrochemically operated sequential logic systems (e.g., flip-flops), multi-valued logic, and multi-state memory have been designed, which can improve computational power without increasing spatial requirements. Applying multi-valued digits in data storage and information processing could exponentially increase memory capacity. Our approach is applicable to highly diverse electrochromic thin films that operate at practical voltages (< 1.5 V).

  19. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...... computations of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems.3,16,17,18 For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence...

  20. Molecular approach of uranyl/mineral surfaces: theoretical approach

    International Nuclear Information System (INIS)

    Roques, J.

    2009-01-01

    As migration of radio-toxic elements through the geosphere is one of the processes which may affect the safety of a radioactive waste storage site, the author shows that numerical modelling is a support to experimental result exploitation, and allows the development of new interpretation and prediction codes. He shows that molecular modelling can be used to study processes of interaction between an actinide ion (notably a uranyl ion) and a mineral surface (a TiO 2 substrate). He also reports the predictive theoretical study of the interaction between an uranyl ion and a gibbsite substrate

  1. Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

    Science.gov (United States)

    Zhao, Lei; Cheng, Jiangtao

    2017-09-07

    In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

  2. Surface enhanced raman spectroscopy analytical, biophysical and life science applications

    CERN Document Server

    Schlücker, Sebastian

    2013-01-01

    Covering everything from the basic theoretical and practical knowledge to new exciting developments in the field with a focus on analytical and life science applications, this monograph shows how to apply surface-enhanced Raman scattering (SERS) for solving real world problems. From the contents: * Theory and practice of SERS * Analytical applications * SERS combined with other analytical techniques * Biophysical applications * Life science applications including various microscopies Aimed at analytical, surface and medicinal chemists, spectroscopists, biophysicists and materials scientists. Includes a Foreword by the renowned Raman spectroscopist Professor Wolfgang Kiefer, the former Editor-in-Chief of the Journal of Raman Spectroscopy.

  3. Molecular catalysis science: Perspective on unifying the fields of catalysis.

    Science.gov (United States)

    Ye, Rong; Hurlburt, Tyler J; Sabyrov, Kairat; Alayoglu, Selim; Somorjai, Gabor A

    2016-05-10

    Colloidal chemistry is used to control the size, shape, morphology, and composition of metal nanoparticles. Model catalysts as such are applied to catalytic transformations in the three types of catalysts: heterogeneous, homogeneous, and enzymatic. Real-time dynamics of oxidation state, coordination, and bonding of nanoparticle catalysts are put under the microscope using surface techniques such as sum-frequency generation vibrational spectroscopy and ambient pressure X-ray photoelectron spectroscopy under catalytically relevant conditions. It was demonstrated that catalytic behavior and trends are strongly tied to oxidation state, the coordination number and crystallographic orientation of metal sites, and bonding and orientation of surface adsorbates. It was also found that catalytic performance can be tuned by carefully designing and fabricating catalysts from the bottom up. Homogeneous and heterogeneous catalysts, and likely enzymes, behave similarly at the molecular level. Unifying the fields of catalysis is the key to achieving the goal of 100% selectivity in catalysis.

  4. 7th International Summer Institute in Surface Science

    CERN Document Server

    Howe, Russell

    1986-01-01

    This volume contains review articles which were written by the invited speak­ ers of the seventh International Summer Institute in Surface Science (ISISS), held at the University of Wisconsin - Milwaukee in July 1985. The form of ISISS is a set of tutorial review lectures presented over a one-week period by internationally recognized experts on various aspects of surface science. Each speaker is asked, in addition, to write a review article on his lecture topic. No single volume in the series Chemistry and Physics of Solid Surfaces can possibly cover the entire field of modern surface science. However, the series as a whole is intended to provide experts and students alike with a comprehensive set of reviews and literature references, particularly empha­ sizing the gas-solid interface. The collected articles from previous Summer Institutes have been published under the following titles: Surface Science: Recent Progress and Perspectives, Crit. Rev. Solid State Sci. 4, 125-559 (1974) Chemistry and Physics of ...

  5. Molecular identification of a malaria merozoite surface sheddase.

    Directory of Open Access Journals (Sweden)

    Philippa K Harris

    2005-11-01

    Full Text Available Proteolytic shedding of surface proteins during invasion by apicomplexan parasites is a widespread phenomenon, thought to represent a mechanism by which the parasites disengage adhesin-receptor complexes in order to gain entry into their host cell. Erythrocyte invasion by merozoites of the malaria parasite Plasmodium falciparum requires the shedding of ectodomain components of two essential surface proteins, called MSP1 and AMA1. Both are released by the same merozoite surface "sheddase," but the molecular identity and mode of action of this protease is unknown. Here we identify it as PfSUB2, an integral membrane subtilisin-like protease (subtilase. We show that PfSUB2 is stored in apical secretory organelles called micronemes. Upon merozoite release it is secreted onto the parasite surface and translocates to its posterior pole in an actin-dependent manner, a trafficking pattern predicted of the sheddase. Subtilase propeptides are usually selective inhibitors of their cognate protease, and the PfSUB2 propeptide is no exception; we show that recombinant PfSUB2 propeptide binds specifically to mature parasite-derived PfSUB2 and is a potent, selective inhibitor of MSP1 and AMA1 shedding, directly establishing PfSUB2 as the sheddase. PfSUB2 is a new potential target for drugs designed to prevent erythrocyte invasion by the malaria parasite.

  6. Molecular Dynamics Simulations of Slip on Curved Surfaces

    Directory of Open Access Journals (Sweden)

    Ross D.A.

    2016-07-01

    Full Text Available We present Molecular Dynamics (MD simulations of liquid water confined within nanoscale geometries, including slit-like and cylindrical graphitic pores. These equilibrium results are used for calculating friction coefficients, which in turn can be used to calculate slip lengths. The slip length is a material property independent of the fluid flow rate. It is therefore a better quantity for study than the fluid velocity at the wall, also known as the slip velocity. Once the slip length has been found as a function of surface curvature, it can be used to parameterise Lattice Boltzmann (LB simulations. These larger scale simulations are able to tell us about how fluid transport is affected by slip in complex geometries; not just limited to single pores. Applications include flow and transport in nano-porous engine valve deposits and gas shales. The friction coefficient is found to be a function of curvature and is higher for fluid on convex surfaces and lower for concave surfaces. Both concave and convex surfaces approach the same value of the friction coefficient, which is constant above some critical radius of curvature, here found to be 7.4 ± 2.9 nm. The constant value of the friction coefficient is 10,000 ± 600 kg m−2 s−1, which is equivalent to a slip length of approximately 67 ± 4 nm.

  7. Surface science of single-site heterogeneous olefin polymerization catalysts

    OpenAIRE

    Kim, Seong H.; Somorjai, Gabor A.

    2006-01-01

    This article reviews the surface science of the heterogeneous olefin polymerization catalysts. The specific focus is on how to prepare and characterize stereochemically specific heterogeneous model catalysts for the Ziegler–Natta polymerization. Under clean, ultra-high vacuum conditions, low-energy electron irradiation during the chemical vapor deposition of model Ziegler–Natta catalysts can be used to create a “single-site” catalyst film with a surface structure that produces only isotactic ...

  8. Surface science station of the infrared beamline at SPring-8

    International Nuclear Information System (INIS)

    Sakurai, M.; Moriwaki, T.; Kimura, H.; Nishida, S.; Nanba, T.

    2001-01-01

    An experimental station for surface science has been constructed at the infrared beamline (BL43IR) of SPring-8, Japan. The station utilizes synchrotron radiation in the energy range of 100-20000 cm -1 to perform infrared reflection absorption spectroscopy (IRAS) of surfaces. It consists of an experimental section, a preparation chamber, gas handling equipment and a pair of focusing optics. In situ observation of vibrational spectra is possible using both IRAS and high-resolution electron energy loss spectroscopy

  9. Molecular Contamination on Anodized Aluminum Components of the Genesis Science Canister

    Science.gov (United States)

    Burnett, D. S.; McNamara, K. M.; Jurewicz, A.; Woolum, D.

    2005-01-01

    Inspection of the interior of the Genesis science canister after recovery in Utah, and subsequently at JSC, revealed a darkening on the aluminum canister shield and other canister components. There has been no such observation of film contamination on the collector surfaces, and preliminary spectroscopic ellipsometry measurements support the theory that the films observed on the anodized aluminum components do not appear on the collectors to any significant extent. The Genesis Science Team has made an effort to characterize the thickness and composition of the brown stain and to determine if it is associated with molecular outgassing.Detailed examination of the surfaces within the Genesis science canister reveals that the brown contamination is observed to varying degrees, but only on surfaces exposed in space to the Sun and solar wind hydrogen. In addition, the materials affected are primarily composed of anodized aluminum. A sharp line separating the sun and shaded portion of the thermal closeout panel is shown. This piece was removed from a location near the gold foil collector within the canister. Future plans include a reassembly of the canister components to look for large-scale patterns of contamination within the canister to aid in revealing the root cause.

  10. The development of surface science in China: Retrospect and prospects

    Energy Technology Data Exchange (ETDEWEB)

    Xie Xide (Fudan University, Shanghai (China))

    1994-01-01

    It is generally agreed that the year of 1977 marked the birth of surface science in China, therefore the length of its history of development is only half of that shown in the title of this volume. Since 1977 laboratories with modern facilities for surface studies have been established in various universities and research institutes. Three open laboratories better equipped than others have been set up in Beijing, Xiamen and Shanghai for surface physics, surface chemistry and applied surface physics, respectively. Five National Conferences on Physics of Surfaces and Interfaces were held in 1982, 1984, 1985, 1988 and 1991. In 1993 China is going to host the Fourth International Conference on the Structure of Surfaces in Shanghai August 16-19 which will serve as a milestone in the history of development of surface science in China. With the access to many overseas laboratories, quite a number of Chinese scientists and students have had opportunities to work and study abroad and have brought back with them experiences acquired. During the Conferences just mentioned, one could witness a number of steady progresses made over the years. In the present review, a brief description about the establishment of some major research facilities and progresses of some of the research is given with emphasis on work related to semiconductor surfaces, interfaces, superlattices, heterojunctions and quantum wells. Although the review nominally covers the development of research in surface science in China, due to the limitation of the capabilities of the author, mostly work done at Fudan University is included. For this the author would like to express her deep apology to many Chinese colleagues whose works have not been properly mentioned

  11. Molecular nutrition research: the modern way of performing nutritional science.

    Science.gov (United States)

    Norheim, Frode; Gjelstad, Ingrid Merethe Fange; Hjorth, Marit; Vinknes, Kathrine J; Langleite, Torgrim M; Holen, Torgeir; Jensen, Jørgen; Dalen, Knut Tomas; Karlsen, Anette S; Kielland, Anders; Rustan, Arild C; Drevon, Christian A

    2012-12-03

    In spite of amazing progress in food supply and nutritional science, and a striking increase in life expectancy of approximately 2.5 months per year in many countries during the previous 150 years, modern nutritional research has a great potential of still contributing to improved health for future generations, granted that the revolutions in molecular and systems technologies are applied to nutritional questions. Descriptive and mechanistic studies using state of the art epidemiology, food intake registration, genomics with single nucleotide polymorphisms (SNPs) and epigenomics, transcriptomics, proteomics, metabolomics, advanced biostatistics, imaging, calorimetry, cell biology, challenge tests (meals, exercise, etc.), and integration of all data by systems biology, will provide insight on a much higher level than today in a field we may name molecular nutrition research. To take advantage of all the new technologies scientists should develop international collaboration and gather data in large open access databases like the suggested Nutritional Phenotype database (dbNP). This collaboration will promote standardization of procedures (SOP), and provide a possibility to use collected data in future research projects. The ultimate goals of future nutritional research are to understand the detailed mechanisms of action for how nutrients/foods interact with the body and thereby enhance health and treat diet-related diseases.

  12. Molecular biogeochemical provinces in the Atlantic Surface Ocean

    Science.gov (United States)

    Koch, B. P.; Flerus, R.; Schmitt-Kopplin, P.; Lechtenfeld, O. J.; Bracher, A.; Cooper, W.; Frka, S.; Gašparović, B.; Gonsior, M.; Hertkorn, N.; Jaffe, R.; Jenkins, A.; Kuss, J.; Lara, R. J.; Lucio, M.; McCallister, S. L.; Neogi, S. B.; Pohl, C.; Roettgers, R.; Rohardt, G.; Schmitt, B. B.; Stuart, A.; Theis, A.; Ying, W.; Witt, M.; Xie, Z.; Yamashita, Y.; Zhang, L.; Zhu, Z. Y.; Kattner, G.

    2010-12-01

    One of the most important aspects to understand marine organic carbon fluxes is to resolve the molecular mechanisms which convert fresh, labile biomolecules into semi-labile and refractory dissolved and particulate organic compounds in the ocean. In this interdisciplinary project, which was performed on a cruise with RV Polarstern, we carried out a detailed molecular characterisation of dissolved organic matter (DOM) on a North-South transect in the Atlantic surface ocean in order to relate the data to different biological, climatic, oceanographic, and meteorological regimes as well as to terrestrial input from riverine and atmospheric sources. Our goal was to achieve a high resolution data set for the biogeochemical characterisation of the sources and reactivity of DOM. We applied ultrahigh resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS), nutrient, trace element, amino acid, and lipid analyses and other biogeochemical measurements for 220 samples from the upper water column (0-200m) and eight deep profiles. Various spectroscopic techniques were applied continuously in a constant sample water flow supplied by a fish system and the moon pool. Radiocarbon dating enabled assessing DOC residence time. Bacterial abundance and production provided a metabolic context for the DOM characterization work and pCO2 concentrations. Combining molecular organic techniques and inductively coupled plasma mass spectrometry (ICP-MS) established an important link between organic and inorganic biogeochemical studies. Multivariate statistics, primarily based on FT-ICR-MS data for 220 samples, allowed identifying geographical clusters which matched ecological provinces proposed previously by Longhurst (2007). Our study demonstrated that marine DOM carries molecular information reflecting the “history” of ocean water masses. This information can be used to define molecular biogeochemical provinces and to improve our understanding of element fluxes in

  13. Surface and Electrical Characterization of Conjugated Molecular Wires

    Science.gov (United States)

    Demissie, Abel Tesfahun

    This thesis describes the surface and electrical characterization of ultrathin organic films and interfaces. These films were synthesized on the surface of gold by utilizing layer by layer synthesis via imine condensation. Film growth by imine click (condensation) chemistry is particularly useful for molecular electronics experiments because it provides a convenient means to obtain and extend ?-conjugation in the growth direction. However, in the context of film growth from a solid substrate, the reaction yield per step has not been characterized previously, though it is critically important. To address these issues, my research focused on a comprehensive characterization of oligophenyleneimine (OPI) wires via Rutherford backscattering spectrometry (RBS), X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE), reflection-absorption infrared spectroscopy (RAIRS), and cyclic voltammetry (CV). In addition, we had the unique opportunity of developing the first of its kind implementation of nuclear reaction analysis (NRA) to probe the intensity of carbon atoms after each addition step. Overall the combination of various techniques indicated that film growth proceeds in a quantitative manner. Furthermore, the NRA experiment was optimized to measure the carbon content in self-assembled monolayers of alkyl thiols. The results indicated well-resolved coverage values for ultrathin films with consecutive steps of 2 carbon atoms per molecule. Another fundamental problem in molecular electronics is the vast discrepancy in the values of measured resistance per molecule between small and large area molecular junctions. In collaboration with researchers at the National University of Singapore, we addressed these issues by comparing the electrical properties of OPI wires with the eutectic gallium indium alloy (EGaIn) junction (1000 mum2), and conducting probe atomic force microscopy (CP-AFM) junction (50 nm2). Our results showed that intensive (i.e., area

  14. Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...... dynamics (MD) simulations of a hydrophilic air-water-silica system using the MD package FASTTUBE. We employ quantum chemistry calculation to obtain air-silica interaction parameters for the simulations. Our simulations are based in the following force fields: i) The silica-silica interaction is based...... of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...

  15. Molecular ordering of ethanol at the calcite surface.

    Science.gov (United States)

    Pasarín, I S; Yang, M; Bovet, N; Glyvradal, M; Nielsen, M M; Bohr, J; Feidenhans'l, R; Stipp, S L S

    2012-02-07

    To produce biominerals, such as shells, bones, and teeth, living beings create organic compounds that control the growth of the solid phase. Investigating the atomic scale behavior of individual functional groups at the mineral-fluid interface provides fundamental information that is useful for constructing accurate predictive models for natural systems. Previous investigations of the activity of coccolith-associated polysaccharides (CAP) on calcite, using atomic force microscopy (AFM) [Henriksen, K., Young, J. R., Bown, P. R., and Stipp, S. L. S. Palentology 2004, 43 (Part 3), 725-743] and molecular dynamics (MD) modeling [Yang, M., Stipp, S. L. S., and Harding, J. H. Cryst. Growth Des. 2008, 8 (11), 4066-4074], have suggested that OH functional groups control polysaccharide attachment. The purpose of this work was to characterize, using X-ray reflectivity (XR) combined with molecular dynamics (MD) simulations, the structuring on calcite of a layer of the simplest carbon chain molecule that contains an OH group, ethanol (CH(3)-CH(2)-OH). We found evidence that EtOH forms a highly ordered structure at the calcite surface, where the first layer molecules bond with calcite. The ethanol molecules stand up perpendicularly at the interface or nearly so. As a consequence, the fatty, CH(3) ends form a new surface, about 6 Å from the termination of the bulk calcite, and beyond that, there is a thin gap where ethanol density is low. Following is a more disordered layer that is two to three ethanol molecules thick, about 14 Å, where density more resembles that of bulk liquid ethanol. The good agreement between theory and experiment gives confidence that a theoretical approach can offer information about behavior in more complex systems.

  16. 8th International Summer Institute in Surface Science

    CERN Document Server

    Howe, Russell

    1988-01-01

    This volume contains review articles written by the invited speakers at the eighth International Summer Institute in Surface Science (ISISS 1987), held at the University of Wisconsin-Milwaukee in August of 1987. During the course of ISISS, invited speakers, all internationally recognized experts in the various fields of surface science, present tutorial review lectures. In addition, these experts are asked to write review articles on their lecture topic. Former ISISS speakers serve as advisors concerning the selection of speakers and lecture topics. Em­ phasis is given to those areas which have not been covered in depth by recent Summer Institutes, as well as to areas which have recently gained in significance and in which important progress has been made. Because of space limitations, no individual volume of Chemistry and Physics of Solid Surfaces can possibly cover the whole area of modem surface science, or even give a complete survey of recent pro­ gress in the field. However, an attempt is made to pres...

  17. Molecular Dynamics Studies of Overbased Detergents on a Water Surface.

    Science.gov (United States)

    Bodnarchuk, M S; Dini, D; Heyes, D M; Breakspear, A; Chahine, S

    2017-07-25

    Molecular dynamics (MD) simulations are reported of model overbased detergent nanoparticles on a model water surface which mimic their behavior on a Langmuir trough or large water droplet in engine oil. The simulations predict that the structure of the nanoparticle on a water surface is different to when it is immersed in a bulk hydrophobic solvent. The surfactant tails are partly directed out of the water, while the carbonate core maximizes its extent of contact with the water. Umbrella sampling calculations of the potential of mean force between two particles showed that they are associated with varying degrees with a maximum binding free energy of ca. 10 k B T for the salicylate stabilized particle, ca. 8 k B T for a sulfurized alkyl phenate stabilized particle, and ca. 5 k B T for a sulfonate stabilized particle. The differences in the strength of attraction depend on the proximity of nearest approach and the energy penalty associated with the disruption of the hydration shell of water molecules around the calcium carbonate core when the two particles approach. This is greatest for the sulfonate particle, which partially loses the surfactant ions to the solution, and least for the salicylate, which forms the weakest water "cage". The particles are separated by a water hydration layer, even at the point of closest approach.

  18. ISIS muons for materials and molecular science studies

    International Nuclear Information System (INIS)

    King, Philip J C; Cottrell, Stephen P; Hillier, Adrian D; Cox, Stephen F J; De Renzi, Roberto

    2013-01-01

    This paper marks the first 25 years of muon production at ISIS and the creation in that time of a facility dedicated to the use of these elementary particles as unique microscopic probes in condensed matter and molecular science. It introduces the basic techniques of muon spin rotation, relaxation and resonance, collectively known as μSR, that were already in use by specialist groups at other accelerator labs by the mid-1980s. It describes how these techniques have been implemented and made available at ISIS, beginning in 1987, and how they have evolved and improved since then. Ever widening applications embrace magnetism, superconductivity, interstitial diffusion and charge transport, semiconductors and dielectrics, chemical physics and radical chemistry. Over these first 25 years, a fully supported user facility has been established, open to all academic and industrial users. It presently comprises four scheduled instruments, optimized for different types of measurement, together with auxiliary equipment for radiofrequency or microwave spin manipulation and future plans for pump–probe laser excitation. (comment)

  19. Revolution in Field Science: Apollo Approach to Inaccessible Surface Exploration

    Science.gov (United States)

    Clark, P. E.

    2010-07-01

    The extraordinary challenge mission designers, scientists, and engineers, faced in planning the first human expeditions to the surface of another solar system body led to the development of a distinctive and even revolutionary approach to field work. Not only were those involved required to deal effectively with the extreme limitation in resources available for and access to a target as remote as the lunar surface; they were required to developed a rigorous approach to science activities ranging from geological field work to deploying field instruments. Principal aspects and keys to the success of the field work are discussed here, including the highly integrated, intensive, and lengthy science planning, simulation, and astronaut training; the development of a systematic scheme for description and documentation of geological sites and samples; and a flexible yet disciplined methodology for site documentation and sample collection. The capability for constant communication with a ‘backroom’ of geological experts who make requests and weigh in on surface operations was innovative and very useful in encouraging rapid dissemination of information to the greater community in general. An extensive archive of the Apollo era science activity related documents provides evidence of the principal aspects and keys to the success of the field work. The Apollo Surface Journal allows analysis of the astronaut’s performance in terms of capability for traveling on foot, documentation and sampling of field stations, and manual operation of tools and instruments, all as a function of time. The application of these analysis as ‘lessons learned’ for planning the next generation of human or robotic field science activities on the Moon and elsewhere are considered here as well.

  20. Molecular Formula and Molecular Weight - NBDC NikkajiRDF | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us NBDC NikkajiRDF Molecular Formula and Molecular Weight Data detail Data name Molecular Formula and Molecul...- Description of data contents This RDF data includes molecular formula and molecular weight of chemical sub...ikkajiRDF_MFMW.tar.gz File size: 404 MB Simple search URL - Data acquisition method The data was converted from data of molecul...ar formulas and molecular weights in Basic Information ( http://dbarchive.biosciencedbc.j... Policy | Contact Us Molecular Formula and Molecular Weight - NBDC NikkajiRDF | LSDB Archive ...

  1. Molecular beam photoionization and gas-surface scattering

    International Nuclear Information System (INIS)

    Ceyer, S.T.

    1979-09-01

    The energetics of the ethylene ion-molecule reactions was investigated in more detail than previously possible in two body collision experiments by photoionization of the neutral van der Waals ethylene dimer. The stability of the (C 2 H 4 ) + C 2 H 4 ion-molecule collision complex has been determined to be 18.2 +- 0.5 kcal. The highest potential barriers along the reaction coordinate for decomposition of this collision complex into C 4 H 7 + + H and C 3 H 5 + + CH 3 have been determined to be 0 +- 1.5 and 8.7 +- 1.5 kcal. In a similar manner, the energetics of the solvated ethylene dimer ion was investigated by the photoionization of the ethylene trimer. The absolute proton affinity of NH 3 (203.6 +- 1.3 kcal/mole) and the proton solvation energies by more than one NH 3 have been determined by molecular beam photoionization. In addition, the NH 3 + -NH 3 interaction energy (0.79 +- 0.05 eV) was measured by photoionization of the neutral van der Waals dimer. These experiments have shown that photoionization of van der Waals clusters is a very powerful method of determining the energetics of gas phase proton solvation. The scattering of helium atomic beams from a high Miller index platinum surface that exhibits ordered, periodic steps on the atomic scale to probe the effect of atomic steps on the scattering distribution is explored. Rainbow scattering is observed when the step edges are perpendicular to the incident helium atoms. The design, construction and operation of a beam-surface scattering apparatus are described. The first data obtained in this apparatus are presented and the interesting dynamical aspects of the oxidation of D, D 2 and CO are discussed. 75 references

  2. Science Academies' Refresher Course on Advances in Molecular ...

    Indian Academy of Sciences (India)

    microRNAs, Ribozyme; molecular oncology; Genes in development and differentiation; Epigenetics and gene regulation; molecular biology of viruses; Restriction enzymes and modifications; Ge- netic engineering; Neurobiology; Bioinformatics- structural, functional and comparative genomics;. Metagenomics; Genome ...

  3. Surface science and model catalysis with ionic liquid-modified materials.

    Science.gov (United States)

    Steinrück, H-P; Libuda, J; Wasserscheid, P; Cremer, T; Kolbeck, C; Laurin, M; Maier, F; Sobota, M; Schulz, P S; Stark, M

    2011-06-17

    Materials making use of thin ionic liquid (IL) films as support-modifying functional layer open up a variety of new possibilities in heterogeneous catalysis, which range from the tailoring of gas-surface interactions to the immobilization of molecularly defined reactive sites. The present report reviews recent progress towards an understanding of "supported ionic liquid phase (SILP)" and "solid catalysts with ionic liquid layer (SCILL)" materials at the microscopic level, using a surface science and model catalysis type of approach. Thin film IL systems can be prepared not only ex-situ, but also in-situ under ultrahigh vacuum (UHV) conditions using atomically well-defined surfaces as substrates, for example by physical vapor deposition (PVD). Due to their low vapor pressure, these systems can be studied in UHV using the full spectrum of surface science techniques. We discuss general strategies and considerations of this approach and exemplify the information available from complementary methods, specifically photoelectron spectroscopy and surface vibrational spectroscopy. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Surface molecular aggregation structure and surface physicochemical properties of poly(fluoroalkyl acrylate) thin films

    International Nuclear Information System (INIS)

    Honda, K; Yamaguchi, H; Takahara, A; Kobayashi, M; Morita, M

    2008-01-01

    Effect of side chain length on the molecular aggregation states and surface properties of poly(fluoroalkyl acrylate)s [PFA-C y , where y is fluoromethylene number in R f group] thin films were systematically investigated. Spin-coated PFA-C y thin films were characterized by static and dynamic contact angle measurements, X-ray photoelectron spectroscopy (XPS), and grazing- incidence X-ray diffraction (GIXD). The receding contact angles showed small values for PFA-C y with short side chain (y≤6) and increased above y≥8. GIXD revealed that fluoroalkyl side chain of PFA-C y with y≥8 was crystallized and formed ordered structures at the surface region as well as bulk one. These results suggest that water repellent mechanism of PFA-C y can be attributed to the presence of highly ordered fluoroalkyl side chains at the outermost surfaces. The results of XPS in the dry and hydrated states and contact angle measurement in water support the mechanism of lowering contact angle for water by exposure of carbonyl group to the water interface through reorientation of short fluoroalkyl chains. The surface nanotextured PFA-C 8 through imprinting of anodic aluminum oxide mold showed extremely high hydrophobicity as well as high oleophobicity

  5. Molecular dynamics simulation of potentiometric sensor response: the effect of biomolecules, surface morphology and surface charge.

    Science.gov (United States)

    Lowe, B M; Skylaris, C-K; Green, N G; Shibuta, Y; Sakata, T

    2018-05-10

    The silica-water interface is critical to many modern technologies in chemical engineering and biosensing. One technology used commonly in biosensors, the potentiometric sensor, operates by measuring the changes in electric potential due to changes in the interfacial electric field. Predictive modelling of this response caused by surface binding of biomolecules remains highly challenging. In this work, through the most extensive molecular dynamics simulation of the silica-water interfacial potential and electric field to date, we report a novel prediction and explanation of the effects of nano-morphology on sensor response. Amorphous silica demonstrated a larger potentiometric response than an equivalent crystalline silica model due to increased sodium adsorption, in agreement with experiments showing improved sensor response with nano-texturing. We provide proof-of-concept that molecular dynamics can be used as a complementary tool for potentiometric biosensor response prediction. Effects that are conventionally neglected, such as surface morphology, water polarisation, biomolecule dynamics and finite-size effects, are explicitly modelled.

  6. Molecular Dynamics Simulation of Water Nanodroplets on Silica Surfaces at High Air Pressures

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Jaffe, Richard Lawrence; Walther, Jens Honore

    2010-01-01

    e.g., nanobubbles. In the present work we study the role of air on the wetting of hydrophilic systems. We conduct molecular dynamics simulations of a water nanodroplet on an amorphous silica surface at different air pressures. The interaction potentials describing the silica, water, and air......Silicon dioxides-water systems are abundant in nature and play fundamental roles in a diversity of novel science and engineering applications. Although extensive research has been devoted to study the nature of the interaction between silica and water a complete understanding of the system has...... perform extensive simulations of the water- air equilibrium and calibrate the water-air interaction to match the experimental solubility of N2 and O2 in water. For the silica-water system we calibrate the water-silica interaction to match the experimental contact angle of 27º. We subsequently study...

  7. Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

    International Nuclear Information System (INIS)

    Sanz-Navarro, Carlos F.

    2002-01-01

    The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

  8. Surface science in hernioplasty: The role of plasma treatments

    Science.gov (United States)

    Nisticò, Roberto; Magnacca, Giuliana; Martorana, Selanna

    2017-10-01

    The aim of this review is to clarify the importance of surface modifications induced in biomaterials for hernia-repair application. Starting from the pioneering experiences involving proto-materials as ancient prosthesis, a historical excursus between the biomaterials used in hernioplasty was realized. Subsequently, after the revolutionary discovery of stereoregular polymerization followed by the PP application in the biomedical field performed by the surgeon F. Usher, a comparative study on different hernia-repair meshes available was realized in order to better understand all the outstanding problems and possible future developments. Furthermore, since many unsolved problems on prosthetic devices implantation are linked to phenomena occurring at the interface between the biomaterials surface and the body fluids, the importance of surface science in hernioplasty was highlighted and case studies of new surface-modified generations of prosthesis presented. The results discussed in the following evidence how the surface study are becoming increasingly important for a proper knowledge of issues related to the interaction between the living matter and the artificial prostheses.

  9. Reducing Motional Decoherence in Ion Traps with Surface Science Methods

    Science.gov (United States)

    Haeffner, Hartmut

    2014-03-01

    Many trapped ions experiments ask for low motional heating rates while trapping the ions close to trapping electrodes. However, in practice small ion-electrode distances lead to unexpected high heating rates. While the mechanisms for the heating is still unclear, it is now evident that surface contamination of the metallic electrodes is at least partially responsible for the elevated heating rates. I will discuss heating rate measurements in a microfabricated surface trap complemented with basic surface science studies. We monitor the elemental surface composition of the Cu-Al alloy trap with an Auger spectrometer. After bake-out, we find a strong Carbon and Oxygen contamination and heating rates of 200 quanta/s at 1 MHz trap frequency. After removing most of the Carbon and Oxygen with Ar-Ion sputtering, the heating rates drop to 4 quanta/s. Interestingly, we still measure the decreased heating rate even after the surface oxidized from the background gas throughout a 40-day waiting time in UHV.

  10. Announcing the International Journal of Molecular Sciences Junior Scientists Travel Awards 2016

    Directory of Open Access Journals (Sweden)

    International Journal of Molecular Sciences Editorial Office

    2016-03-01

    Full Text Available With the goal of recognizing outstanding contributions to the field of molecular sciences by early-career investigators, including assistant professors, postdoctoral students and PhD students, [...

  11. Surface science studies of ethene containing model interstellar ices

    Science.gov (United States)

    Puletti, F.; Whelan, M.; Brown, W. A.

    2011-05-01

    The formation of saturated hydrocarbons in the interstellar medium (ISM) is difficult to explain only by taking into account gas phase reactions. This is mostly due to the fact that carbonium ions only react with H_2 to make unsaturated hydrocarbons, and hence no viable route to saturated hydrocarbons has been postulated to date. It is therefore likely that saturation processes occur via surface reactions that take place on interstellar dust grains. One of the species of interest in this family of reactions is C_2H_4 (ethene) which is an intermediate in several molecular formation routes (e.g. C_2H_2 → C_2H_6). To help to understand some of the surface processes involving ethene, a study of ethene deposited on a dust grain analogue surface (highly oriented pyrolytic graphite) held under ultra-high vacuum at 20 K has been performed. The adsorption and desorption of ethene has been studied both in water-free and water-dominated model interstellar ices. A combination of temperature programmed desorption (TPD) and reflection absorption infrared spectroscopy (RAIRS) have been used to identify the adsorbed and trapped species and to determine the kinetics of the desorption processes. In all cases, ethene is found to physisorb on the carbonaceous surface. As expected water has a very strong influence on the desorption of ethene, as previously observed for other model interstellar ice systems.

  12. EDITORIAL: Three decades of scanning tunnelling microscopy that changed the course of surface science Three decades of scanning tunnelling microscopy that changed the course of surface science

    Science.gov (United States)

    Ramachandra Rao, M. S.; Margaritondo, Giorgio

    2011-11-01

    envisaged. AFM observations of thin-film surfaces give us a picture of surface topography and morphology and any visible defects. The growing importance of ultra-thin films for magnetic recording in hard disk drive systems requires an in-depth understanding of the fundamental mechanisms occurring during growth. This special issue of Journal of Physics D: Applied Physics covers all of the different aspects of SPM that illustrate the achievements of this methodology: nanoscale imaging and mapping (Chiang, and Douillard and Charra), piezoresponse force microscopy (Soergel) and STM engineering (Okuyama and Hamada, and Huang et al). Chiang takes the reader on a journey along the STM imaging of atoms and molecules on surfaces. Jesse and Kalinin explore the band excitations that occur during the corresponding processes. Jia et al propose STM and molecular beam epitaxy as a winning experimental combination at the interface of science and technology. Douillard and Charra describe the high-resolution mapping of plasmonic modes using photoemission and scanning tunnelling microscopy. Cricenti et al demonstrate the importance of SPM in material science and biology. Wiebe et al have probed atomic scale magnetism, revealed by spin polarized scanning tunnelling microscopy. In addition, Simon et al present Fourier transform scanning tunnelling spectroscopy and the possibility to obtain constant energy maps and band dispersion using local measurements. Lackinger and Heckl give a perspective of the use of STM to study covalent intermolecular coupling reactions on surfaces. Okuyama and Hamada investigated hydrogen bond imaging and engineering with STM. Soergel describes the study of substrate-dependent self-assembled CuPc molecules using piezo force microscope (PFM). We are very grateful to the authors and reviewers for the papers in this special issue of Journal of Physics D: Applied Physics. Their contributions have provided a comprehensive picture of the evolution, status and potential of

  13. Molecular Gastronomy: A Food Fad or an Interface for Science-based Cooking?

    NARCIS (Netherlands)

    Linden, van der E.; McClements, D.J.; Ubbink, J.

    2008-01-01

    A review is given over the field of molecular gastronomy and its relation to science and cooking. We begin with a brief history of the field of molecular gastronomy, the definition of the term itself, and the current controversy surrounding this term. We then highlight the distinction between

  14. Reactivity of etoricoxib based on computational study of molecular orbitals, molecular electrostatic potential surface and Mulliken charge analysis

    Science.gov (United States)

    Sachdeva, Ritika; Soni, Abhinav; Singh, V. P.; Saini, G. S. S.

    2018-05-01

    Etoricoxib is one of the selective cyclooxygenase inhibitor drug which plays a significant role in the pharmacological management of arthritis and pain. The theoretical investigation of its reactivity is done using Density Functional Theory calculations. Molecular Electrostatic Potential Surface of etoricoxib and its Mulliken atomic charge distribution are used for the prediction of its electrophilic and nucleophilic sites. The detailed analysis of its frontier molecular orbitals is also done.

  15. Molecular recognition of chromophore molecules to amine terminated surfaces

    International Nuclear Information System (INIS)

    Flores-Perez, Rosangelly; Ivanisevic, Albena

    2007-01-01

    We report the design and characterization of quartz surfaces that can bind to three retinal based chromophores. The amine terminated surfaces were engineered in order to mimic the environment of the opsin protein that accommodates binding of chromophore molecules in the human eye. Each surface coupling step was characterized by water contact angle measurements, ellipsometry, atomic force microscopy, X-ray photoelectron spectroscopy, and transmission infrared spectroscopy. The spectroscopic techniques confirmed that the three chromophore molecules can bind to the surface using a Schiff base mode. Our data suggests that the availability of the amine groups on the surface is critical in the accommodation of the binding of different chromophores

  16. Vibrational energy on surfaces: Ultrafast flash-thermal conductance of molecular monolayers

    Science.gov (United States)

    Dlott, Dana

    2008-03-01

    Vibrational energy flow through molecules remains a perennial problem in chemical physics. Usually vibrational energy dynamics are viewed through the lens of time-dependent level populations. This is natural because lasers naturally pump and probe vibrational transitions, but it is also useful to think of vibrational energy as being conducted from one location in a molecule to another. We have developed a new technique where energy is driven into a specific part of molecules adsorbed on a metal surface, and ultrafast nonlinear coherent vibrational spectroscopy is used to watch the energy arrive at another part. This technique is the analog of a flash thermal conductance apparatus, except it probes energy flow with angstrom spatial and femtosecond temporal resolution. Specific examples to be presented include energy flow along alkane chains, and energy flow into substituted benzenes. Ref: Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Ultrafast flash thermal conductance of molecular chains, Science 317, 787-790 (2007). This material is based upon work supported by the National Science Foundation under award DMR 0504038 and the Air Force Office of Scientific Research under award FA9550-06-1-0235.

  17. Surface science models of CoMoS hydrodesulfurisation catalysts

    Energy Technology Data Exchange (ETDEWEB)

    De Jong, A.M.; De Beer, V.H.J.; Van Veen, J.A.R.; Niemantsverdriet, J.W. [Schuit Institute of Catalysis, Eindhoven University of Technology, Eindhoven (Netherlands)

    1997-07-01

    Characterization of supported catalysts with surface spectroscopic techniques is often limited due to restraints imposed by the support material. The use of flat conducting substrates as a model support offers a way to apply these techniques to their full potential. Such surface science models of silica and alumina supported CoMoS catalysts have been made by impregnating thin SiO{sub 2} and Al{sub 2}O{sub 3} films with a solution of nitrilotriacetic acid (NTA) complexes of cobalt and molybdenum. X-ray Photoelectron Spectroscopy (XPS) spectra indicate that the order in which cobalt and molybdenum transfer to the sulfided state is reversed with respect to oxidic Co and Mo systems prepared by conventional methods, implying that NTA complexation retards the sulfidation of cobalt to temperatures where MoS{sub 2} is already formed. Catalytic tests show that the CoMoS model catalysts exhibit activities for thiophene desulfurisation and product distributions similar to those of their high surface area counterparts. 25 refs.

  18. Chemical Modification of Semiconductor Surfaces for Molecular Electronics.

    Science.gov (United States)

    Vilan, Ayelet; Cahen, David

    2017-03-08

    Inserting molecular monolayers within metal/semiconductor interfaces provides one of the most powerful expressions of how minute chemical modifications can affect electronic devices. This topic also has direct importance for technology as it can help improve the efficiency of a variety of electronic devices such as solar cells, LEDs, sensors, and possible future bioelectronic ones. The review covers the main aspects of using chemistry to control the various aspects of interface electrostatics, such as passivation of interface states and alignment of energy levels by intrinsic molecular polarization, as well as charge rearrangement with the adjacent metal and semiconducting contacts. One of the greatest merits of molecular monolayers is their capability to form excellent thin dielectrics, yielding rich and unique current-voltage characteristics for transport across metal/molecular monolayer/semiconductor interfaces. We explain the interplay between the monolayer as tunneling barrier on the one hand, and the electrostatic barrier within the semiconductor, due to its space-charge region, on the other hand, as well as how different monolayer chemistries control each of these barriers. Practical tools to experimentally identify these two barriers and distinguish between them are given, followed by a short look to the future. This review is accompanied by another one, concerning the formation of large-area molecular junctions and charge transport that is dominated solely by molecules.

  19. Molecular modeling of alkyl monolayers on the Si (100)-2 x 1 surface

    NARCIS (Netherlands)

    Lee, M.V.; Guo, D.; Linford, M.R.; Zuilhof, H.

    2004-01-01

    Molecular modeling was used to simulate various surfaces derived from the addition of 1-alkenes and 1-alkynes to Si=Si dimers on the Si(100)-2 × 1 surface. The primary aim was to better understand the interactions between adsorbates on the surface and distortions of the underlying silicon crystal

  20. Educational challenges of molecular life science: Characteristics and implications for education and research.

    Science.gov (United States)

    Tibell, Lena A E; Rundgren, Carl-Johan

    2010-01-01

    Molecular life science is one of the fastest-growing fields of scientific and technical innovation, and biotechnology has profound effects on many aspects of daily life-often with deep, ethical dimensions. At the same time, the content is inherently complex, highly abstract, and deeply rooted in diverse disciplines ranging from "pure sciences," such as math, chemistry, and physics, through "applied sciences," such as medicine and agriculture, to subjects that are traditionally within the remit of humanities, notably philosophy and ethics. Together, these features pose diverse, important, and exciting challenges for tomorrow's teachers and educational establishments. With backgrounds in molecular life science research and secondary life science teaching, we (Tibell and Rundgren, respectively) bring different experiences, perspectives, concerns, and awareness of these issues. Taking the nature of the discipline as a starting point, we highlight important facets of molecular life science that are both characteristic of the domain and challenging for learning and education. Of these challenges, we focus most detail on content, reasoning difficulties, and communication issues. We also discuss implications for education research and teaching in the molecular life sciences.

  1. Hydrologic Science and Satellite Measurements of Surface Water (Invited)

    Science.gov (United States)

    Alsdorf, D. E.; Mognard, N. M.; Lettenmaier, D. P.

    2010-12-01

    While significant advances continue to be made for satellite measurements of surface waters, important science and application opportunities remain. Examples include the following: (1) Our current methods of measuring floodwater dynamics are either sparsely distributed or temporally inadequate. As an example, flood depths are measured by using high water marks, which capture only the peak of the flood wave, not its temporal variability. (2) Discharge is well measured at individual points along stream networks using in-situ gauges, but these do not capture within-reach hydraulic variability such as the water surface slope changes on the rising and falling limbs of flood waves. (3) Just a 1.0 mm/day error in ET over the Congo Basin translates to a 35,000 m3/s discharge error. Knowing the discharge of the Congo River and its many tributaries should significantly improve our understanding of the water balance throughout the basin. The Congo is exemplary of many other basins around the globe. (4) Arctic hydrology is punctuated by millions of unmeasured lakes. Globally, there might be as many as 30 million lakes larger than a hectare. Storage changes in these lakes are nearly unknown, but in the Arctic such changes are likely an indication of global warming. (5) Well over 100 rivers cross international boundaries, yet the sharing of water data is poor. Overcoming this helps to better manage the entire river basin while also providing a better assessment of potential water related disasters. The Surface Water and Ocean Topography (SWOT, http://swot.jpl.nasa.gov/) mission is designed to meet these needs by providing global measurements of surface water hydrodynamics. SWOT will allow estimates of discharge in rivers wider than 100m (50m goal) and storage changes in water bodies larger than 250m by 250m (and likely as small as one hectare).

  2. Designing molecular printboards: a photolithographic platform for recodable surfaces

    Czech Academy of Sciences Publication Activity Database

    Abt, D.; Schmidt, B. V. K. J.; Pop-Georgievski, Ognen; Quick, A. S.; Danilov, D.; Kostina, Nina Yu.; Bruns, M.; Wenzel, W.; Wegener, M.; Rodriguez-Emmenegger, Cesar; Barner-Kowollik, C.

    2015-01-01

    Roč. 21, č. 38 (2015), s. 13186-13190 ISSN 0947-6539 R&D Projects: GA ČR(CZ) GJ15-09368Y Institutional support: RVO:61389013 Keywords : cyclodextrin * molecular printboard * photoconjugation Subject RIV: BO - Biophysics Impact factor: 5.771, year: 2015

  3. Molecular mass spectrometry imaging in biomedical and life science research

    Czech Academy of Sciences Publication Activity Database

    Pól, Jaroslav; Strohalm, Martin; Havlíček, Vladimír; Volný, Michael

    2010-01-01

    Roč. 134, č. 5 (2010), s. 423-443 ISSN 0948-6143 R&D Projects: GA MŠk LC545; GA ČR GPP206/10/P018 Institutional research plan: CEZ:AV0Z50200510 Keywords : Mass spectrometry * Chemical imaging * Molecular imaging Subject RIV: EE - Microbiology, Virology Impact factor: 4.727, year: 2010

  4. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Energy Technology Data Exchange (ETDEWEB)

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  5. Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

    Science.gov (United States)

    Wang, Hong-Fei

    2016-12-01

    Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there have been many progresses in the development of methodology and instrumentation in the SFG-VS toolbox that have significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

  6. En route to surface-bound electric field-driven molecular motors.

    Science.gov (United States)

    Jian, Huahua; Tour, James M

    2003-06-27

    Four caltrop-shaped molecules that might be useful as surface-bound electric field-driven molecular motors have been synthesized. The caltrops are comprised of a pair of electron donor-acceptor arms and a tripod base. The molecular arms are based on a carbazole or oligo(phenylene ethynylene) core with a strong net dipole. The tripod base uses a silicon atom as its core. The legs of the tripod bear sulfur-tipped bonding units, as acetyl-protected benzylic thiols, for bonding to a gold surface. The geometry of the tripod base allows the caltrop to project upward from a metallic surface after self-assembly. Ellipsometric studies show that self-assembled monolayers of the caltrops are formed on Au surfaces with molecular thicknesses consistent with the desired upright-shaft arrangement. As a result, the zwitterionic molecular arms might be controllable when electric fields are applied around the caltrops, thereby constituting field-driven motors.

  7. Ultrafast phenomena in molecular sciences femtosecond physics and chemistry

    CERN Document Server

    Bañares, Luis

    2014-01-01

    This book presents the latest developments in Femtosecond Chemistry and Physics for the study of ultrafast photo-induced molecular processes. Molecular systems, from the simplest H2 molecule to polymers or biological macromolecules, constitute central objects of interest for Physics, Chemistry and Biology, and despite the broad range of phenomena that they exhibit, they share some common behaviors. One of the most significant of those is that many of the processes involving chemical transformation (nuclear reorganization, bond breaking, bond making) take place in an extraordinarily short time, in or around the femtosecond temporal scale (1 fs = 10-15 s). A number of experimental approaches - very particularly the developments in the generation and manipulation of ultrashort laser pulses - coupled with theoretical progress, provide the ultrafast scientist with powerful tools to understand matter and its interaction with light, at this spatial and temporal scale. This book is an attempt to reunite some of the ...

  8. Molecular dynamics simulation of uranium compound adsorption on solid surface

    International Nuclear Information System (INIS)

    Omori, Yuki; Takizawa, Yuji; Okamoto, Tsuyoshi

    2010-01-01

    Particles mixed in the UF6 gas have the property of accumulating on the inside of piping or units. This type of accumulation will cause material unaccounted for (MUF) in the UF6 gas processing facilities. Development of a calculation model for estimating the accumulation rate of uranium compounds has been expected. And predicting possible part of the units where uranium compounds adsorb will contribute to design an effective detection system. The purpose of this study is to take the basic knowledge of the particle's adsorption mechanism from the microscopic point of view. In simulation analysis, UF5 model particle is produced, then two types of solid surfaces are prepared; one is a solid surface at rest and the other is a moving solid surface. The result obtained by the code 'PABS' showed that when the solid surface moves at a lower velocity, the particle's adsorption process dominates over the particle's breakup one. Besides the velocity of the solid surface, other principal factors affecting an adsorption ratio were also discussed. (author)

  9. Hydrogenation of nitriles on a well-characterized nickel surface: From surface science studies to liquid phase catalytic activity measurements

    Energy Technology Data Exchange (ETDEWEB)

    Gardin, Denis Emmanuel [Univ. of California, Berkeley, CA (United States)

    1993-12-01

    Nitrile hydrogenation is the most commonly used method for preparing diverse amines. This thesis is aimed at the mechanism and factors affecting the performance of Ni-based catalysts in nitrile hydrogenations. Surface science techniques are used to study bonding of nitriles and amines to a Ni(111) surface and to identify surface intermediates. Liquid-phase hydrogenations of cyclohexene and 1-hexene on a Pt foil were carried out successfully. Finally, knowledge about the surface structure, surface chemical bond, dynamics of surface atoms (diffusion, growth), and reactivity of metal surfaces from solid-gas interface studies, is discussed.

  10. A Molecular-Level Account of the Antigenic Hantaviral Surface

    Directory of Open Access Journals (Sweden)

    Sai Li

    2016-05-01

    Full Text Available Hantaviruses, a geographically diverse group of zoonotic pathogens, initiate cell infection through the concerted action of Gn and Gc viral surface glycoproteins. Here, we describe the high-resolution crystal structure of the antigenic ectodomain of Gn from Puumala hantavirus (PUUV, a causative agent of hemorrhagic fever with renal syndrome. Fitting of PUUV Gn into an electron cryomicroscopy reconstruction of intact Gn-Gc spike complexes from the closely related but non-pathogenic Tula hantavirus localized Gn tetramers to the membrane-distal surface of the virion. The accuracy of the fitting was corroborated by epitope mapping and genetic analysis of available PUUV sequences. Interestingly, Gn exhibits greater non-synonymous sequence diversity than the less accessible Gc, supporting a role of the host humoral immune response in exerting selective pressure on the virus surface. The fold of PUUV Gn is likely to be widely conserved across hantaviruses.

  11. Surface physics of materials materials science and technology

    CERN Document Server

    Blakely, J M

    2013-01-01

    Surface Physics of Materials presents accounts of the physical properties of solid surfaces. The book contains selected articles that deal with research emphasizing surface properties rather than experimental techniques in the field of surface physics. Topics discussed include transport of matter at surfaces; interaction of atoms and molecules with surfaces; chemical analysis of surfaces; and adhesion and friction. Research workers, teachers and graduate students in surface physics, and materials scientist will find the book highly useful.

  12. Adhesion of Photon-Driven Molecular Motors to Surfaces via 1,3-Dipolar Cycloadditions : Effect of Interfacial Interactions on Molecular Motion

    NARCIS (Netherlands)

    Carroll, Gregory T.; London, Gabor; Fernández Landaluce, Tatiana; Rudolf, Petra; Feringa, Ben L.

    We report the attachment of altitudinal light-driven molecular motors to surfaces using 1,3-dipolar cycloaddition reactions. Molecular motors were designed containing azide or alkyne groups for attachment to alkyne- or azide-modified surfaces. Surface attachment was characterized by UV-vis, IR, XPS,

  13. An adaptive interpolation scheme for molecular potential energy surfaces

    Science.gov (United States)

    Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

    2016-08-01

    The calculation of potential energy surfaces for quantum dynamics can be a time consuming task—especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within a given accuracy compared to the non-adaptive version.

  14. On the stability of surface-confined nanoporous molecular networks

    Energy Technology Data Exchange (ETDEWEB)

    Ghijsens, Elke; Adisoejoso, Jinne, E-mail: Jinne.adisoejoso@chem.kuleuven.be, E-mail: tobe@chem.es.osaka-u.ac.jp, E-mail: Steven.DeFeyter@chem.kuleuven.be; Van Gorp, Hans; Destoop, Iris; Ivasenko, Oleksandr; Van der Auweraer, Mark; De Feyter, Steven, E-mail: Jinne.adisoejoso@chem.kuleuven.be, E-mail: tobe@chem.es.osaka-u.ac.jp, E-mail: Steven.DeFeyter@chem.kuleuven.be [Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven—University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven (Belgium); Noguchi, Aya; Tahara, Kazukuni; Tobe, Yoshito, E-mail: Jinne.adisoejoso@chem.kuleuven.be, E-mail: tobe@chem.es.osaka-u.ac.jp, E-mail: Steven.DeFeyter@chem.kuleuven.be [Graduate School of Engineering Science, Division of Frontier Materials Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan)

    2015-03-14

    Self-assembly of molecular building blocks into two-dimensional nanoporous networks has been a topic of broad interest for many years. However, various factors govern the specific outcome of the self-assembly process, and understanding and controlling these are key to successful creation. In this work, the self-assembly of two alkylated dehydrobenzo[12]annulene building blocks was compared at the liquid-solid interface. It turned out that only a small chemical modification within the building blocks resulted in enhanced domain sizes and stability of the porous packing relative to the dense linear packing. Applying a thermodynamic model for phase transition revealed some key aspects for network formation.

  15. Inelastic surface collisions and the desorption of massive molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Macfarlane, R D [Texas A and M Univ., College Station (USA). Dept. of Chemistry

    1983-01-01

    The interaction of high energy ions in the region of electronic stopping (1 MeV u/sup -1/) stimulates the desorption of massive molecular ions of biomolecules such as insulin. The experimental details of the measurements are given with some examples of application for analytical mass spectrometry. Studies on the role of the incident ion (accelerator beam experiments) are reviewed as well as the contribution of the matrix to the desorption-ionization process. How the electronic relaxation process couples to desorption-ionization is a central question in understanding the overall mechanism of the process.

  16. Relativistic quantum chemistry the fundamental theory of molecular science

    CERN Document Server

    Reiher, Markus

    2014-01-01

    Einstein proposed his theory of special relativity in 1905. For a long time it was believed that this theory has no significant impact on chemistry. This view changed in the 1970s when it was realized that (nonrelativistic) Schrödinger quantum mechanics yields results on molecular properties that depart significantly from experimental results. Especially when heavy elements are involved, these quantitative deviations can be so large that qualitative chemical reasoning and understanding is affected. For this to grasp the appropriate many-electron theory has rapidly evolved. Nowadays relativist

  17. Molecularly-Limited Fractal Surface Area of Mineral Powders

    Directory of Open Access Journals (Sweden)

    Petr Jandacka

    2016-05-01

    Full Text Available The topic of the specific surface area (SSA of powders is not sufficiently described in the literature in spite of its nontrivial contribution to adsorption and dissolution processes. Fractal geometry provides a way to determine this parameter via relation SSA ~ x(D − 3s(2 − D, where x (m is the particle size and s (m is a scale. Such a relation respects nano-, micro-, or macro-topography on the surface. Within this theory, the fractal dimension 2 ≤ D < 3 and scale parameter s plays a significant role. The parameter D may be determined from BET or dissolution measurements on several samples, changing the powder particle sizes or sizes of adsorbate molecules. If the fractality of the surface is high, the SSA does not depend on the particle size distribution and vice versa. In this paper, the SSA parameter is analyzed from the point of view of adsorption and dissolution processes. In the case of adsorption, a new equation for the SSA, depending on the term (2 − D∙(s2 − sBET/sBET, is derived, where sBET and s2 are effective cross-sectional diameters for BET and new adsorbates. Determination of the SSA for the dissolution process appears to be very complicated, since the fractality of the surface may change in the process. Nevertheless, the presented equations have good application potential.

  18. Surface engineering: molecularly imprinted affinity membranes by photograft polymerization

    Science.gov (United States)

    Matuschewski, Heike; Sergeyeva, Tatiana A.; Bendig, Juergen; Piletsky, Sergey A.; Ulbricht, Matthies; Schedler, Uwe

    2001-02-01

    Commercial polymer microfiltration membranes were surface-modified with a graft copolymer of a functional monomer and a crosslinker in the presence of a template (triazine-herbicide). As result, membranes covered with a thin layer of imprinted polymer (MIP) selective to the template were obtained. The influence of the polymerization conditions on membrane recognition properties was studied by membranes

  19. Surface plasmon-enhanced molecular fluorescence induced by gold nanostructures

    International Nuclear Information System (INIS)

    Teng, Y.; Ueno, K.; Shi, X.; Aoyo, D.; Misawa, H.; Qiu, J.

    2012-01-01

    The authors report on surface plasmon-enhanced fluorescence of Eosin Y molecules induced by gold nanostructures. Al 2 O 3 films deposited by atomic layer deposition with sub-nanometer resolution were used as the spacer layer to control the distance between molecules and the gold surface. As the thickness of the Al 2 O 3 film increased, the fluorescence intensity first increased and then decreased. The highest enhancement factor is achieved with a 1 nm Al 2 O 3 film. However, the trend for the fluorescence lifetime is the opposite. It first decreased and then increased. The changes in the fluorescence quantum yield were also calculated. The yield shows a similar trend to the fluorescence intensity. The competition between the surface plasmon-induced increase in the radiative decay rate and the gold-induced fluorescence quenching is responsible for the observed phenomenon. In addition, this competition strongly depends on the thickness of the spacer layer between Eosin Y molecules and the gold surface. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. Sea Surface Height, Absolute, Aviso, 0.25 degrees, Global, Science Quality

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Aviso Absolute Sea Surface Height is the Sea Surface Height Deviation plus the long term mean dynamic height. This is Science Quality data.

  1. Integration of molecular pathology, epidemiology and social science for global precision medicine.

    Science.gov (United States)

    Nishi, Akihiro; Milner, Danny A; Giovannucci, Edward L; Nishihara, Reiko; Tan, Andy S; Kawachi, Ichiro; Ogino, Shuji

    2016-01-01

    The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science.

  2. Electronic structure of surface-supported bis(phthalocyaninato) terbium(III) single molecular magnets.

    Science.gov (United States)

    Vitali, Lucia; Fabris, Stefano; Conte, Adriano Mosca; Brink, Susan; Ruben, Mario; Baroni, Stefano; Kern, Klaus

    2008-10-01

    The electronic structure of isolated bis(phthalocyaninato) terbium(III) molecules, a novel single-molecular-magnet (SMM), supported on the Cu(111) surface has been characterized by density functional theory and scanning tunneling spectroscopy. These studies reveal that the interaction with the metal surface preserves both the molecular structure and the large spin magnetic moment of the metal center. The 4f electron states are not perturbed by the adsorption while a strong molecular/metal interaction can induce the suppression of the minor spin contribution delocalized over the molecular ligands. The calculations show that the inherent spin magnetic moment of the molecule is only weakly affected by the interaction with the surface and suggest that the SMM character might be preserved.

  3. Molecular dynamics simulations of water on a hydrophilic silica surface at high air pressures

    DEFF Research Database (Denmark)

    Zambrano, H.A.; Walther, Jens Honore; Jaffe, R.L.

    2014-01-01

    Wepresent a force field forMolecular Dynamics (MD) simulations ofwater and air in contactwith an amorphous silica surface. We calibrate the interactions of each species present in the systemusing dedicated criteria such as the contact angle of a water droplet on a silica surface, and the solubility...

  4. Electronic structure, molecular bonding and potential energy surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ruedenberg, K. [Ames Laboratory, IA (United States)

    1993-12-01

    By virtue of the universal validity of the generalized Born-Oppenheimer separation, potential energy surfaces (PES`) represent the central conceptual as well as quantitative entities of chemical physics and provide the basis for the understanding of most physicochemical phenomena in many diverse fields. The research in this group deals with the elucidation of general properties of PES` as well as with the quantitative determination of PES` for concrete systems, in particular pertaining to reactions involving carbon, oxygen, nitrogen and hydrogen molecules.

  5. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    Energy Technology Data Exchange (ETDEWEB)

    López-Moreno, S., E-mail: sinlopez@uacam.mx [Centro de Investigación en Corrosión, Universidad Autónoma de Campeche, Av. Héroe de Nacozari 480, Campeche, Campeche 24029 (Mexico); Romero, A. H. [Physics Department, West Virginia University, Morgantown, West Virginia 26506-6315 (United States)

    2015-04-21

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O{sub 2} molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

  6. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    Science.gov (United States)

    López-Moreno, S.; Romero, A. H.

    2015-04-01

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

  7. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    International Nuclear Information System (INIS)

    López-Moreno, S.; Romero, A. H.

    2015-01-01

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O 2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered

  8. 3S'83 Symposium on surface science. Contributions

    International Nuclear Information System (INIS)

    Braun, P.; Betz, G.; Husinsky, W.; Soellner, E.; Stoeri, H.; Varga, P.

    1983-01-01

    This symposium included the topics: electronic structure; ion-surface-interaction; surface structure; adsorption and reactivity; surface analysis; 60 papers were presented, only part of which pertain to INIS. (G.Q.)

  9. Hydration of excess electrons trapped in charge pockets on molecular surfaces

    Science.gov (United States)

    Jalbout, Abraham F.; Del Castillo, R.; Adamowicz, Ludwik

    2007-01-01

    In this work we strive to design a novel electron trap located on a molecular surface. The process of electron trapping involves hydration of the trapped electron. Previous calculations on surface electron trapping revealed that clusters of OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), while the hydrogen atoms on the opposite side of the surface form pockets of positive charge that can attract extra negative charge. The excess electron density on such surfaces can be further stabilized by interactions with water molecules. Our calculations show that these anionic systems are stable with respect to vertical electron detachment (VDE).

  10. Synthesis and Surface-Specific Analysis of Molecular Constituents Relevant to Biogenic Secondary Organic Aerosol Material

    Science.gov (United States)

    Be, A. G.; Upshur, M. A.; Chase, H. M.; Geiger, F.; Thomson, R. J.

    2017-12-01

    Secondary organic aerosol (SOA) particles formed from the oxidation of biogenic volatile organic compounds (BVOCs) remain a principal, yet elusive, class of airborne particulate matter that impacts the Earth's radiation budget. Given the characteristic molecular complexity comprising biogenic SOA particles, chemical information selective to the gas-aerosol interface may be valuable in the investigation of such systems, as surface considerations likely dictate the phenomena driving particle evolution mechanisms and climate effects. In particular, cloud activation processes may be parameterized using the surface tension depression that coincides with partitioning of surface-active organic species to the gas-droplet interface. However, the extent to which surface chemical processes, such as cloud droplet condensation, are influenced by the chemical structure and reactivity of individual surface-active molecules in SOA particles is largely unknown. We seek to study terpene-derived organic species relevant to the surfaces of biogenic SOA particles via synthesis of putative oxidation products followed by analysis using surface-selective physicochemical measurements. Using dynamic surface tension measurements, considerable differences are observed in the surface tension depression of aqueous pendant droplets that contain synthetically prepared ozonolysis products derived from abundant terpene precursors. Furthermore, sum frequency generation spectroscopy is utilized for comparison of the surface vibrational spectral responses of synthesized reference compounds with those observed for laboratory aerosol toward probing the surface composition of SOA material. Such ongoing findings highlight the underlying importance of molecular structure and reactivity when considering the surface chemistry of biogenic terpene-derived atmospheric aerosols.

  11. Rosalind Franklin and the DNA molecular structure: A case of history of science to learn about the nature of science

    Directory of Open Access Journals (Sweden)

    José Antonio Acevedo-Díaz

    2016-08-01

    Full Text Available The Rosalind Franklin’s case regarding the elucidation of the molecular structure of DNA is presented as an interesting story of the history of science to address a set of questions related to the nature of science (NOS from an explicit and reflective approach. The teaching proposal is aimed to the pre-service teachers training in NOS issues and its didactics. Attention is given to both epistemic and non-epistemic aspects in the narration and the NOS questions asked for reflecting about them. Also, some methodological recommendations for implementing the didactic proposal in science classroom are offered. This involves the follows: (i in small groups, the students read the controversy and respond to some questions on NOS; (ii they present their responses to the whole-class; and (iii they revise their initial responses in light of the whole-class discussion.

  12. Surface Charge Transfer Doping of Monolayer Phosphorene via Molecular Adsorption.

    Science.gov (United States)

    He, Yuanyuan; Xia, Feifei; Shao, Zhibin; Zhao, Jianwei; Jie, Jiansheng

    2015-12-03

    Monolayer phosphorene has attracted much attention owing to its extraordinary electronic, optical, and structural properties. Rationally tuning the electrical transport characteristics of monolayer phosphorene is essential to its applications in electronic and optoelectronic devices. Herein, we study the electronic transport behaviors of monolayer phosphorene with surface charge transfer doping of electrophilic molecules, including 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ), NO2, and MoO3, using density functional theory combined with the nonequilibrium Green's function formalism. F4TCNQ shows optimal performance in enhancing the p-type conductance of monolayer phosphorene. Static electronic properties indicate that the enhancement is originated from the charge transfer between adsorbed molecule and phosphorene layer. Dynamic transport behaviors demonstrate that additional channels for hole transport in host monolayer phosphorene were generated upon the adsorption of molecule. Our work unveils the great potential of surface charge transfer doping in tuning the electronic properties of monolayer phosphorene and is of significance to its application in high-performance devices.

  13. Educational Challenges of Molecular Life Science: Characteristics and Implications for Education and Research

    Science.gov (United States)

    Tibell, Lena A. E.; Rundgren, Carl-Johan

    2010-01-01

    Molecular life science is one of the fastest-growing fields of scientific and technical innovation, and biotechnology has profound effects on many aspects of daily life--often with deep, ethical dimensions. At the same time, the content is inherently complex, highly abstract, and deeply rooted in diverse disciplines ranging from "pure…

  14. Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

    Science.gov (United States)

    Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

    2014-01-01

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

  15. Molecular orbital study of the chemisorption of carbon monoxide on a tungsten (100) surface

    International Nuclear Information System (INIS)

    Lee, T.H.; Rabalais, J.W.

    1978-01-01

    The adsorption energies of carbon monoxide chemisorbed at various sites on a tungsten (100) surface have been calculated by extended Hueckel molecular orbital theory (EHMO). The concept of a 'surface molecule' in which CO is bonded to an array of tungsten atoms Wsub(n) has been employed. Dissociative adsorption in which C occupies a four-fold, five-coordination site and O occupies either a four- or two-fold site has been found to be the most stable form for CO on a W surface. Stable one-fold and two-fold sites of molecularly adsorbed CO have also been found in which the CO group is normal to the surface plane and the C atom is nearest the surface. Adsorption energies and molecular orbitals for the stable molecularly and dissociatively adsorbed CO sites are compared with the experimental data on various types of adsorbed CO, i.e. virgin-, α-, and β-CO. Models are suggested for each of these adsorption types. The strongest bonding interactions occur between the CO 5sigma orbital and the totally symmetric 5d and 6s orbitals of the Wsub(n) cluster. Possible mechanisms for conversion of molecularly adsorbed CO to dissociatively adsorbed CO are proposed and the corresponding activation energies are estimated. (Auth.)

  16. Memory effects in nonadiabatic molecular dynamics at metal surfaces

    DEFF Research Database (Denmark)

    Olsen, Thomas; Schiøtz, Jakob

    2010-01-01

    We study the effect of temporal correlation in a Langevin equation describing nonadiabatic dynamics at metal surfaces. For a harmonic oscillator, the Langevin equation preserves the quantum dynamics exactly and it is demonstrated that memory effects are needed in order to conserve the ground state...... energy of the oscillator. We then compare the result of Langevin dynamics in a harmonic potential with a perturbative master equation approach and show that the Langevin equation gives a better description in the nonperturbative range of high temperatures and large friction. Unlike the master equation......, this approach is readily extended to anharmonic potentials. Using density functional theory, we calculate representative Langevin trajectories for associative desorption of N-2 from Ru(0001) and find that memory effects lower the dissipation of energy. Finally, we propose an ab initio scheme to calculate...

  17. Molecular ordering of ethanol at the calcite surface

    DEFF Research Database (Denmark)

    Pasarín, I. S.; Yang, M.; Bovet, Nicolas Emile

    2012-01-01

    To produce biominerals, such as shells, bones, and teeth, living beings create organic compounds that control the growth of the solid phase. Investigating the atomic scale behavior of individual functional groups at the mineral-fluid interface provides fundamental information that is useful...... for constructing accurate predictive models for natural systems. Previous investigations of the activity of coccolith-associated polysaccharides (CAP) on calcite, using atomic force microscopy (AFM) [ Henriksen, K., Young, J. R., Bown, P. R., and Stipp, S. L. S.Palentology 2004, 43 (Part 3), 725...... dynamics (MD) simulations, the structuring on calcite of a layer of the simplest carbon chain molecule that contains an OH group, ethanol (CH 3-CH2-OH). We found evidence that EtOH forms a highly ordered structure at the calcite surface, where the first layer molecules bond with calcite. The ethanol...

  18. Active molecular plasmonics: tuning surface plasmon resonances by exploiting molecular dimensions

    Science.gov (United States)

    Chen, Kai; Leong, Eunice Sok Ping; Rukavina, Michael; Nagao, Tadaaki; Liu, Yan Jun; Zheng, Yuebing

    2015-06-01

    Molecular plasmonics explores and exploits the molecule-plasmon interactions on metal nanostructures to harness light at the nanoscale for nanophotonic spectroscopy and devices. With the functional molecules and polymers that change their structural, electrical, and/or optical properties in response to external stimuli such as electric fields and light, one can dynamically tune the plasmonic properties for enhanced or new applications, leading to a new research area known as active molecular plasmonics (AMP). Recent progress in molecular design, tailored synthesis, and self-assembly has enabled a variety of scenarios of plasmonic tuning for a broad range of AMP applications. Dimension (i.e., zero-, two-, and threedimensional) of the molecules on metal nanostructures has proved to be an effective indicator for defining the specific scenarios. In this review article, we focus on structuring the field of AMP based on the dimension of molecules and discussing the state of the art of AMP. Our perspective on the upcoming challenges and opportunities in the emerging field of AMP is also included.

  19. Active molecular plasmonics: tuning surface plasmon resonances by exploiting molecular dimensions

    Directory of Open Access Journals (Sweden)

    Chen Kai

    2015-06-01

    Full Text Available Molecular plasmonics explores and exploits the molecule–plasmon interactions on metal nanostructures to harness light at the nanoscale for nanophotonic spectroscopy and devices. With the functional molecules and polymers that change their structural, electrical, and/or optical properties in response to external stimuli such as electric fields and light, one can dynamically tune the plasmonic properties for enhanced or new applications, leading to a new research area known as active molecular plasmonics (AMP. Recent progress in molecular design, tailored synthesis, and self-assembly has enabled a variety of scenarios of plasmonic tuning for a broad range of AMP applications. Dimension (i.e., zero-, two-, and threedimensional of the molecules on metal nanostructures has proved to be an effective indicator for defining the specific scenarios. In this review article, we focus on structuring the field of AMP based on the dimension of molecules and discussing the state of the art of AMP. Our perspective on the upcoming challenges and opportunities in the emerging field of AMP is also included.

  20. The Environmental and Molecular Sciences Laboratory project -- Continuous evolution in leadership

    International Nuclear Information System (INIS)

    Knutson, D.E.; McClusky, J.K.

    1994-10-01

    The Environmental and Molecular Sciences Laboratory (EMSL) construction project at Pacific Northwest Laboratory (PNL) in Richland, Washington, is a $230M Major Systems Acquisition for the US Department of Energy (DOE). The completed laboratory will be a national user facility that provides unparalleled capabilities for scientists involved in environmental molecular science research. This project, approved for construction by the Secretary of Energy in October 1993, is underway. The United States is embarking on an environmental cleanup effort that dwarfs previous scientific enterprise. Using current best available technology, the projected costs of cleaning up the tens of thousands of toxic waste sites, including DOE sites, is estimated to exceed one trillion dollars. The present state of scientific knowledge regarding the effects of exogenous chemicals on human biology is very limited. Long term environmental research at the molecular level is needed to resolve the concerns, and form the building blocks for a structure of cost effective process improvement and regulatory reform

  1. The Environmental and Molecular Sciences Laboratory project -- Continuous evolution in leadership

    Energy Technology Data Exchange (ETDEWEB)

    Knutson, D.E.; McClusky, J.K.

    1994-10-01

    The Environmental and Molecular Sciences Laboratory (EMSL) construction project at Pacific Northwest Laboratory (PNL) in Richland, Washington, is a $230M Major Systems Acquisition for the US Department of Energy (DOE). The completed laboratory will be a national user facility that provides unparalleled capabilities for scientists involved in environmental molecular science research. This project, approved for construction by the Secretary of Energy in October 1993, is underway. The United States is embarking on an environmental cleanup effort that dwarfs previous scientific enterprise. Using current best available technology, the projected costs of cleaning up the tens of thousands of toxic waste sites, including DOE sites, is estimated to exceed one trillion dollars. The present state of scientific knowledge regarding the effects of exogenous chemicals on human biology is very limited. Long term environmental research at the molecular level is needed to resolve the concerns, and form the building blocks for a structure of cost effective process improvement and regulatory reform.

  2. 52nd colloid and surface science symposium. Proceedings volume

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, E.L. Jr.; Corbett, H.G.

    1978-05-01

    Abstracts are presented under the headings: cell/surface interactions, surface properties and reactions of catalysts, solution chemistry of surfactants, dynamic systems, microorganism/surface interactions, gas-solid interactions, biological surfaces, solid sorbents, lung surfactant and intestinal absorption, pigments, and liquid systems. (DLC)

  3. The hydrophobic effect: Molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Mouritsen, Ole G.; Peters, Günther H.J.

    2004-01-01

    Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C36H74 or n-alcohol C35H71OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding......-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together...... at both surfaces. The ordering is characteristically different between the surfaces and of longer range at the hydrophilic surface. Furthermore, the dynamic properties of water are different at the two surfaces and different from the bulk behavior. In particular, at the hydrophobic surface, time...

  4. The Soft-Confined Method for Creating Molecular Models of Amorphous Polymer Surfaces

    KAUST Repository

    Liu, Hongyi; Li, Yan; Krause, Wendy E.; Rojas, Orlando J.; Pasquinelli, Melissa A.

    2012-01-01

    The goal of this work was to use molecular dynamics (MD) simulations to build amorphous surface layers of polypropylene (PP) and cellulose and to inspect their physical and interfacial properties. A new method to produce molecular models for these surfaces was developed, which involved the use of a "soft" confining layer comprised of a xenon crystal. This method compacts the polymers into a density distribution and a degree of molecular surface roughness that corresponds well to experimental values. In addition, calculated properties such as density, cohesive energy density, coefficient of thermal expansion, and the surface energy agree with experimental values and thus validate the use of soft confining layers. The method can be applied to polymers with a linear backbone such as PP as well as those whose backbones contain rings, such as cellulose. The developed PP and cellulose surfaces were characterized by their interactions with water. It was found that a water nanodroplet spreads on the amorphous cellulose surfaces, but there was no significant change in the dimension of the droplet on the PP surface; the resulting MD water contact angles on PP and amorphous cellulose surfaces were determined to be 106 and 33°, respectively. © 2012 American Chemical Society.

  5. The Soft-Confined Method for Creating Molecular Models of Amorphous Polymer Surfaces

    KAUST Repository

    Liu, Hongyi

    2012-02-09

    The goal of this work was to use molecular dynamics (MD) simulations to build amorphous surface layers of polypropylene (PP) and cellulose and to inspect their physical and interfacial properties. A new method to produce molecular models for these surfaces was developed, which involved the use of a "soft" confining layer comprised of a xenon crystal. This method compacts the polymers into a density distribution and a degree of molecular surface roughness that corresponds well to experimental values. In addition, calculated properties such as density, cohesive energy density, coefficient of thermal expansion, and the surface energy agree with experimental values and thus validate the use of soft confining layers. The method can be applied to polymers with a linear backbone such as PP as well as those whose backbones contain rings, such as cellulose. The developed PP and cellulose surfaces were characterized by their interactions with water. It was found that a water nanodroplet spreads on the amorphous cellulose surfaces, but there was no significant change in the dimension of the droplet on the PP surface; the resulting MD water contact angles on PP and amorphous cellulose surfaces were determined to be 106 and 33°, respectively. © 2012 American Chemical Society.

  6. Coupling molecular catalysts with nanostructured surfaces for efficient solar fuel production

    Science.gov (United States)

    Jin, Tong

    Solar fuel generation via carbon dioxide (CO2) reduction is a promising approach to meet the increasing global demand for energy and to minimize the impact of energy consumption on climate change. However, CO2 is thermodynamically stable; its activation often requires the use of appropriate catalysts. In particular, molecular catalysts with well-defined structures and tunability have shown excellent activity in photochemical CO2 reduction. These homogenous catalysts, however, suffer from poor stability under photochemical conditions and difficulty in recycling from the reaction media. Heterogenized molecular catalysts, particularly those prepared by coupling molecular catalysts with solid-state surfaces, have attracted more attention in recent years as potential solutions to address the issues associated with molecular catalysts. In this work, solar CO2 reduction is investigated using systems coupling molecular catalysts with robust nanostructured surfaces. In Chapter 2, heterogenization of macrocyclic cobalt(III) and nickel (II) complexes on mesoporous silica surface was achieved by different methods. Direct ligand derivatization significantly lowered the catalytic activity of Co(III) complex, while grafting the Co(III) complex onto silica surface through Si-O-Co linkage resulted in hybrid catalysts with excellent activity in CO2 reduction in the presence of p-terphenyl as a molecular photosensitizer. An interesting loading effect was observed, in which the optimal activity was achieved at a medium Co(III) surface density. Heterogenization of the Ni(II) complex on silica surface has also been implemented, the poor photocatalytic activity of the hybrid catalyst can be attributed to the intrinsic nature of the homogeneous analogue. This study highlighted the importance of appropriate linking strategies in preparing functional heterogenized molecular catalysts. Coupling molecular complexes with light-harvesting surfaces could avoid the use of expensive molecular

  7. Heat-resistant organic molecular layer as a joint interface for metal reduction on plastics surfaces

    International Nuclear Information System (INIS)

    Sang, Jing; Aisawa, Sumio; Hirahara, Hidetoshi; Kudo, Takahiro; Mori, Kunio

    2016-01-01

    Graphical abstract: - Highlights: • In situ adsorption behaviors of TES on PA6 surface were clarified by QCM. • Highest adsorption of TES on PA6 was obtained in pH 3 and 0.1 M solution. • Molecular layers of TES with uniform structures were prepared on PA6 surface. • TES layer improved PA6 local heat resistance from 150 °C to 230 °C. • TES molecular layer successfully reduced Ag ion to Ag"0. - Abstract: Heat-resistant organic molecular layers have been fabricated by triazine-based silane coupling agent for metal reduction on plastic surfaces using adsorption method. These molecular layers were used as an interfacial layer between polyamide (PA6) and metal solution to reduce Ag"+ ion to Ag"0. The interfacial behaviors of triazine molecular layer at the interfaces between PA6 and Ag solution were investigated using quartz crystal microbalance (QCM). The kinetics of molecular adsorption on PA6 was investigated by using triazine-based silane coupling agent solutions at different pH and concentration. X-ray photoelectron spectroscopy (XPS), atomic force microscope (AFM), and local nano thermal analysis were employed to characterize the surfaces and interfaces. The nano thermal analysis results show that molecular layers of triazine-based silane coupling agent greatly improved heat resistance of PA6 resin from 170 °C up to 230 °C. This research developed an in-depth insight for molecular behaviors of triazine-based silane coupling agent at the PA6 and Ag solution interfaces and should be of significant value for interfacial research between plastics and metal solution in plating industry.

  8. Heat-resistant organic molecular layer as a joint interface for metal reduction on plastics surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Sang, Jing [Department of Frontier Materials and Function Engineering, Graduate School of Engineering, Iwate University, 4-3-5 Ueda, Morioka 020-8551 (Japan); Aisawa, Sumio, E-mail: aisawa@iwate-u.ac.jp [Department of Frontier Materials and Function Engineering, Graduate School of Engineering, Iwate University, 4-3-5 Ueda, Morioka 020-8551 (Japan); Hirahara, Hidetoshi [Department of Frontier Materials and Function Engineering, Graduate School of Engineering, Iwate University, 4-3-5 Ueda, Morioka 020-8551 (Japan); Kudo, Takahiro [Sulfur Chemical Institute, 210, Collabo MIU, 4-3-5, Ueda, Morioka 020-0066 (Japan); Mori, Kunio [Department of Frontier Materials and Function Engineering, Graduate School of Engineering, Iwate University, 4-3-5 Ueda, Morioka 020-8551 (Japan); Sulfur Chemical Institute, 210, Collabo MIU, 4-3-5, Ueda, Morioka 020-0066 (Japan)

    2016-04-15

    Graphical abstract: - Highlights: • In situ adsorption behaviors of TES on PA6 surface were clarified by QCM. • Highest adsorption of TES on PA6 was obtained in pH 3 and 0.1 M solution. • Molecular layers of TES with uniform structures were prepared on PA6 surface. • TES layer improved PA6 local heat resistance from 150 °C to 230 °C. • TES molecular layer successfully reduced Ag ion to Ag{sup 0}. - Abstract: Heat-resistant organic molecular layers have been fabricated by triazine-based silane coupling agent for metal reduction on plastic surfaces using adsorption method. These molecular layers were used as an interfacial layer between polyamide (PA6) and metal solution to reduce Ag{sup +} ion to Ag{sup 0}. The interfacial behaviors of triazine molecular layer at the interfaces between PA6 and Ag solution were investigated using quartz crystal microbalance (QCM). The kinetics of molecular adsorption on PA6 was investigated by using triazine-based silane coupling agent solutions at different pH and concentration. X-ray photoelectron spectroscopy (XPS), atomic force microscope (AFM), and local nano thermal analysis were employed to characterize the surfaces and interfaces. The nano thermal analysis results show that molecular layers of triazine-based silane coupling agent greatly improved heat resistance of PA6 resin from 170 °C up to 230 °C. This research developed an in-depth insight for molecular behaviors of triazine-based silane coupling agent at the PA6 and Ag solution interfaces and should be of significant value for interfacial research between plastics and metal solution in plating industry.

  9. Seventh BES [Basic Energy Sciences] catalysis and surface chemistry research conference

    International Nuclear Information System (INIS)

    1990-03-01

    Research programs on catalysis and surface chemistry are presented. A total of fifty-seven topics are included. Areas of research include heterogeneous catalysis; catalysis in hydrogenation, desulfurization, gasification, and redox reactions; studies of surface properties and surface active sites; catalyst supports; chemical activation, deactivation; selectivity, chemical preparation; molecular structure studies; sorption and dissociation. Individual projects are processed separately for the data bases

  10. Seventh BES (Basic Energy Sciences) catalysis and surface chemistry research conference

    Energy Technology Data Exchange (ETDEWEB)

    1990-03-01

    Research programs on catalysis and surface chemistry are presented. A total of fifty-seven topics are included. Areas of research include heterogeneous catalysis; catalysis in hydrogenation, desulfurization, gasification, and redox reactions; studies of surface properties and surface active sites; catalyst supports; chemical activation, deactivation; selectivity, chemical preparation; molecular structure studies; sorption and dissociation. Individual projects are processed separately for the data bases. (CBS)

  11. Molecularly oriented surface relief formation in polymethacrylates comprising N-benzylideneaniline derivative side groups

    Science.gov (United States)

    Kawatsuki, Nobuhiro; Hosoda, Risa; Kondo, Mizuho; Sasaki, Tomoyuki; Ono, Hiroshi

    2014-12-01

    Molecularly oriented surface relief (SR) formation in polymethacrylates with N-benzylideneaniline (NBA) derivative side groups is investigated by holographic exposure using a 325 nm He-Cd laser. Because the NBA moieties show a photoinduced orientation perpendicular to the polarization of light, polarization holography successfully forms a molecularly oriented SR structure in accordance with the polarization distribution that includes p-polarized components. Although intensity holography induces molecular orientation, it does not generate a satisfactory SR structure. In all the holographic modes, the SR depth depends on the direction of the C=N bonds in the NBA moieties and the photoproducts affect the SR formation ability.

  12. A preliminary exploration of Advanced Molecular Bio-Sciences Research Center

    International Nuclear Information System (INIS)

    Yamada, Yutaka; Yanai, Takanori; Onodera, Jun'ichi; Yamagami, Mutsumi; Sakata, Hiroshi; Sota, Masahiro; Takemura, Tatsuo; Koyama, Kenji; Sato, Fumiaki

    2000-01-01

    Low-dose and low-dose-rate radiation effects on life-span, pathological changes, hemopoiesis and cytokine production in experimental animals have been investigated in our laboratory. In the intermediate period of the investigation, an expert committee on radiation biology, which was composed of two task groups, was organized. The purposes of the committee were to assess of previous studies and plan future research for Advanced Molecular Bio-Sciences Research Center (AMBIC). In its report, the committee emphasized the necessity of molecular research in radiation biology and ecology, and proposed six subjects for the research: 1) Molecular carcinogenesis of low-dose radiation; 2) Radiation effects on the immune system and hemopoietic system; 3) Molecular mechanisms of hereditary effect; 4) Non cancer effect of low-dose radiation; 5) Gene targeting for ion transport system in plants; 6) Bioremediation with transgenic plant and bacteria. Exploration of the AMBIC project will continue under the committee's direction. (author)

  13. A preliminary exploration of the advanced molecular bio-sciences research center

    International Nuclear Information System (INIS)

    Yanai, Takanori; Yamada, Yutaka; Tanaka, Kimio; Yamagami, Mutsumi; Sota, Masahiro; Takemura, Tatsuo; Koyama, Kenji; Sato, Fumiaki

    2001-01-01

    Low dose and low dose rate radiation effects on lifespan, pathological changes, hemopoiesis and cytokine production in mice have been investigated in our laboratory. In the intermediate period of the investigation, an expert committee on radiation biology was organized. The purposes of the committee were to assess previous studies and advise on a future research plan for the Advanced Molecular Bio-Sciences Research Center (AMBIC). The committee emphasized the necessity of molecular research in radiation biology, and proposed the following five subjects: 1) molecular carcinogenesis by low dose radiation; 2) radiation effects on the immune and hemopoietic systems; 3) molecular mechanisms of hereditary effect; 4) noncancer diseases of low dose radiation, and 5) cellular mechanisms by low dose radiation. (author)

  14. Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge.

    Science.gov (United States)

    Fuchs, Julian E; Bender, Andreas; Glen, Robert C

    2015-09-01

    The Centre for Molecular Informatics, formerly Unilever Centre for Molecular Science Informatics (UCMSI), at the University of Cambridge is a world-leading driving force in the field of cheminformatics. Since its opening in 2000 more than 300 scientific articles have fundamentally changed the field of molecular informatics. The Centre has been a key player in promoting open chemical data and semantic access. Though mainly focussing on basic research, close collaborations with industrial partners ensured real world feedback and access to high quality molecular data. A variety of tools and standard protocols have been developed and are ubiquitous in the daily practice of cheminformatics. Here, we present a retrospective of cheminformatics research performed at the UCMSI, thereby highlighting historical and recent trends in the field as well as indicating future directions.

  15. Molecular dynamics simulation of temperature effects on low energy near-surface cascades and surface damage in Cu

    Science.gov (United States)

    Zhu, Guo; Sun, Jiangping; Guo, Xiongxiong; Zou, Xixi; Zhang, Libin; Gan, Zhiyin

    2017-06-01

    The temperature effects on near-surface cascades and surface damage in Cu(0 0 1) surface under 500 eV argon ion bombardment were studied using molecular dynamics (MD) method. In present MD model, substrate system was fully relaxed for 1 ns and a read-restart scheme was introduced to save total computation time. The temperature dependence of damage production was calculated. The evolution of near-surface cascades and spatial distribution of adatoms at varying temperature were analyzed and compared. It was found that near-surface vacancies increased with temperature, which was mainly due to the fact that more atoms initially located in top two layers became adatoms with the decrease of surface binding energy. Moreover, with the increase of temperature, displacement cascades altered from channeling-like structure to branching structure, and the length of collision sequence decreased gradually, because a larger portion of energy of primary knock-on atom (PKA) was scattered out of focused chain. Furthermore, increasing temperature reduced the anisotropy of distribution of adatoms, which can be ascribed to that regular registry of surface lattice atoms was changed with the increase of thermal vibration amplitude of surface atoms.

  16. Molecular dynamics simulation of temperature effects on low energy near-surface cascades and surface damage in Cu

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Guo; Sun, Jiangping; Guo, Xiongxiong; Zou, Xixi; Zhang, Libin; Gan, Zhiyin, E-mail: ganzhiyin@126.com

    2017-06-15

    The temperature effects on near-surface cascades and surface damage in Cu(0 0 1) surface under 500 eV argon ion bombardment were studied using molecular dynamics (MD) method. In present MD model, substrate system was fully relaxed for 1 ns and a read-restart scheme was introduced to save total computation time. The temperature dependence of damage production was calculated. The evolution of near-surface cascades and spatial distribution of adatoms at varying temperature were analyzed and compared. It was found that near-surface vacancies increased with temperature, which was mainly due to the fact that more atoms initially located in top two layers became adatoms with the decrease of surface binding energy. Moreover, with the increase of temperature, displacement cascades altered from channeling-like structure to branching structure, and the length of collision sequence decreased gradually, because a larger portion of energy of primary knock-on atom (PKA) was scattered out of focused chain. Furthermore, increasing temperature reduced the anisotropy of distribution of adatoms, which can be ascribed to that regular registry of surface lattice atoms was changed with the increase of thermal vibration amplitude of surface atoms.

  17. Role of molecular properties of ulvans on their ability to elaborate antiadhesive surfaces.

    Science.gov (United States)

    Gadenne, Virginie; Lebrun, Laurent; Jouenne, Thierry; Thebault, Pascal

    2015-03-01

    Antiadhesive properties of polysaccharides (such ulvans) once immobilized on a surface are described in the literature but the parameters governing their antifouling properties are not yet well identified. In the present study, the relationship between molecular parameters of ulvans and the inhibition of bacterial adhesion was investigated. To this aim, various ulvans were grafted on silicon wafers under two different experimental immobilization conditions. Results showed that the experimental immobilization conditions and the polysaccharides molecular weight led to specific layer conformations which exhibited a key role in the surface antiadhesive properties. © 2014 Wiley Periodicals, Inc.

  18. Molecular weight evaluation of poly-dimethylsiloxane on solid surfaces using silver deposition/TOF-SIMS

    Science.gov (United States)

    Inoue, Masae; Murase, Atsushi

    2004-06-01

    Molecular ions include information about end groups, functional groups and molecular weight. A method for directly detecting this in the high-mass region of the spectrum (>1000 amu) from poly-dimethylsiloxane (PDMS) on a solid surface was investigated. It was found that a TOF-SIMS analysis of silver-deposited surfaces (silver deposition/TOF-SIMS) is useful for this purpose. Two methods for silver deposition, the diode sputtering method and the vacuum evaporation coating method, were tried. The former required the sample to be cooled so as to prevent the damage of the sample surface due to thermal oxidation; the latter caused no damage to sample surfaces at room temperature. Using silver deposition/TOF-SIMS analysis, silver-cationized quasi-molecular ions were clearly detected from PDMS on solid surfaces and their images were observed without the interference of deposited silver. By applying to the analysis of paint defects, etc., it was confirmed that this technique is useful to analyze practical industrial materials. Silver-cationized ions were detected not only from PDMS, but also from other organic materials, such as some kinds of lubricant additives and fluorine oils on solid surfaces. Therefore, silver deposition/TOF-SIMS was proved to be useful for the analysis of thin substances on solid surfaces.

  19. Role of surface studies in science and technology

    Energy Technology Data Exchange (ETDEWEB)

    Karkhanavala, M D [Bhabha Atomic Research Centre, Bombay (India). Chemistry Div.

    1977-01-01

    Reactivity of solids is influenced by the surface properties such as structure, dislocations and composition. Corrosion and erosion are essentially surface phenomena. Surface studies, therefore, assume importance in prevention and minimization of corrosion and erosion. Discussion is illustrated with examples drawn from the field of nuclear power reactor technology.

  20. Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

    Science.gov (United States)

    Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

    2018-04-01

    Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

  1. Potato agriculture, late blight science, and the molecularization of plant pathology.

    Science.gov (United States)

    Turner, R Steven

    2008-01-01

    By the mid-1980s nucleic-acid based methods were penetrating the farthest reaches of biological science, triggering rivalries among practitioners, altering relationships among subfields, and transforming the research front. This article delivers a "bottom up" analysis of that transformation at work in one important area of biological science, plant pathology, by tracing the "molecularization" of efforts to understand and control one notorious plant disease -- the late blight of potatoes. It mobilizes the research literature of late blight science as a tool through which to trace the changing typography of the research front from 1983 to 2003. During these years molecularization intensified the traditional fragmentation of the late blight research community, even as it dramatically integrated study of the causal organism into broader areas of biology. In these decades the pathogen responsible for late blight, the oomycete "Phytophthora infestans," was discovered to be undergoing massive, frightening, and still largely unexplained genetic diversification -- a circumstance that lends the episode examined here an urgency that reinforces its historiographical significance as a case-study in the molecularization of the biological sciences.

  2. Report of the workshop on accelerator-based atomic and molecular science

    International Nuclear Information System (INIS)

    Meyerhof, W.E.

    1981-01-01

    This Workshop, held in New London, NH on July 27-30, 1980, had a registration of 43, representing an estimated one-third of all principal investigators in the United States in this research subfield. The workshop was organized into 5 working groups for the purpose of (1) identifying some vital physics problems which experimental and theoretical atomic and molecular science can address with current and projected techniques; (2) establishing facilities and equipment needs required to realize solutions to these problems; (3) formulating suggestions for a coherent national policy concerning this discipline; (4) assessing and projecting the manpower situation; and (5) evaluating the relations of this interdisciplinary science to other fields. Recommedations deal with equipment and operating costs for small accelerator laboratories, especially at universities; instrumentation of ion beam lines dedicated to atomic and molecular science at some large accelerators; development of low-velocity, high charge-state ion sources; synchrotron light sources; improvement or replacement of tandem van de Graaff accelerators; high-energy beam lines for atomic physics; the needs for postdoctoral support in this subfield; new accelerator development; need for representatives from atomic and molecular science on program committees for large national accelerator facilities; and the contributions the field can make to applied physics problems

  3. Integration of Molecular Pathology, Epidemiology, and Social Science for Global Precision Medicine

    Science.gov (United States)

    Nishi, Akihiro; Milner, Danny A; Giovannucci, Edward L.; Nishihara, Reiko; Tan, Andy S.; Kawachi, Ichiro; Ogino, Shuji

    2015-01-01

    Summary The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations, and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial, and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors, and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference, and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology, and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors, and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging, and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science. PMID:26636627

  4. Water Adsorption on Clean and Defective Anatase TiO2 (001) Nanotube Surfaces: A Surface Science Approach.

    Science.gov (United States)

    Kenmoe, Stephane; Lisovski, Oleg; Piskunov, Sergei; Bocharov, Dmitry; Zhukovskii, Yuri F; Spohr, Eckhard

    2018-04-11

    We use ab initio molecular dynamics simulations to study the adsorption of thin water films with 1 and 2 ML coverage on anatase TiO 2 (001) nanotubes. The nanotubes are modeled as 2D slabs, which consist of partially constrained and partially relaxed structural motifs from nanotubes. The effect of anion doping on the adsorption is investigated by substituting O atoms with N and S impurities on the nanotube slab surface. Due to strain-induced curvature effects, water adsorbs molecularly on defect-free surfaces via weak bonds on Ti sites and H bonds to surface oxygens. While the introduction of an S atom weakens the interaction of the surface with water, which adsorbs molecularly, the presence of an N impurity renders the surface more reactive to water, with a proton transfer from the water film and the formation of an NH group at the N site. At 2 ML coverage, a further surface-assisted proton transfer takes place in the water film, resulting in the formation of an OH - group and an NH 2 + cationic site on the surface.

  5. Control of chemical bonding of the ZnO surface grown by molecular beam epitaxy

    International Nuclear Information System (INIS)

    Ogata, K.; Komuro, T.; Hama, K.; Koike, K.; Sasa, S.; Inoue, M.; Yano, M.

    2004-01-01

    Toward the fabrication of enzyme modified field effect transistors (EnFETs) as one of organic/inorganic hybridized structures, surface bonding of the ZnO grown by molecular beam epitaxy was controlled by ex situ treatments. Angle resolved X-ray photoelectron spectroscopy (XPS) measurement revealed that O-H bonds exist at the surface of ZnO. It was found that the number of O-H bond could be changed with reversibility using plasma and thermal treatments

  6. Novel ion-molecular surface reaction to result in CH3 adsorbates on (111) surface of chemical vapor deposition diamond from ethane and surface anionic sites

    International Nuclear Information System (INIS)

    Komatsu, Shojiro; Okada, Katsuyuki; Shimizu, Yoshiki; Moriyoshi, Yusuke

    2001-01-01

    The existence of CH 3 adsorbates on (111) surface of chemical vapor deposited diamond, which was observed by scanning tunneling microscopy, was explained by the following S N 2 (bimolecular, substitutional, and nucleophilic) type surface reaction; C(s) - +C 2 H 6 ->C(s)-CH 3 +CH 3 - , where C(s) denotes a surface carbon atom. The activation energy was estimated to be 36.78 kcal/mol and the reaction proved to be exothermic with the enthalpy change of -9.250 kcal/mol, according to ab initio molecular orbital calculations at MP2/3-21+G * //RHF/3-21G * level; this result is consistent with typical substrate temperatures, namely about 900 degree C, for chemical vapor deposition of diamond. Charge transfer from the highest occupied molecular orbital of the surface anionic site to the lowest unoccupied molecular orbital of ethane, that is antibonding at the CH 3 - CH 3 bond, has been clearly visualized. A characteristic configuration of an ethane molecule which is associated with an anionic vacant site C(s) - on hydrogenated (111) surface of diamond was also found. [copyright] 2001 American Institute of Physics

  7. Surface functionalization of SPR chip for specific molecular interaction analysis under flow condition

    Directory of Open Access Journals (Sweden)

    Tao Ma

    2017-03-01

    Full Text Available Surface functionalization of sensor chip for probe immobilization is crucial for the biosensing applications of surface plasmon resonance (SPR sensors. In this paper, we report a method circulating the dopamine aqueous solution to coat polydopamine film on sensing surface for surface functionalization of SPR chip. The polydopamine film with available thickness can be easily prepared by controlling the circulation time and the biorecognition elements can be immobilized on the polydopamine film for specific molecular interaction analysis. These operations are all performed under flow condition in the fluidic system, and have the advantages of easy implementation, less time consuming, and low cost, because the reagents and devices used in the operations are routinely applied in most laboratories. In this study, the specific absorption between the protein A probe immobilized on the sensing surface and human immunoglobulin G in the buffer is monitored based on this surface functionalization strategy to demonstrated its feasibility for SPR biosensing applications.

  8. Tunable Complex Stability in Surface Molecular Recognition Mediated by Self-Complementary Quadruple Hydrogen Bonds

    NARCIS (Netherlands)

    Zou, S(han); Zhang, Zhihong; Forch, Renate; Knoll, Wolfgang; Schönherr, Holger; Vancso, Gyula J.

    2003-01-01

    We show that surfaces modified with asymmetric 2-ureido-4[1H]-pyrimidinone-hydroxyalkane disulfide adsorbates exhibit efficient and controllable self-complementary molecular recognition of the pyrimidinone moieties. Two novel asymmetric 2-ureido-4[1H]-pyrimidinone-hydroxyalkane disulfide adsorbates,

  9. High-Resolution Scanning Tunneling Microscopy Studies of Molecular Nanostructures on Surfaces

    DEFF Research Database (Denmark)

    Song, Xin

    . First, to study the role of hydrogen bonding in self-assembly, we investigate the monomolecular self-assembled system of pyrene-4,5,9,10-tetrone and phenanthrene- 9,10-dione molecules on Au(111) and HOPG surface respectively and the binary molecular self-assembled system of stearic acid and guanine...

  10. Comparison of molecular dynamics and kinetic modeling of gas-surface interactions

    NARCIS (Netherlands)

    Frezzotti, A.; Gaastra - Nedea, S.V.; Markvoort, A.J.; Spijker, P.; Gibelli, L.

    2008-01-01

    The interaction of a dilute monatomic gas with a solid surface is studied byMolecular Dynamics (MD) simulations and by numerical solutions of a recently proposed kinetic model. Following previous investigations, the heat transport between parallel walls and Couette flow have been adopted as test

  11. DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

    NARCIS (Netherlands)

    JUFFER, AH; BERENDSEN, HJC

    1993-01-01

    A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

  12. Surface enhanced raman scattering on tardigrada - Towards monitoring and imaging molecular structures in live cryptobiotic organisms

    DEFF Research Database (Denmark)

    Kneipp, Harald; Møbjerg, Nadja; Jørgensen, Aslak

    2013-01-01

    Tardigrades are microscopic metazoans which are able to survive extreme physical and chemical conditions by entering a stress tolerant state called cryptobiosis. At present, the molecular mechanisms behind cryptobiosis are still poorly understood. We show that surface enhanced Raman scattering su...

  13. Free-Molecular Gas Flow in Channels (Pores) with Physico-Chemical Transformation on the Surface

    Czech Academy of Sciences Publication Activity Database

    Levdansky, V.V.; Smolík, Jiří; Moravec, Pavel

    2006-01-01

    Roč. 49, 13-14 (2006), s. 2356-2365 ISSN 0017-9310 Institutional research plan: CEZ:AV0Z40720504 Keywords : free-molecular flow * surface * spatial distribution Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.482, year: 2006

  14. Squeezing Molecularly thin Lubricant Films between curved Corrugated Surfaces with long range Elasticity

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    2010-01-01

    3H8, C4H10, C8H18, C9H20, C10H22, C14H30 and C16H34, confined between corrugated gold surfaces. Well defined molecular layers develop in the lubricant film when the width is of the order of a few atomic diameters. An external squeezing pressure induces discontinuous, thermally activated changes...

  15. Adsorption and recognition characteristics of surface molecularly imprinted polymethacrylic acid/silica toward genistein.

    Science.gov (United States)

    Zhang, Yanyan; Gao, Baojiao; An, Fuqiang; Xu, Zeqing; Zhang, Tingting

    2014-09-12

    In this paper, on the basis of surface-initiated graft polymerization, a new surface molecular imprinting technique is established by molecular design. And molecularly imprinted polymer MIP-PMAA/SiO2 is successfully prepared with genistein as template. The adsorption and recognition characteristics of MIP-PMAA/SiO2 for genistein are studied in depth by using static method, dynamic method and competitive adsorption experiment. The experimental results show that MIP-PMAA/SiO2 possesses very strong adsorption affinity and specific recognition for genistein. The saturated adsorption capacity could reach to 0.36mmolg(-1). The selectivity coefficients relative to quercetin and rutin are 5.4 and 11.8, respectively. Besides, MIP-PMAA/SiO2 is regenerated easily and exhibits excellent reusability. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-02-21

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

  17. The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Ferguson, Ken R. [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Department of Applied Physics, Stanford University, 348 Via Pueblo, Stanford, CA 94305 (United States); Bucher, Maximilian; Bozek, John D.; Carron, Sebastian; Castagna, Jean-Charles [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Coffee, Ryan [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Curiel, G. Ivan; Holmes, Michael; Krzywinski, Jacek; Messerschmidt, Marc; Minitti, Michael; Mitra, Ankush; Moeller, Stefan; Noonan, Peter; Osipov, Timur; Schorb, Sebastian; Swiggers, Michele; Wallace, Alexander; Yin, Jing [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Bostedt, Christoph, E-mail: bostedt@slac.stanford.edu [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States)

    2015-04-17

    A description of the Atomic, Molecular and Optical Sciences (AMO) instrument at the Linac Coherent Light Source is presented. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument. The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump–probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.

  18. Molecular biology in marine science: Scientific questions, technological approaches, and practical implications

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    This report describes molecular techniques that could be invaluable in addressing process-oriented problems in the ocean sciences that have perplexed oceanographers for decades, such as understanding the basis for biogeochemical processes, recruitment processes, upper-ocean dynamics, biological impacts of global warming, and ecological impacts of human activities. The coupling of highly sophisticated methods, such as satellite remote sensing, which permits synoptic monitoring of chemical, physical, and biological parameters over large areas, with the power of modern molecular tools for ``ground truthing`` at small scales could allow scientists to address questions about marine organisms and the ocean in which they live that could not be answered previously. Clearly, the marine sciences are on the threshold of an exciting new frontier of scientific discovery and economic opportunity.

  19. Surface charge method for molecular surfaces with curved areal elements I. Spherical triangles

    Science.gov (United States)

    Yu, Yi-Kuo

    2018-03-01

    Parametrizing a curved surface with flat triangles in electrostatics problems creates a diverging electric field. One way to avoid this is to have curved areal elements. However, charge density integration over curved patches appears difficult. This paper, dealing with spherical triangles, is the first in a series aiming to solve this problem. Here, we lay the ground work for employing curved patches for applying the surface charge method to electrostatics. We show analytically how one may control the accuracy by expanding in powers of the the arc length (multiplied by the curvature). To accommodate not extremely small curved areal elements, we have provided enough details to include higher order corrections that are needed for better accuracy when slightly larger surface elements are used.

  20. Molecular-level chemistry of model single-crystal oxide surfaces with model halogenated compounds

    Science.gov (United States)

    Adib, Kaveh

    Synchrotron-based X-ray photoelectron spectroscopy (XPS), temperature-programmed desorption (TPD) and low energy electron diffraction (LEED) have been used to investigate, at a molecular level, the chemistry of different terminations of single crystal iron-oxide surfaces with probe molecules (CCl4 and D2O). Comparisons of the reactivity of these surfaces towards CCl4, indicate that the presence of an uncapped surface Fe cation (strong Lewis acid site) and an adjacent oxygen site capped by that cation can effect the C-Cl bond cleavage in CCl4, resulting in dissociatively adsorbed Cl-adatoms and carbon-containing fragments. If in addition to these sites, an uncapped surface oxygen (Lewis base) site is also available, the carbon-containing moiety can then move that site, coordinate itself with that uncapped oxygen, and stabilize itself. At a later step, the carbon-containing fragment may form a strong covalent bond with the uncapped oxygen and may even abstract that surface oxygen. On the other hand, if an uncapped oxygen is not available to stabilize the carbon-containing fragment, the surface coordination will not occur and upon the subsequent thermal annealing of the surface the Cl-adatoms and the carbon-containing fragments will recombine and desorb as CCl4. Finally, the presence of surface deuteroxyls blocking the strong Lewis acid and base sites of the reactive surface, passivates this surface. Such a deuteroxylated surface will be unreactive towards CCl 4. Such a molecular level understanding of the surface chemistry of metal-oxides will have applications in the areas of selective catalysis, including environmental catalysis, and chemical sensor technology.

  1. Measurement of molecular length of self-assembled monolayer probed by localized surface plasmon resonance

    Science.gov (United States)

    Ito, Juri; Kajikawa, Kotaro

    2016-02-01

    We propose a method to measure the variation of the molecular length of self-assembled monolayers (SAMs) when it is exposed to solutions at different pH conditions. The surface immobilized gold nanospheres (SIGNs) shows strong absorption peak at the wavelengths of 600-800 nm when p-polarized light is illuminated. The peak wavelength depends on the length of the gap distance between the SIGNs and the substrate. The gap is supported by the SAM molecules. According to the analytical calculation based on multiple expansion, the relation between the peak wavelength of the SIGN structures and the gap distance is calculated, to evaluate the molecular length of the SAM through the optical absorption spectroscopy for the SIGN structures. The molecular length of the SIGN structure was measured in air, water, acidic, and basic solutions. It was found that the molecular lengths are longer in acidic solutions.

  2. Surface based detection schemes for molecular interferometry experiments - implications and possible applications

    Science.gov (United States)

    Juffmann, Thomas; Milic, Adriana; Muellneritsch, Michael; Arndt, Markus

    2011-03-01

    Surface based detection schemes for molecular interferometry experiments might be crucial in the search for the quantum properties of larger and larger objects since they provide single particle sensitivity. Here we report on molecular interferograms of different biomolecules imaged using fluorescence microscopy. Being able to watch the build-up of an interferogram live and in situ reveals the matter-wave behavior of these complex molecules in an unprecedented way. We examine several problems encountered due to van-der-Waals forces between the molecules and the diffraction grating and discuss possible ways to circumvent these. Especially the advent of ultra-thin (1-100 atomic layers) diffraction masks might path the way towards molecular holography. We also discuss other possible applications such as coherent molecular microscopy.

  3. Environmental Molecular Sciences Laboratory Operations System: Version 4.0 - system requirements specification

    Energy Technology Data Exchange (ETDEWEB)

    Kashporenko, D.

    1996-07-01

    This document is intended to provide an operations standard for the Environmental Molecular Sciences Laboratory OPerations System (EMSL OPS). It is directed toward three primary audiences: (1) Environmental Molecular Sciences Laboratory (EMSL) facility and operations personnel; (2) laboratory line managers and staff; and (3) researchers, equipment operators, and laboratory users. It is also a statement of system requirements for software developers of EMSL OPS. The need for a finely tuned, superior research environment as provided by the US Department of Energy`s (DOE) Environmental Molecular Sciences Laboratory has never been greater. The abrupt end of the Cold War and the realignment of national priorities caused major US and competing overseas laboratories to reposition themselves in a highly competitive research marketplace. For a new laboratory such as the EMSL, this means coming into existence in a rapidly changing external environment. For any major laboratory, these changes create funding uncertainties and increasing global competition along with concomitant demands for higher standards of research product quality and innovation. While more laboratories are chasing fewer funding dollars, research ideas and proposals, especially for molecular-level research in the materials and biological sciences, are burgeoning. In such an economically constrained atmosphere, reduced costs, improved productivity, and strategic research project portfolio building become essential to establish and maintain any distinct competitive advantage. For EMSL, this environment and these demands require clear operational objectives, specific goals, and a well-crafted strategy. Specific goals will evolve and change with the evolution of the nature and definition of DOE`s environmental research needs. Hence, EMSL OPS is designed to facilitate migration of these changes with ease into every pertinent job function, creating a facile {open_quotes}learning organization.{close_quotes}

  4. Dynamics of the contact between a ruthenium surface with a single nanoasperity and a flat ruthenium surface: Molecular dynamics simulations

    International Nuclear Information System (INIS)

    Barros de Oliveira, Alan; Fortini, Andrea; Buldyrev, Sergey V.; Srolovitz, David

    2011-01-01

    We study the dynamics of the contact between a pair of surfaces (with properties designed to mimic ruthenium) via molecular dynamics simulations. In particular, we study the contact between a ruthenium surface with a single nanoasperity and a flat ruthenium surface. The results of such simulations suggest that contact behavior is highly variable. The goal of this study is to investigate the source and degree of this variability. We find that during compression, the behavior of the contact force displacement curves is reproducible, while during contact separation, the behavior is highly variable. Examination of the contact surfaces suggests that two separation mechanisms are in operation and give rise to this variability. One mechanism corresponds to the formation of a bridge between the two surfaces that plastically stretches as the surfaces are drawn apart and eventually separate in shear. This leads to a morphology after separation in which there are opposing asperities on the two surfaces. This plastic separation/bridge formation mechanism leads to a large work of separation. The other mechanism is a more brittle-like mode in which a crack propagates across the base of the asperity (slightly below the asperity/substrate junction) leading to most of the asperity on one surface or the other after separation and a slight depression facing this asperity on the opposing surface. This failure mode corresponds to a smaller work of separation. This failure mode corresponds to a smaller work of separation. Furthermore, contacts made from materials that exhibit predominantly brittle-like behavior will tend to require lower work of separation than those made from ductile-like contact materials.

  5. Experimental innovations in surface science a guide to practical laboratory methods and instruments

    CERN Document Server

    Yates, John T

    2015-01-01

    This book is a new edition of a classic text on experimental methods and instruments in surface science. It offers practical insight useful to chemists, physicists, and materials scientists working in experimental surface science. This enlarged second edition contains almost 300 descriptions of experimental methods. The more than 50 active areas with individual scientific and measurement concepts and activities relevant to each area are presented in this book. The key areas covered are: Vacuum System Technology, Mechanical Fabrication Techniques, Measurement Methods, Thermal Control, Delivery of Adsorbates to Surfaces, UHV Windows, Surface Preparation Methods, High Area Solids, Safety. The book is written for researchers and graduate students.

  6. Sea Surface Height Deviation, Aviso, 0.25 degrees, Global, Science Quality

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Aviso Sea Surface Height Deviation is the deviation from the mean geoid as measured from 1993 - 1995. This is Science Quality data.

  7. Molecular Dynamics Study of Thermally Augmented Nanodroplet Motion on Chemical Energy Induced Wettability Gradient Surfaces.

    Science.gov (United States)

    Chakraborty, Monojit; Chowdhury, Anamika; Bhusan, Richa; DasGupta, Sunando

    2015-10-20

    Droplet motion on a surface with chemical energy induced wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics of molecular movement near the solid-liquid interface including the contact line friction. The simulations mimic experiments in a comprehensive manner wherein microsized droplets are propelled by the surface wettability gradient against forces opposed to motion. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature are varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction is observed to be a strong function of temperature at atomistic scales, confirming their experimentally observed inverse functionality. Additionally, the MD simulation results are successfully compared with those from an analytical model for self-propelled droplet motion on gradient surfaces.

  8. Exploring Surface Analysis Techniques for the Detection of Molecular Contaminants on Spacecraft

    Science.gov (United States)

    Rutherford, Gugu N.; Seasly, Elaine; Thornblom, Mark; Baughman, James

    2016-01-01

    Molecular contamination is a known area of concern for spacecraft. To mitigate this risk, projects involving space flight hardware set requirements in a contamination control plan that establishes an allocation budget for the exposure of non-volatile residues (NVR) onto critical surfaces. The purpose of this work will focus on non-contact surface analysis and in situ monitoring to mitigate molecular contamination on space flight hardware. By using Scanning Electron Microscopy and Energy Dispersive Spectroscopy (SEM-EDS) with Raman Spectroscopy, an unlikely contaminant was identified on space flight hardware. Using traditional and surface analysis methods provided the broader view of the contamination sources allowing for best fit solutions to prevent any future exposure.

  9. Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping

    Science.gov (United States)

    Lu, Jianfeng; Zhou, Zhennan

    2018-02-01

    To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limit, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer and thus connects the surface hopping approach to the mean-field path-integral molecular dynamics. A multiscale integrator for the infinite swapping limit is also proposed to enable efficient sampling based on the limiting dynamics. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path-integral molecular dynamics with surface hopping.

  10. Scattering of atomic and molecular ions from single crystal surfaces of Cu, Ag and Fe

    International Nuclear Information System (INIS)

    Zoest, J.M. van.

    1986-01-01

    This thesis deals with analysis of crystal surfaces of Cu, Ag and Fe with Low Energy Ion scattering Spectroscopy (LEIS). Different atomic and molecular ions with fixed energies below 7 keV are scattered by a metal single crystal (with adsorbates). The energy and direction of the scattered particles are analysed for different selected charge states. In that way information can be obtained concerning the composition and atomic and electronic structure of the single crystal surface. Energy spectra contain information on the composition of the surface, while structural atomic information is obtained by direction measurements (photograms). In Ch.1 a description is given of the experimental equipment, in Ch.2 a characterization of the LEIS method. Ch.3 deals with the neutralization of keV-ions in surface scattering. Two different ways of data interpretation are presented. First a model is treated in which the observed directional dependence of neutralization action of the first atom layer of the surface is presented by a laterally varying thickness of the neutralizing layer. Secondly it is shown that the data can be reproduced by a more realistic, physical model based on atomic transition matrix elements. In Ch.4 the low energy hydrogen scattering is described. The study of the dissociation of H 2 + at an Ag surface r0230ted in a model based on electronic dissociation, initialized by electron capture into a repulsive (molecular) state. In Ch.5 finally the method is applied to the investigation of the surface structure of oxidized Fe. (Auth.)

  11. Implementation of molecularly imprinted polymer beads for surface enhanced Raman detection.

    Science.gov (United States)

    Kamra, Tripta; Zhou, Tongchang; Montelius, Lars; Schnadt, Joachim; Ye, Lei

    2015-01-01

    Molecularly imprinted polymers (MIPs) have a predesigned molecular recognition capability that can be used to build robust chemical sensors. MIP-based chemical sensors allow label-free detection and are particularly interesting due to their simple operation. In this work we report the use of thiol-terminated MIP microspheres to construct surfaces for detection of a model organic analyte, nicotine, by surface enhanced Raman scattering (SERS). The nicotine-imprinted microspheres are synthesized by RAFT precipitation polymerization and converted into thiol-terminated microspheres through aminolysis. The thiol groups on the MIP surface allow the microspheres to be immobilized on a gold-coated substrate. Three different strategies are investigated to achieve surface enhanced Raman scattering in the vicinity of the imprinted sites: (1) direct sputtering of gold nanoparticles, (2) immobilization of gold colloids through the MIP's thiol groups, and (3) trapping of the MIP microspheres in a patterned SERS substrate. For the first time we show that large MIP microspheres can be turned into selective SERS surfaces through the three different approaches of assembly. The MIP-based sensing surfaces are used to detect nicotine to demonstrate the proof of concept. As synthesis and surface functionalization of MIP microspheres and nanoparticles are well established, the methods reported in this work are handy and efficient for constructing label-free chemical sensors, in particular for those based on SERS detection.

  12. Proportional Reasoning Ability and Concepts of Scale: Surface Area to Volume Relationships in Science

    Science.gov (United States)

    Taylor, Amy; Jones, Gail

    2009-01-01

    The "National Science Education Standards" emphasise teaching unifying concepts and processes such as basic functions of living organisms, the living environment, and scale. Scale influences science processes and phenomena across the domains. One of the big ideas of scale is that of surface area to volume. This study explored whether or not there…

  13. Confinement properties of 2D porous molecular networks on metal surfaces

    International Nuclear Information System (INIS)

    Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

    2016-01-01

    Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article

  14. Soft X-Ray Microscopy and Spectroscopy at the Molecular Environmental Science Beamline at the Advanced Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Bluhm, Hendrik; Andersson, Klas J.; Araki, Tohru; Benzerara, Karim; Brown, Gordon E.; Dynes, Jay J.; Ghosal, Sutapa; Gilles, Mary K.; Hansen, Hans C.; Hemminger, J. C.; Hitchcock, Adam P.; Ketteler, Guido; Kilcoyne, Arthur L.; Kneedler, Eric M.; Lawrence, John R.; Leppard, Gary G.; Majzlam, Juraj; Mun, B. S.; Myneni, Satish C.; Nilsson, Anders R.; Ogasawara, Hirohito; Ogletree, D. F.; Pecher, Klaus H.; Salmeron, Miquel B.; Shuh, David K.; Tonner, Brian; Tyliszczak, Tolek; Warwick, Tony; Yoon, T. H.

    2006-02-01

    We present examples of the application of synchrotron-based spectroscopies and microscopies to environmentally-relevant samples. The experiments were performed at the Molecular Environmental Science beamline (11.0.2) at the Advanced Light Source, Lawrence Berkeley National Laboratory. Examples range from the study of water monolayers on Pt(111) single crystal surfaces using X-ray emission spectroscopy and the examination of alkali halide solution/water vapor interfaces using ambient pressure photoemission spectroscopy, to the investigation of actinides, river-water biofilms, Al-containing colloids and mineral-bacteria suspensions using scanning transmission X-ray spectromicroscopy. The results of our experiments show that spectroscopy and microscopy in the soft X-ray energy range are excellent tools for the investigation of environmentally relevant samples under realistic conditions, i.e. with water or water vapor present at ambient temperature.

  15. Molecular dynamics simulations study of nano bubble attachment at hydrophobic surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Dang, Liem X.; Miller, Jan D.

    2018-01-01

    Bubble attachment phenomena are examined using Molecular Dynamics Simulations (MDS) for the first time. The simulation involves a nitrogen nano bubble containing 906 nitrogen molecules in a water phase with 74,000 water molecules at molybdenite surfaces. During a simulation period of 1 ns, film rupture and displacement occurs. The attached nanobubble at the hydrophobic molybdenite face surface results in a contact angle of about 90º. This spontaneous attachment is due to a “water exclusion zone” at the molybdenite face surface and can be explained by a van der Waals (vdW) attractive force, as discussed in the literature. In contrast, the film is stable at the hydrophilic quartz (001) surface and the bubble does not attach. Contact angles determined from MD simulations are reported, and these results agree well with experimental and MDS sessile drop results. In this way, film stability and bubble attachment are described with respect to interfacial water structure for surfaces of different polarity. Interfacial water molecules at the hydrophobic molybdenite face surface have relatively weak interactions with the surface when compared to the hydrophilic quartz (001) surface, as revealed by the presence of a 3 Å “water exclusion zone” at the molybdenite/water interface. The molybdenite armchair-edge and zigzag-edge surfaces show a comparably slow process for film rupture and displacement when compared to the molybdenite face surface, which is consistent with their relatively weak hydrophobic character.

  16. Molecular-dynamics theory of the temperature-dependent surface phonons of W(001)

    International Nuclear Information System (INIS)

    Wang, C.Z.; Fasolino, A.; Tosatti, E.

    1987-04-01

    We study the temperature-dependent zone-boundary surface phonons across the c(2x2)→1x1 reconstruction phase transition of the clean W(001) surface. Velocity-velocity correlations and hence the phonon spectral densities are calculated by molecular dynamics for the surface atoms of a finite thickness (001) slab, with interatomic potentials established in a previous study of the surface statics. Our calculated k = (1/2,1/2)(2π/a) surface phonon are dominated by three main low-frequency modes. Of these, the longitudinal and the shear horizontal are reconstruction-related and display critical broadening and softening at the phase transition, while the third, the shear vertical, is basically unaffected. The reconstruction phase mode, shear horizontal, appears to be responsible for the phase fluctuations which destroy long-range order at the transition. (author). 30 refs, 12 figs

  17. On the computation of molecular surface correlations for protein docking using fourier techniques.

    Science.gov (United States)

    Sakk, Eric

    2007-08-01

    The computation of surface correlations using a variety of molecular models has been applied to the unbound protein docking problem. Because of the computational complexity involved in examining all possible molecular orientations, the fast Fourier transform (FFT) (a fast numerical implementation of the discrete Fourier transform (DFT)) is generally applied to minimize the number of calculations. This approach is rooted in the convolution theorem which allows one to inverse transform the product of two DFTs in order to perform the correlation calculation. However, such a DFT calculation results in a cyclic or "circular" correlation which, in general, does not lead to the same result as the linear correlation desired for the docking problem. In this work, we provide computational bounds for constructing molecular models used in the molecular surface correlation problem. The derived bounds are then shown to be consistent with various intuitive guidelines previously reported in the protein docking literature. Finally, these bounds are applied to different molecular models in order to investigate their effect on the correlation calculation.

  18. Molecular weight-dependent degradation and drug release of surface-eroding poly(ethylene carbonate).

    Science.gov (United States)

    Bohr, Adam; Wang, Yingya; Harmankaya, Necati; Water, Jorrit J; Baldursdottír, Stefania; Almdal, Kristoffer; Beck-Broichsitter, Moritz

    2017-06-01

    Poly(ethylene carbonate) (PEC) is a unique biomaterial showing significant potential for controlled drug delivery applications. The current study investigated the impact of the molecular weight on the biological performance of drug-loaded PEC films. Following the preparation and thorough physicochemical characterization of diverse PEC (molecular weights: 85, 110, 133, 174 and 196kDa), the degradation and drug release behavior of rifampicin- and bovine serum albumin-loaded PEC films was investigated in vitro (in the presence and absence of cholesterol esterase), in cell culture (RAW264.7 macrophages) and in vivo (subcutaneous implantation in rats). All investigated samples degraded by means of surface erosion (mass loss, but constant molecular weight), which was accompanied by a predictable, erosion-controlled drug release pattern. Accordingly, the obtained in vitro degradation half-lives correlated well with the observed in vitro half-times of drug delivery (R 2 =0.96). Here, the PEC of the highest molecular weight resulted in the fastest degradation/drug release. When incubated with macrophages or implanted in animals, the degradation rate of PEC films superimposed the results of in vitro incubations with cholesterol esterase. Interestingly, SEM analysis indicated a distinct surface erosion process for enzyme-, macrophage- and in vivo-treated polymer films in a molecular weight-dependent manner. Overall, the molecular weight of surface-eroding PEC was identified as an essential parameter to control the spatial and temporal on-demand degradation and drug release from the employed delivery system. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Molecular weight-dependent degradation and drug release of surface-eroding poly(ethylene carbonate)

    DEFF Research Database (Denmark)

    Bohr, Adam; Wang, Yingya; Harmankaya, Necati

    2017-01-01

    .7 macrophages) and in vivo (subcutaneous implantation in rats). All investigated samples degraded by means of surface erosion (mass loss, but constant molecular weight), which was accompanied by a predictable, erosion-controlled drug release pattern. Accordingly, the obtained in vitro degradation half......Poly(ethylene carbonate) (PEC) is a unique biomaterial showing significant potential for controlled drug delivery applications. The current study investigated the impact of the molecular weight on the biological performance of drug-loaded PEC films. Following the preparation and thorough...... to control the spatial and temporal on-demand degradation and drug release from the employed delivery system....

  20. Molecular resonances, fusion reactions and surface transparency of interaction between heavy ions

    International Nuclear Information System (INIS)

    Abe, Yasuhisa.

    1980-01-01

    A review of the Band Crossing Model is given, including recent results on the 16 O + 16 O system. Surface Transparency is discussed in the light of the recent development in our understanding of the fusion reaction mechanisms and by calculating the number of open channels available to direct reactions. The existence of the Molecular Resonance Region is suggested in several systems by the fact that Band Crossing Region overlaps with the Transparent Region. A systematic study predicts molecular resonances in the 14 C + 14 C and 12 C + 14 C systems as prominent as those observed in the 16 O + 16 O and 12 C + 16 O systems

  1. Two sides of the coin. Part 2. Colloid and surface science meets real biointerfaces.

    Science.gov (United States)

    Ninham, Barry W; Larsson, Kåre; Lo Nostro, Pierandrea

    2017-11-01

    Part 1 revisited developments in lipid and surfactant self assembly over the past 40 years [1]. New concepts emerged. Here we explore how these developments can be used to make sense of and bring order to a range of complex biological phenomena. Together with Part 1, this contribution is a fundamental revision of intuition at the boundaries of Colloid Science and Biological interfaces from a perspective of nearly 50 years. We offer new insights on a unified treatment of self assembly of lipids, surfactants and proteins in the light of developments presented in Part 1. These were in the enabling disciplines in molecular forces, hydration, oil and electrolyte specificity; and in the role of non Euclidean geometries-across the whole gammut of physical, colloid and surface chemistry, biophysics and membrane biology and medicine. It is where the early founders of the cell theory of biology and the physiologists expected advances to occur as D'Arcy Thompson predicted us 100 years ago. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Molecular polymorphism of a cell surface proteoglycan: distinct structures on simple and stratified epithelia.

    Science.gov (United States)

    Sanderson, R D; Bernfield, M

    1988-12-01

    Epithelial cells are organized into either a single layer (simple epithelia) or multiple layers (stratified epithelia). Maintenance of these cellular organizations requires distinct adhesive mechanisms involving many cell surface molecules. One such molecule is a cell surface proteoglycan, named syndecan, that contains both heparan sulfate and chondroitin sulfate chains. This proteoglycan binds cells to fibrillar collagens and fibronectin and thus acts as a receptor for interstitial matrix. The proteoglycan is restricted to the basolateral surface of simple epithelial cells, but is located over the entire surface of stratified epithelial cells, even those surfaces not contacting matrix. We now show that the distinct localization in simple and stratified epithelia correlates with a distinct proteoglycan structure. The proteoglycan from simple epithelia (modal molecular size, 160 kDa) is larger than that from stratified epithelia (modal molecular size, 92 kDa), but their core proteins are identical in size and immunoreactivity. The proteoglycan from simple epithelia has more and larger heparan sulfate and chondroitin sulfate chains than the proteoglycan from stratified epithelia. Thus, the cell surface proteoglycan shows a tissue-specific structural polymorphism due to distinct posttranslational modifications. This polymorphism likely reflects distinct proteoglycan functions in simple and stratified epithelia, potentially meeting the different adhesive requirements of the cells in these different organizations.

  3. Electron induced conformational changes of an imine-based molecular switch on a Au(111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Lotze, Christian; Henningsen, Nils; Franke, Katharina; Schulze, Gunnar; Pascual, Jose Ignacio [Inst. f. Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Inst. f. Organische Chemie, Freie Universitaet Berlin (Germany)

    2009-07-01

    Azobenzene-based molecules exhibit a cis-trans configurational photoisomerisation in solution. Recently, the adsorption properties of azobenzene derivatives have been investigated on different metal surfaces in order to explore the possible changes in the film properties induced by external stimuli. In azobenzene, the diazo-bridge is a key group for the isomerization process. Its interaction with a metal surface is dominated through the N lone-pair electrons, which reduces the efficiency of the conformational change. In order to reduce the molecule-surface interaction, we explore an alternative molecular architecture by substituting the diazo-bridge (-N=N-) of azobenzene by an imine-group (-N=CH-). We have investigated the imine-based compound para-carboxyl-di-benzene-imine (PCI) adsorbed on a Au(111) surface. The carboxylic terminations mediates the formation of strongly bonded molecular dimers, which align in ordered rows preferentially following the fcc regions of the Au(111) herringbone reconstruction. Low temperature scanning tunneling microscopy was used to induce conformational changes between trans and cis state of individual molecules in a molecular monolayer.

  4. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  5. Operation of micro and molecular machines: a new concept with its origins in interface science.

    Science.gov (United States)

    Ariga, Katsuhiko; Ishihara, Shinsuke; Izawa, Hironori; Xia, Hong; Hill, Jonathan P

    2011-03-21

    A landmark accomplishment of nanotechnology would be successful fabrication of ultrasmall machines that can work like tweezers, motors, or even computing devices. Now we must consider how operation of micro- and molecular machines might be implemented for a wide range of applications. If these machines function only under limited conditions and/or require specialized apparatus then they are useless for practical applications. Therefore, it is important to carefully consider the access of functionality of the molecular or nanoscale systems by conventional stimuli at the macroscopic level. In this perspective, we will outline the position of micro- and molecular machines in current science and technology. Most of these machines are operated by light irradiation, application of electrical or magnetic fields, chemical reactions, and thermal fluctuations, which cannot always be applied in remote machine operation. We also propose strategies for molecular machine operation using the most conventional of stimuli, that of macroscopic mechanical force, achieved through mechanical operation of molecular machines located at an air-water interface. The crucial roles of the characteristics of an interfacial environment, i.e. connection between macroscopic dimension and nanoscopic function, and contact of media with different dielectric natures, are also described.

  6. Surface transport mechanisms in molecular glasses probed by the exposure of nano-particles

    Science.gov (United States)

    Ruan, Shigang; Musumeci, Daniele; Zhang, Wei; Gujral, Ankit; Ediger, M. D.; Yu, Lian

    2017-05-01

    For a glass-forming liquid, the mechanism by which its surface contour evolves can change from bulk viscous flow at high temperatures to surface diffusion at low temperatures. We show that this mechanistic change can be conveniently detected by the exposure of nano-particles native in the material. Despite its high chemical purity, the often-studied molecular glass indomethacin contains low-concentration particles approximately 100 nm in size and 0.3% in volume fraction. Similar particles are present in polystyrene, another often-used model. In the surface-diffusion regime, particles are gradually exposed in regions vacated by host molecules, for example, the peak of a surface grating and the depletion zone near a surface crystal. In the viscous-flow regime, particle exposure is not observed. The surface contour around an exposed particle widens over time in a self-similar manner as 3 (Bt)1/4, where B is a surface mobility constant and the same constant obtained by surface grating decay. This work suggests that in a binary system composed of slow- and fast-diffusing molecules, slow-diffusing molecules can be stranded in surface regions vacated by fast-diffusing molecules, effectively leading to phase separation.

  7. Monitoring peptide-surface interaction by means of molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Nonella, Marco, E-mail: mnonella@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland); Seeger, Stefan, E-mail: sseeger@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland)

    2010-12-09

    Graphical abstract: Protein-surface interactions play a crucial role in a wide field of research areas like biology, biotechnology, or pharmacology. Only recently, it has been shown that not only peptide adsorption represents an important process but also spreading and clustering of adsorbed proteins. By means of classical molecular dynamics, peptide adsorption as well as the dynamics of adsorbed peptides have been investigated in order to gain deeper insight into such processes. The picture shows a snapshot of an adsorbed peptide on a silica surface showing strong direct hydrogen bonding. Research highlights: {yields} Simulation of peptide surface interaction. {yields} Dynamics of hydrogen bond formation and destruction. {yields} Internal flexibility of adsorbed peptides. - Abstract: Protein adsorption and protein surface interactions have become an important research topic in recent years. Very recently, for example, it has been shown that protein clusters can undergo a surface-induced spreading after adsorption. Such phenomena emphasize the need of a more detailed insight into protein-silica interaction at an atomic level. Therefore, we have studied a model system consisting of a short peptide, a silica slab, and water molecules by means of classical molecular dynamics simulations. The study reveals that, besides of electrostatic interactions caused by the chosen charge distribution, the peptide interacts with the silica surface through formation of direct peptide-surface hydrogen bonds as well as indirect peptide-water-surface hydrogen bonds. The number of created hydrogen bonds varies considerably among the simulated structures. The strength of hydrogen bonding determines the mobility of the peptide on the surface and the internal flexibility of the adsorbed peptide.

  8. Mineral Surface Reactivity in teaching of Science Materials

    Science.gov (United States)

    Del Hoyo Martínez, Carmen

    2013-04-01

    In the last fifty years, science materials issues has required the study of air pollution, water and soil to prevent and remedy the adverse effects of waste originating from anthropogenic activity and the development of new energies and new materials. The teaching of this discipline has been marked by lectures on general lines, materials, disciplines, who explained biased objects of reality, but often forgot the task of reconstruction and integration of such visions. Moving from that model, otherwise quite static, to a dynamic relational model, would in our view, a real revolution in education. This means taking a systematic approach to complex both in interpreting reality and in favor when learning. Children relationships are as important or more than single objects, and it is to discover fundamental organizational principles of phenomena we seek to interpret or in other words, find the pattern that connects. Thus, we must work on relationships and also take into account the relation between the observer and the observed. Educate about relationships means that studies should always be considered within a framework of probabilities, not absolute certainties. This model of systemic thinking, dealing with complexity, is a possibility to bring coherence to our educational work, because the complexity is not taught, complexity is live, so that complex thinking is extended (and fed) in a form educate complex. It is the task of teaching to help people move from level to level of decision reviews. This means that systems thinking should be extended in a local action, action that engages the individual and the environment. Science Materials has emerged as a discipline of free choice for pupils attending chemical engineering which has been assigned 6.0 credits. The chemical engineer's professional profile within the current framework is defined as a professional knowledge as a specialization technical / functional, working in a learning organization and the formation of

  9. Density functional theory in surface science and heterogeneous catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Scheffler, M.; Toulhoat, H.

    2006-01-01

    Solid surfaces are used extensively as catalysts throughout the chemical industry, in the energy sector, and in environmental protection. Recently, density functional theory has started providing new insight into the atomic-scale mechanisms of heterogeneous catalysis, helping to interpret the large...

  10. The influence of lithology on surface water sources | Science ...

    Science.gov (United States)

    Understanding the temporal and spatial variability of surface water sources within a basin is vital to our ability to manage the impacts of climate variability and land cover change. Water stable isotopes can be used as a tool to determine geographic and seasonal sources of water at the basin scale. Previous studies in the Coastal Range of Oregon reported that the variation in the isotopic signatures of surface water does not conform to the commonly observed “rainout effect”, which exhibits a trend of increasing isotopic depletion with rising elevation. The primary purpose of this research is to investigate the mechanisms governing seasonal and spatial variations in the isotopic signature of surface waters within the Marys River Basin, located in the leeward side of the Oregon Coastal Range. Surface water and precipitation samples were collected every 2-3 weeks for isotopic analysis of δ18O and δ2H for one year. Results indicate a significant difference in isotopic signature between watersheds underlain by basalt and sandstone. The degree of separation was the most distinct during the summer when low flows reflect deeper groundwater sources, whereas isotopic signatures during the rainy season (fall and winter) showed a greater degree of similarity between the two lithologies. This indicates that baseflow within streams drained by sandstone versus basalt is being supplied from two distinctly separate water sources. In addition, Marys River flow at the outle

  11. A study of structure and properties of molecularly thin methanol film using the modified surface forces apparatus.

    Science.gov (United States)

    Zhao, Gutian; Cai, Di; Wu, Gensheng; Tan, Qiyan; Xiang, Li; Zhang, Yin; Xiang, Nan

    2014-11-01

    A novel approach for studying the adsorption and evaporation processes of molecularly thin methanol film by the modified surface forces apparatus (M-SFA) is reported. This method can be used precisely to measure the thickness, morphology, and mechanical properties of the film confined between two mica surfaces in a real-time manner at gas atmosphere. By observing the adsorption and evaporation processes of the methanol molecule, it is found that the first adsorbed layer of the methanol film on the mica surface behaves as a solid-like structure. The thickness of this layer is measured to be about 3.2 Å, approximately equal to the diameter of a methanol molecule. Besides, this first adsorbed layer can carry normalized loads of more than 5.6 atm due to the carrying capacity conserved by the bond of mica-OH. The outer layers of the methanol film are further adsorbed with the increase of the exposure time, which are liquid-like and can be easily eliminated out from the substrate. The present study suggests that the interacting mode between hydroxy and mica is of great potential in material science and biomedical systems. © 2014 Wiley Periodicals, Inc.

  12. Art Advancing Science: Filmmaking Leads to Molecular Insights at the Nanoscale.

    Science.gov (United States)

    Reilly, Charles; Ingber, Donald E

    2017-12-26

    Many have recognized the potential value of facilitating activities that span the art-science interface for the benefit of society; however, there are few examples that demonstrate how pursuit of an artistic agenda can lead to scientific insights. Here, we describe how we set out to produce an entertaining short film depicting the fertilization of the egg by sperm as a parody of a preview for another Star Wars movie to excite the public about science, but ended up developing a simulation tool for multiscale modeling. To produce an aesthetic that communicates mechanical continuity across spatial scales, we developed custom strategies that integrate physics-based animation software from the entertainment industry with molecular dynamics simulation tools, using experimental data from research publications. Using this approach, we were able to depict biological physicality across multiple spatial scales, from how sperm tails move to collective molecular behavior within the axoneme to how the molecular motor, dynein, produces force at the nanometer scale. The dynein simulations, which were validated by replicating results of past simulations and cryo-electron microscopic studies, also predicted a potential mechanism for how ATP hydrolysis drives dynein motion along the microtubule as well as how dynein changes its conformation when it goes through the power stroke. Thus, pursuit of an artistic work led to insights into biology at the nanoscale as well as the development of a highly generalizable modeling and simulation technology that has utility for nanoscience and any other area of scientific investigation that involves analysis of complex multiscale systems.

  13. New molecular descriptors based on local properties at the molecular surface and a boiling-point model derived from them.

    Science.gov (United States)

    Ehresmann, Bernd; de Groot, Marcel J; Alex, Alexander; Clark, Timothy

    2004-01-01

    New molecular descriptors based on statistical descriptions of the local ionization potential, local electron affinity, and the local polarizability at the surface of the molecule are proposed. The significance of these descriptors has been tested by calculating them for the Maybridge database in addition to our set of 26 descriptors reported previously. The new descriptors show little correlation with those already in use. Furthermore, the principal components of the extended set of descriptors for the Maybridge data show that especially the descriptors based on the local electron affinity extend the variance in our set of descriptors, which we have previously shown to be relevant to physical properties. The first nine principal components are shown to be most significant. As an example of the usefulness of the new descriptors, we have set up a QSPR model for boiling points using both the old and new descriptors.

  14. Nonequilibrium Molecular Simulations of New Ionic Lubricants at Metallic Surfaces: Prediction of the Friction.

    Science.gov (United States)

    Mendonça, Ana C F; Pádua, Agílio A H; Malfreyt, Patrice

    2013-03-12

    We report nonequilibrium molecular dynamics of ionic liquids interacting with metallic surfaces. A specific set of interaction parameters for ionic liquids composed of alkylammonium cations and alkylsulfonate anions with an iron surface, which has been previously developed (J. Chem. Theory Comput.2012, 8, 3348) is used here. We develop a procedure for a quantitative prediction of the friction coefficient at different loads and shear rates. The simulated friction coefficient agrees very well with the available experimental ones. The dependence of friction on the load, shear velocity, surface topology, and length of alkyl side chains in the ionic liquid is also investigated. The changes in the frictional forces are explained in terms of the specific arrangements and orientations of groups forming the ionic liquid at the vicinity of the surface.

  15. Solvation of excess electrons trapped in charge pockets on molecular surfaces

    Science.gov (United States)

    Jalbout, Abraham F.

    This work considers the ability of hydrogen fluoride (HF) to solvate excess electrons located on cyclic hydrocarbon surfaces. The principle applied involves the formation of systems in which excess electrons can be stabilized not only on concentrated molecular surface charge pockets but also by HF. Recent studies have shown that OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), at the same time, the hydrogen atoms on the opposite side of this surface form a pocket of positive charge can attract the excess electron. This density can be further stabilized by the addition of an HF molecule that can form an 'anion with an internally solvated electron' (AISE) state. These systems are shown to be stable with respect to vertical electron detachment (VDE).

  16. Surface activation of cyclo olefin polymer by oxygen plasma discharge: a molecular dynamics study

    International Nuclear Information System (INIS)

    Soberon, Felipe

    2014-01-01

    Thermoplastic substrates made of cyclo olefin polymer (COP) are treated with oxygen plasma discharges to introduce polar groups at the surface. This is the first step in the process of surface functionalization of COP substrates used in biosensor devices. A molecular dynamics model of basic COP structure is implemented using the second-generation reactive empirical bond order (REBO) potentials for hydrocarbon–oxygen interactions. The model includes covalent bond and Van der Waals interactions. The bombardment of a COP surface with mono-energetic atomic oxygen ions, energy in the range 1-35 eV, is simulated and reported here. The dynamics of the substrate modification reveals that the substrate top layer is de-hydrogenated and subsequently builds up an oxygen–carbon matrix layer, ∼10 Å thick. Analysis of the modified substrates indicates that surface yield is predominantly peroxide groups. (paper)

  17. Molecular-scale shear response of the organic semiconductor β -DBDCS (100) surface

    Science.gov (United States)

    Álvarez-Asencio, Rubén; Moreno-Ramírez, Jorge S.; Pimentel, Carlos; Casado, Santiago; Matta, Micaela; Gierschner, Johannes; Muccioli, Luca; Yoon, Seong-Jun; Varghese, Shinto; Park, Soo Young; Gnecco, Enrico; Pina, Carlos M.

    2017-09-01

    In this work we present friction-force microscopy (FFM) lattice-resolved images acquired on the (100) facet of the semiconductor organic oligomer (2 Z ,2'Z )-3 , 3' -(1,4-phenylene)bis(2-(4-butoxyphenyl)acrylonitrile) (β -DBDCS) crystal in water at room temperature. Stick-slip contrast, lateral contact stiffness, and friction forces are found to depend strongly on the sliding direction due to the anisotropic packing of the molecular chains forming the crystal surface along the [010] and [001] directions. The anisotropy also causes the maximum value of the normal force applicable before wearing to increase by a factor of 3 when the scan is performed along the [001] direction on the (100) face. Altogether, our results contribute to achieving a better understanding of the molecular origin of friction anisotropy on soft crystalline surfaces, which has been often hypothesized but rarely investigated in the literature.

  18. Molecular dynamics study of room temperature ionic liquids with water at mica surface

    Directory of Open Access Journals (Sweden)

    Huanhuan Zhang

    2018-04-01

    Full Text Available Water in room temperature ionic liquids (RTILs could impose significant effects on their interfacial properties at a charged surface. Although the interfaces between RTILs and mica surfaces exhibit rich microstructure, the influence of water content on such interfaces is little understood, in particular, considering the fact that RTILs are always associated with water due to their hygroscopicity. In this work, we studied how different types of RTILs and different amounts of water molecules affect the RTIL-mica interfaces, especially the water distribution at mica surfaces, using molecular dynamics (MD simulation. MD results showed that (1 there is more water and a thicker water layer adsorbed on the mica surface as the water content increases, and correspondingly the average location of K+ ions is farther from mica surface; (2 more water accumulated at the interface with the hydrophobic [Emim][TFSI] than in case of the hydrophilic [Emim][BF4] due to the respective RTIL hydrophobicity and ion size. A similar trend was also observed in the hydrogen bonds formed between water molecules. Moreover, the 2D number density map of adsorbed water revealed that the high-density areas of water seem to be related to K+ ions and silicon/aluminum atoms on mica surface. These results are of great importance to understand the effects of hydrophobicity/hydrophicility of RTIL and water on the interfacial microstructure at electrified surfaces. Keywords: Room temperature ionic liquids, Hydrophobicity/hydrophicility, Water content, Electrical double layer, Mica surface

  19. Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces

    International Nuclear Information System (INIS)

    Wang Xiaojing; Wang Wei; Han Peilin; Kubo, Momoji; Miyamoto, Akira

    2008-01-01

    An accelerated quantum chemical molecular dynamical code 'Colors-Excite' was used to investigate the photolysis of alkyl nitrites series, RONO (R=CH 3 and C(CH 3 ) 3 ) on copper surfaces. Our calculations showed that the photo-dissociated processes are associated with the alkyl substituents of RONO when adsorbed on copper surfaces. For R=CH 3 , a two-step photolysis reaction occurred, yielding diverse intermediate products including RO radical, NO, and HNO, consistent with those reported in gas phase. While for R=C(CH 3 ) 3 , only one-step photolysis reaction occurred and gave intermediate products of RO radical and NO. Consequently, pure RO species were achieved to adsorb on metal surfaces by removing the NO species in photolysis reaction. The detailed photo-dissociated behaviors of RONO on copper surfaces with different alkyl substituents which are uncovered by the present simulation can be extended to explain the diverse dissociative mechanism experimentally observed. The quantum chemical molecular dynamical code 'Colors-Excite' is proved to be highly applicable to the photo-dissociations on metal surfaces

  20. ESCA and electron diffraction studies of InP surface heated under As molecular beam exposure

    International Nuclear Information System (INIS)

    Sugiura, Hideo; Yamaguchi, Masafumi; Shibukawa, Atsushi

    1983-01-01

    Chemical composition of InP substrate surface heattreated under As molecular beam exposure in an ultrahigh vacuum chamber was studied with ESCA, and surface reconstruction of the substrate was examined by in-situ electron diffraction. The InP substrate heated under the exposure of As molecular beam has mirror surface up to 590 0 C while the surface of InP heated above 400 0 C in vacuum is roughened. The ESCA study shows that thin InAs layer (thickness 0 C under the exposure of As. The electron diffraction study indicates that the InP is cleaned at about 500 0 C in As pressures of 10 -7 - 10 -5 Torr. The InP surface is prevented from thermally decomposing by the coverage of the InAs layer, which may be formed through the following process: 2InPO 4 + As 4 → 2InAs + P 2 O 5 + As 2 O 3 . (author)

  1. Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations.

    Science.gov (United States)

    Ge, Zhenpeng; Wang, Yi

    2017-04-20

    Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such simulations generally require detailed knowledge of the surface composition of the NP under investigation. Even for some well-characterized nanoparticles, however, this knowledge is not always available. An example is nanodiamond, a nanoscale diamond particle with surface dominated by oxygen-containing functional groups. In this work, we explore using the harmonic restraint method developed by Venable et al., to estimate the surface charge density (σ) of nanodiamonds. Based on the Gouy-Chapman theory, we convert the experimentally determined zeta potential of a nanodiamond to an effective charge density (σ eff ), and then use the latter to estimate σ via molecular dynamics simulations. Through scanning a series of nanodiamond models, we show that the above method provides a straightforward protocol to determine the surface charge density of relatively large (> ∼100 nm) NPs. Overall, our results suggest that despite certain limitation, the above protocol can be readily employed to guide the model construction for MD simulations, which is particularly useful when only limited experimental information on the NP surface composition is available to a modeler.

  2. Modelling episodic acidification of surface waters: the state of science.

    Science.gov (United States)

    Eshleman, K N; Wigington, P J; Davies, T D; Tranter, M

    1992-01-01

    Field studies of chemical changes in surface waters associated with rainfall and snowmelt events have provided evidence of episodic acidification of lakes and streams in Europe and North America. Modelling these chemical changes is particularly challenging because of the variability associated with hydrological transport and chemical transformation processes in catchments. This paper provides a review of mathematical models that have been applied to the problem of episodic acidification. Several empirical approaches, including regression models, mixing models and time series models, support a strong hydrological interpretation of episodic acidification. Regional application of several models has suggested that acidic episodes (in which the acid neutralizing capacity becomes negative) are relatively common in surface waters in several regions of the US that receive acid deposition. Results from physically based models have suggested a lack of understanding of hydrological flowpaths, hydraulic residence times and biogeochemical reactions, particularly those involving aluminum. The ability to better predict episodic chemical responses of surface waters is thus dependent upon elucidation of these and other physical and chemical processes.

  3. Surface science. Adhesion and friction in mesoscopic graphite contacts.

    Science.gov (United States)

    Koren, Elad; Lörtscher, Emanuel; Rawlings, Colin; Knoll, Armin W; Duerig, Urs

    2015-05-08

    The weak interlayer binding in two-dimensional layered materials such as graphite gives rise to poorly understood low-friction characteristics. Accurate measurements of the adhesion forces governing the overall mechanical stability have also remained elusive. We report on the direct mechanical measurement of line tension and friction forces acting in sheared mesoscale graphite structures. We show that the friction is fundamentally stochastic in nature and is attributable to the interaction between the incommensurate interface lattices. We also measured an adhesion energy of 0.227 ± 0.005 joules per square meter, in excellent agreement with theoretical models. In addition, bistable all-mechanical memory cell structures and rotational bearings have been realized by exploiting position locking, which is provided solely by the adhesion energy. Copyright © 2015, American Association for the Advancement of Science.

  4. High-order fractional partial differential equation transform for molecular surface construction.

    Science.gov (United States)

    Hu, Langhua; Chen, Duan; Wei, Guo-Wei

    2013-01-01

    Fractional derivative or fractional calculus plays a significant role in theoretical modeling of scientific and engineering problems. However, only relatively low order fractional derivatives are used at present. In general, it is not obvious what role a high fractional derivative can play and how to make use of arbitrarily high-order fractional derivatives. This work introduces arbitrarily high-order fractional partial differential equations (PDEs) to describe fractional hyperdiffusions. The fractional PDEs are constructed via fractional variational principle. A fast fractional Fourier transform (FFFT) is proposed to numerically integrate the high-order fractional PDEs so as to avoid stringent stability constraints in solving high-order evolution PDEs. The proposed high-order fractional PDEs are applied to the surface generation of proteins. We first validate the proposed method with a variety of test examples in two and three-dimensional settings. The impact of high-order fractional derivatives to surface analysis is examined. We also construct fractional PDE transform based on arbitrarily high-order fractional PDEs. We demonstrate that the use of arbitrarily high-order derivatives gives rise to time-frequency localization, the control of the spectral distribution, and the regulation of the spatial resolution in the fractional PDE transform. Consequently, the fractional PDE transform enables the mode decomposition of images, signals, and surfaces. The effect of the propagation time on the quality of resulting molecular surfaces is also studied. Computational efficiency of the present surface generation method is compared with the MSMS approach in Cartesian representation. We further validate the present method by examining some benchmark indicators of macromolecular surfaces, i.e., surface area, surface enclosed volume, surface electrostatic potential and solvation free energy. Extensive numerical experiments and comparison with an established surface model

  5. Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu [Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003-9303 (United States); Hammond, Karl D. [Department of Chemical Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Wirth, Brian D. [Department of Nuclear Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)

    2015-10-28

    We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (He{sub n}, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes of helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He{sub 4} and He{sub 5} clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.

  6. Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

    Science.gov (United States)

    Stolow, Albert

    polyatomic molecules, including high harmonic generation (HHG). We discuss an experimental method, Channel-Resolved Above Threshold Ionization (CRATI), which directly unveils the electronic channels participating in the attosecond molecular strong field ionization response [10]. This work was supported by the National Research Council of Canada and the Natural Sciences & Engineering Research Council.

  7. Adsorption of molecular additive onto lead halide perovskite surfaces: A computational study on Lewis base thiophene additive passivation

    Science.gov (United States)

    Zhang, Lei; Yu, Fengxi; Chen, Lihong; Li, Jingfa

    2018-06-01

    Organic additives, such as the Lewis base thiophene, have been successfully applied to passivate halide perovskite surfaces, improving the stability and properties of perovskite devices based on CH3NH3PbI3. Yet, the detailed nanostructure of the perovskite surface passivated by additives and the mechanisms of such passivation are not well understood. This study presents a nanoscopic view on the interfacial structure of an additive/perovskite interface, consisting of a Lewis base thiophene molecular additive and a lead halide perovskite surface substrate, providing insights on the mechanisms that molecular additives can passivate the halide perovskite surfaces and enhance the perovskite-based device performance. Molecular dynamics study on the interactions between water molecules and the perovskite surfaces passivated by the investigated additive reveal the effectiveness of employing the molecular additives to improve the stability of the halide perovskite materials. The additive/perovskite surface system is further probed via molecular engineering the perovskite surfaces. This study reveals the nanoscopic structure-property relationships of the halide perovskite surface passivated by molecular additives, which helps the fundamental understanding of the surface/interface engineering strategies for the development of halide perovskite based devices.

  8. Detection of low-molecular-weight domoic acid using surface plasmon resonance sensor

    Czech Academy of Sciences Publication Activity Database

    Yu, Q.; Chen, S.; Taylor, A. D.; Homola, Jiří; Hock, B.; Jiang, S.

    2005-01-01

    Roč. 107, č. 1 (2005), s. 193-201 ISSN 0925-4005. [European Conference on Optical Chemical Sensors and Biosensors EUROPT(R)ODE /7./. Madrid, 04.04.2004-07.04.2004] Grant - others:US FDA (US) FD-U-002250; National Science Foundation(US) CTS-0092699 Institutional research plan: CEZ:AV0Z20670512 Keywords : biosensors * surface plasmon resonance * optical sensors Subject RIV: JB - Sensors, Measurment, Regulation Impact factor: 2.646, year: 2005

  9. Super-Resolution Molecular and Functional Imaging of Nanoscale Architectures in Life and Materials Science

    KAUST Repository

    Habuchi, Satoshi

    2014-06-12

    Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.

  10. Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease.

    Science.gov (United States)

    Ogino, Shuji; Lochhead, Paul; Chan, Andrew T; Nishihara, Reiko; Cho, Eunyoung; Wolpin, Brian M; Meyerhardt, Jeffrey A; Meissner, Alexander; Schernhammer, Eva S; Fuchs, Charles S; Giovannucci, Edward

    2013-04-01

    Epigenetics acts as an interface between environmental/exogenous factors, cellular responses, and pathological processes. Aberrant epigenetic signatures are a hallmark of complex multifactorial diseases (including neoplasms and malignancies such as leukemias, lymphomas, sarcomas, and breast, lung, prostate, liver, and colorectal cancers). Epigenetic signatures (DNA methylation, mRNA and microRNA expression, etc) may serve as biomarkers for risk stratification, early detection, and disease classification, as well as targets for therapy and chemoprevention. In particular, DNA methylation assays are widely applied to formalin-fixed, paraffin-embedded archival tissue specimens as clinical pathology tests. To better understand the interplay between etiological factors, cellular molecular characteristics, and disease evolution, the field of 'molecular pathological epidemiology (MPE)' has emerged as an interdisciplinary integration of 'molecular pathology' and 'epidemiology'. In contrast to traditional epidemiological research including genome-wide association studies (GWAS), MPE is founded on the unique disease principle, that is, each disease process results from unique profiles of exposomes, epigenomes, transcriptomes, proteomes, metabolomes, microbiomes, and interactomes in relation to the macroenvironment and tissue microenvironment. MPE may represent a logical evolution of GWAS, termed 'GWAS-MPE approach'. Although epigenome-wide association study attracts increasing attention, currently, it has a fundamental problem in that each cell within one individual has a unique, time-varying epigenome. Having a similar conceptual framework to systems biology, the holistic MPE approach enables us to link potential etiological factors to specific molecular pathology, and gain novel pathogenic insights on causality. The widespread application of epigenome (eg, methylome) analyses will enhance our understanding of disease heterogeneity, epigenotypes (CpG island methylator

  11. Interactive Multimodal Molecular Set – Designing Ludic Engaging Science Learning Content

    DEFF Research Database (Denmark)

    Thorsen, Tine Pinholt; Christiansen, Kasper Holm Bonde; Jakobsen Sillesen, Kristian

    2014-01-01

    This paper reports on an exploratory study investigating 10 primary school students’ interaction with an interactive multimodal molecular set fostering ludic engaging science learning content in primary schools (8th and 9th grade). The concept of the prototype design was to bridge the physical...... and virtual worlds with electronic tags and, through this, blend the familiarity of the computer and toys, to create a tool that provided a ludic approach to learning about atoms and molecules. The study was inspired by the participatory design and informant design methodologies and included design...

  12. Molecular dynamics simulation of wetting behaviors of Li on W surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Xuegui [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Xiao, Shifang [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Deng, Huiqiu, E-mail: hqdeng@hnu.edu.cn [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Hu, Wangyu, E-mail: wyuhu@hnu.edu.cn [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China)

    2017-04-15

    A modified analytic embedded atom potential has been developed for the Li-W system. The potential has been fitted to physical quantities derived from density functional theory calculations. It is shown that the new potential is capable of reproducing the solubility of solid solution for Li-W systems. The wetting behaviors between solid tungsten and liquid Li are examined by using molecular dynamics simulations. The MD simulation results for the Li droplet wetting on the W surface illustrated that our MAEAM potential model has a good forecasting ability for the contact angle of liquid Li on W the cleaning surface above the wetting temperature. And the results of Li film dewetting from the W surfaces are consistent with relative experimental results. It is believed that the potential can be used to investigate the surfaces wettability of liquid Li on W substrate. We also simulated the lithium droplet on grooved surface. It is shown that the grooving W surfaces can obviously improve the wetting of liquid Li on W surfaces.

  13. Molecular simulation insights on the in vacuo adsorption of amino acids on graphene oxide surfaces with varying surface oxygen densities

    Energy Technology Data Exchange (ETDEWEB)

    Rahmani, Farzin; Nouranian, Sasan, E-mail: sasan@olemiss.edu; Mahdavi, Mina [University of Mississippi, Department of Chemical Engineering (United States); Al-Ostaz, Ahmed [University of Mississippi, Department of Civil Engineering (United States)

    2016-11-15

    In this fundamental study, a series of molecular dynamics simulations were performed in vacuo to investigate the energetics and select geometries of 20 standard amino acids (AAs) on pristine graphene (PG) and graphene oxide (GO) surfaces as a function of graphene surface oxygen density. These interactions are of key interest to graphene/biomolecular systems. Our results indicate that aromatic AAs exhibit the strongest total interactions with the PG surfaces due to π-π stacking. Tryptophan (Trp) has the highest aromaticity due to its indole side chain and, hence, has the strongest interaction among all AAs (−16.66 kcal/mol). Aliphatic, polar, and charged AAs show various levels of affinity to the PG sheets depending on the strength of their side chain hydrophobic interactions. For example, arginine (Arg) with its guanidinium side chain exhibits the strongest interaction with the PG sheets (−13.81 kcal/mol) following aromatic AAs. Also, glycine (Gly; a polar AA) has the weakest interaction with the PG sheets (−7.29 kcal/mol). When oxygen-containing functional groups are added to the graphene sheets, the π-π stacking in aromatic AAs becomes disrupted and perfect parallelism of the aromatic rings is lost. Moreover, hydrogen bonding and/or electrostatic interactions become more pronounced. Charged AAs exhibit the strongest interactions with the GO surfaces. In general, the AA-GO interactions increase with increasing surface oxygen density, and the effect is more pronounced at higher O/C ratios. This study provides a quantitative measure of AA-graphene interactions for the design and tuning of biomolecular systems suitable for biosensing, drug delivery, and gene delivery applications.

  14. Studies of the surface structures of molecular crystals and of adsorbed molecular monolayers on the (111) crystal faces of platinum and silver by low-energy electron diffraction

    International Nuclear Information System (INIS)

    Firment, L.E.

    1977-01-01

    The structures of molecular crystal surfaces were investigated for the first time by the use of low-energy electron diffraction (LEED). The experimental results from a variety of molecular crystals were examined and compared as a first step towards understanding the properties of these surfaces on a microscopic level. The method of sample preparation employed, vapor deposition onto metal single-crystal substrates at low temperatures in ultrahigh vacuum, allowed concurrent study of the structures of adsorbed monolayers on metal surfaces and of the growth processes of molecular films on metal substrates. The systems investigated were ice, ammonia, naphthalene, benzene, the n-paraffins (C 3 to C 8 ), cyclohexane, trioxane, acetic acid, propionic acid, methanol, and methylamine adsorbed and condensed on both Pt(111) and Ag(111) surfaces. Electron-beam-induced damage of the molecular surfaces was observed after electron exposures of 10 -4 A sec cm -2 at 20 eV. Aromatic molecular crystal samples were more resistant to damage than samples of saturated molecules. The quality and orientation of the grown molecular crystal films were influenced by substrate preparation and growth conditions. Forty ordered monolayer structures were observed. 110 figures, 22 tables, 162 references

  15. Molecular dynamics for lateral surface adhesion and peeling behavior of single-walled carbon nanotubes on gold surfaces

    International Nuclear Information System (INIS)

    Huang, Pei-Hsing

    2011-01-01

    Highlights: ► Adhesion and peeling behaviors of SWCNTs are investigated by detailed, fully atomistic MD simulations. ► Adhesion energy of SWCNTs are discussed. ► Dynamical behaviors of SWCNTs in low temperature adhesion are analyzed. ► Adhesion strengths of SWCNTs obtained from MD simulations are compared with the predictions of Hamaker theory and JKR model. - Abstract: Functional gecko-inspired adhesives have attracted a lot of research attention in the last decade. In this work, the lateral surface adhesion and normal peeling-off behavior of single-walled carbon nanotubes (SWCNTs) on gold substrates are investigated by performing detailed, fully atomistic molecular dynamics (MD) simulations. The effects of the diameter and adhered length of CNTs on the adhesive properties were systematically examined. The simulation results indicate that adhesion energies between the SWCNTs and the Au surface varied from 220 to 320 mJ m −2 over the reported chirality range. The adhesion forces on the lateral surface and the tip of the nanotubes obtained from MD simulations agree very well with the predictions of Hamaker theory and Johnson–Kendall–Roberts (JKR) model. The analyses of covalent bonds indicate that the SWCNTs exhibited excellent flexibility and extensibility when adhering at low temperatures (∼100 K). This mechanism substantially increases adhesion time compared to that obtained at higher temperatures (300–700 K), which makes SWCNTs promising for biomimetic adhesives in ultra-low temperature surroundings.

  16. Molecular dynamics for lateral surface adhesion and peeling behavior of single-walled carbon nanotubes on gold surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Pei-Hsing, E-mail: phh@mail.npust.edu.tw [Department of Mechanical Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan (China)

    2011-12-15

    Highlights: Black-Right-Pointing-Pointer Adhesion and peeling behaviors of SWCNTs are investigated by detailed, fully atomistic MD simulations. Black-Right-Pointing-Pointer Adhesion energy of SWCNTs are discussed. Black-Right-Pointing-Pointer Dynamical behaviors of SWCNTs in low temperature adhesion are analyzed. Black-Right-Pointing-Pointer Adhesion strengths of SWCNTs obtained from MD simulations are compared with the predictions of Hamaker theory and JKR model. - Abstract: Functional gecko-inspired adhesives have attracted a lot of research attention in the last decade. In this work, the lateral surface adhesion and normal peeling-off behavior of single-walled carbon nanotubes (SWCNTs) on gold substrates are investigated by performing detailed, fully atomistic molecular dynamics (MD) simulations. The effects of the diameter and adhered length of CNTs on the adhesive properties were systematically examined. The simulation results indicate that adhesion energies between the SWCNTs and the Au surface varied from 220 to 320 mJ m{sup -2} over the reported chirality range. The adhesion forces on the lateral surface and the tip of the nanotubes obtained from MD simulations agree very well with the predictions of Hamaker theory and Johnson-Kendall-Roberts (JKR) model. The analyses of covalent bonds indicate that the SWCNTs exhibited excellent flexibility and extensibility when adhering at low temperatures ({approx}100 K). This mechanism substantially increases adhesion time compared to that obtained at higher temperatures (300-700 K), which makes SWCNTs promising for biomimetic adhesives in ultra-low temperature surroundings.

  17. Intense positron beam and its application to surface science

    International Nuclear Information System (INIS)

    Ito, Y.; Hirose, M.; Kanazawa, I.; Sueoka, O.; Takamura, S.; Okada, S.

    1992-01-01

    Intense pulsed slow positron beam has been produced using the 100 MeV electron LINAC of JAERI · Tokai. In order to use the beam for surface studies such as positron diffraction and positron microscopy, it was transferred from the solenoid magnetic field to field free region and then was brightness-enhanced. The beam size was reduced from 10 mmφ (in the magnetic field) to 0.5 mmφ after two stages of re-moderation. Using the intense brightness-enhanced positron beam we have observed for the first time RHEPD (Reflection High-Energy Positron Diffraction) patterns. A design of re-emission positron microscopy is also described. (author)

  18. Building Surface Science Capacity to Serve the Automobile Industry in Southeastern Michigan, final report

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Weidian

    2013-09-27

    This project, “Building Surface Science Capacity to Serve the Automobile Industry in Southeastern Michigan” was carried out in two phases: (1) the 2009 – 2012 renovation of space in the new EMU Science Complex, which included the Surface Science Laboratory (SSL), a very vigorous research lab at EMU that carries on a variety of research projects to serve the auto and other industries in Michigan; and (2) the 2013 purchase of several pieces of equipment to further enhance the research capability of the SSL. The funding granted by the DoE was proposed to “renovate the space in the Science Complex to include SSL and purchase equipment for tribological and electrochemical impedance measurements in the lab, thus SSL will serve the auto and other industries in Michigan better.” We believe we have fully accomplished the mission.

  19. Frames of scientific evidence: How journalists represent the (un)certainty of molecular medicine in science television programs.

    Science.gov (United States)

    Ruhrmann, Georg; Guenther, Lars; Kessler, Sabrina Heike; Milde, Jutta

    2015-08-01

    For laypeople, media coverage of science on television is a gateway to scientific issues. Defining scientific evidence is central to the field of science, but there are still questions if news coverage of science represents scientific research findings as certain or uncertain. The framing approach is a suitable framework to classify different media representations; it is applied here to investigate the frames of scientific evidence in film clips (n=207) taken from science television programs. Molecular medicine is the domain of interest for this analysis, due to its high proportion of uncertain and conflicting research findings and risks. The results indicate that television clips vary in their coverage of scientific evidence of molecular medicine. Four frames were found: Scientific Uncertainty and Controversy, Scientifically Certain Data, Everyday Medical Risks, and Conflicting Scientific Evidence. They differ in their way of framing scientific evidence and risks of molecular medicine. © The Author(s) 2013.

  20. Dynamics and diffusive-conformational coupling in polymer bulk samples and surfaces: a molecular dynamics study

    International Nuclear Information System (INIS)

    Vree, C; Mayr, S G

    2010-01-01

    The impact of free surfaces on the mobility and conformational fluctuations of model polymer chains is investigated with the help of classical molecular dynamics simulations over a broad temperature range. Below a critical temperature, T*, similar to the critical temperature of the mode coupling theory, the center-of-mass displacements and temporal fluctuations of the radius of gyration of individual chains-as a fingerprint of structural reconfigurations-reveal a strong enhancement close to surfaces, while this effect diminishes with increasing temperature and observation time. Interpreting conformational fluctuations as a random walk in conformational space, identical activation enthalpies for structural reconfigurations and diffusion are obtained within the error bars in the bulk and at the surfaces, thus indicating a coupling of diffusive and conformational dynamics.

  1. Final Report: Molecular Basis for Microbial Adhesion and Geochemical Surface Reactions: A Study Across Scales

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, David Adams [The University of Alabama

    2013-06-27

    Computational chemistry was used to help provide a molecular level description of the interactions of Gram-negative microbial membranes with subsurface materials. The goal is to develop a better understanding of the molecular processes involved in microbial metal binding, microbial attachment to mineral surfaces, and, eventually, oxidation/reduction reactions (electron transfer) that can occur at these surfaces and are mediated by the bacterial exterior surface. The project focused on the interaction of the outer microbial membrane, which is dominated by an exterior lipopolysaccharide (LPS) portion, of Pseudomonas aeruginosa with the mineral goethite and with solvated ions in the environment. This was originally a collaborative project with T.P. Straatsma and B. Lowery of the Pacific Northwest National Laboratory. The University of Alabama effort used electronic structure calculations to predict the molecular behavior of ions in solution and the behavior of the sugars which form a critical part of the LPS. The interactions of the sugars with metal ions are expected to dominate much of the microscopic structure and transport phenomena in the LPS. This work, in combination with the molecular dynamics simulations of Straatsma and the experimental electrochemistry and microscopy measurements of Lowry, both at PNNL, is providing new insights into the detailed molecular behavior of these membranes in geochemical environments. The effort at The University of Alabama has three components: solvation energies and structures of ions in solution, prediction of the acidity of the critical groups in the sugars in the LPS, and binding of metal ions to the sugar anions. An important aspect of the structure of the LPS membrane as well as ion transport in the LPS is the ability of the sugar side groups such as the carboxylic acids and the phosphates to bind positively charged ions. We are studying the acidity of the acidic side groups in order to better understand the ability of

  2. Molecular beam studies of energy transfer in scattering from crystal surfaces

    International Nuclear Information System (INIS)

    Guthrie, W.L.

    1983-01-01

    The translational energy distributions and angular distributions of D 2 O produced from the reaction of incident D 2 and O 2 on a (111) platinum single crystal surface have been measured through the use of a molecular beam-surface scattering apparatus equipped with a time-of-flight spectrometer. The translation energies were measured over the surface temperature range T/sub s/ = 664 K - 913 K and at scattering angles of 7 0 and 40 0 from the surface normal. The D 2 O translational energy, , was found to be approximately half the equilibrium value over the temperature range examined, with /2k varying from 280 K to 480 K. These results are discussed in terms of a non-equilibrium desorption model. The two-photon ionization spectrometer was built to investigate the internal rotational and vibrational energy distributions of NO scattered from Pt(111) surfaces. The rotational energy distributions were measured over the crystal temperature range of T/sub s/ = 400 K - 1200 K. The translational energy distributions and angular distributions were measured using the time-of-flight spectrometer over the crystal temperature range of 400 K - 110 K and for beam translational energies of 0.046 eV, 0.11 eV and 0.24 eV, so that complete energy exchange information for translation, rotation and vibration is available for this gas-surface system. Significant energy transfer was observed in all three modes

  3. Molecular Structure and Dynamics in Thin Water Films at the Silica and Graphite Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Argyris, Dr. Dimitrios [University of Oklahoma; Tummala, Dr. Naga Rajesh [University of Oklahoma; StrioloDr., A [Vanderbilt University; Cole, David R [ORNL

    2008-01-01

    The structure and dynamic properties of interfacial water at the graphite and silica solid surfaces were investigated using molecular dynamics simulations. The effect of surface properties on the characteristics of interfacial water was quantified by computing density profiles, radial distribution functions, surface density distributions, orientation order parameters, and residence and reorientation correlation functions. In brief, our results show that the surface roughness, chemical heterogeneity, and surface heterogeneous charge distribution affect the structural and dynamic properties of the interfacial water molecules, as well as their rate of exchange with bulk water. Most importantly, our results indicate the formation of two distinct water layers at the SiO2 surface covered by a large density of hydroxyl groups. Further analysis of the data suggests a highly confined first layer where the water molecules assume preferential hydrogen-down orientation and a second layer whose behavior and characteristics are highly dependent on those of the first layer through a well-organized hydrogen bond network. The results suggest that water-water interactions, in particular hydrogen bonds, may be largely responsible for macroscopic interfacial properties such as adsorption and contact angle.

  4. Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

    Science.gov (United States)

    Perry, Thomas D.; Cygan, Randall T.; Mitchell, Ralph

    2006-07-01

    Cation binding by polysaccharides is observed in many environments and is important for predictive environmental modeling, and numerous industrial and food technology applications. The complexities of these cation-organic interactions are well suited for predictive molecular modeling and the analysis of conformation and configuration of polysaccharides and their influence on cation binding. In this study, alginic acid was chosen as a model polymer system and representative disaccharide and polysaccharide subunits were developed. Molecular dynamics simulation of the torsion angles of the ether linkage between various monomeric subunits identified local and global energy minima for selected disaccharides. The simulations indicate stable disaccharide configurations and a common global energy minimum for all disaccharide models at Φ = 274 ± 7°, Ψ = 227 ± 5°, where Φ and Ψ are the torsion angles about the ether linkage. The ability of disaccharide subunits to bind calcium ions and to associate with the (101¯4) surface of calcite was also investigated. Molecular models of disaccharide interactions with calcite provide binding energy differences for conformations that are related to the proximity and residence densities of the electron-donating moieties with calcium ions on the calcite surface, which are controlled, in part, by the torsion of the ether linkage between monosaccharide units. Dynamically optimized configurations for polymer alginate models with calcium ions were also derived.

  5. Molecular dynamics simulations of the DNA interaction with metallic nanoparticles and TiO2 surfaces

    International Nuclear Information System (INIS)

    Kholmurodov, Kh.T.; Krasavin, E.A.; Dushanov, E.B.; Hassan, H.K.; Galal, A.; ElHabashy, H.A.; Sweilam, N.H.; Yasuoka, K.

    2013-01-01

    The understanding of the mechanism of DNA interactions and binding with metallic nanoparticles (NPs) and surfaces represents a great interest in today's medicine applications due to diagnostic and treatment of oncology diseases. Recent experimental and simulation studies involve the DNA interaction with highly localized proton beams or metallic NPs (such as Ag, Au, etc.), aimed at targeted cancer therapy through the injection of metal micro- or nanoparticles into the tumor tissue with consequent local microwave or laser heating. The effects of mutational structure changes in DNA and protein structures could result in destroying of native chemical (hydrogen) bonds or, on the contrary, creating of new bonds that do not normally exist there. The cause of such changes might be the alteration of one or several nucleotides (in DNA) or the substitution of specific amino acid residues (in proteins) that can lead to the essential structural destabilization or unfolding. At the atomic or molecular level, the replacement of one nucleotide by another (in DNA double helices) or replacement of one amino acid residue by another (in proteins) cause essential modifications of the molecular force fields of the environment that break locally important hydrogen bonds underlying the structural stability of the biological molecules. In this work, the molecular dynamics(MD) simulations were performed for four DNA models and the flexibilities of the purine and pyrimidine nucleotides during the interaction process with the metallic NPs and TiO 2 surface were clarified

  6. Surface science study of selective ethylene epoxidation catalyzed by the Ag(110) surface: Structural sensitivity

    International Nuclear Information System (INIS)

    Campbell, C.T.

    1984-01-01

    The selective oxidation of ethylene to ethylene epoxide (C 2 H 4 +1/2O 2 →C 2 H 4 O) over Ag is the simplest example of kinetically controlled, selective heterogeneous catalysis. We have studied the steady-state kinetics and selectivity of this reaction for the first time on a clean, well-characterized Ag(110) surface by using a special apparatus which allows rapid (approx.20 s) transfer between a high-pressure catalytic microreactor and an ultrahigh vacuum surface analysis (AES, XPS, LEED, TDS) chamber. The effects of temperature and reactant pressures upon the rate and selectivity are virtually identical on Ag(110) and supported, high surface area Ag catalysts. The absolute specific rate (per Ag surface atom) is, however, some 100-fold higher for Ag(110) than for high surface area catalysts. This is related to the well-known structural sensitivity of this reaction. It is postulated that a small percentage of (110) planes (or [110]-like sites) are responsible for most of the catalytic activity of high surface area catalysts. The high activity of the (110) plane is attributed to its high sticking probability for dissociative oxygen adsorption, since the rate of ethylene epoxidation is shown in a related work [Ref. 1: C. T. Campbell and M. T. Paffett, Surf. Sci. (in press)] to be proportional to the coverage of atomically adsorbed oxygen at constant temperature and ethylene pressure

  7. Hybrid Light-Matter States in a Molecular and Material Science Perspective.

    Science.gov (United States)

    Ebbesen, Thomas W

    2016-11-15

    The notion that light and matter states can be hybridized the way s and p orbitals are mixed is a concept that is not familiar to most chemists and material scientists. Yet it has much potential for molecular and material sciences that is just beginning to be explored. For instance, it has already been demonstrated that the rate and yield of chemical reactions can be modified and that the conductivity of organic semiconductors and nonradiative energy transfer can be enhanced through the hybridization of electronic transitions. The hybridization is not limited to electronic transitions; it can be applied for instance to vibrational transitions to selectively perturb a given bond, opening new possibilities to change the chemical reactivity landscape and to use it as a tool in (bio)molecular science and spectroscopy. Such results are not only the consequence of the new eigenstates and energies generated by the hybridization. The hybrid light-matter states also have unusual properties: they can be delocalized over a very large number of molecules (up to ca. 10 5 ), and they become dispersive or momentum-sensitive. Importantly, the hybridization occurs even in the absence of light because it is the zero-point energies of the molecular and optical transitions that generate the new light-matter states. The present work is not a review but rather an Account from the author's point of view that first introduces the reader to the underlying concepts and details of the features of hybrid light-matter states. It is shown that light-matter hybridization is quite easy to achieve: all that is needed is to place molecules or a material in a resonant optical cavity (e.g., between two parallel mirrors) under the right conditions. For vibrational strong coupling, microfluidic IR cells can be used to study the consequences for chemistry in the liquid phase. Examples of modified properties are given to demonstrate the full potential for the molecular and material sciences. Finally an

  8. Perfect-absorption graphene metamaterials for surface-enhanced molecular fingerprint spectroscopy

    Science.gov (United States)

    Guo, Xiangdong; Hu, Hai; Liao, Baoxin; Zhu, Xing; Yang, Xiaoxia; Dai, Qing

    2018-05-01

    Graphene plasmon with extremely strong light confinement and tunable resonance frequency represents a promising surface-enhanced infrared absorption (SEIRA) sensing platform. However, plasmonic absorption is relatively weak (approximately 1%-9%) in monolayer graphene nanostructures, which would limit its sensitivity. Here, we theoretically propose a hybrid plasmon-metamaterial structure that can realize perfect absorption in graphene with a low carrier mobility of 1000 cm2 V-1 s-1. This structure combines a gold reflector and a gold grating to the graphene plasmon structures, which introduce interference effect and the lightning-rod effect, respectively, and largely enhance the coupling of light to graphene. The vibration signal of trace molecules can be enhanced up to 2000-fold at the hotspot of the perfect-absorption structure, enabling the SEIRA sensing to reach the molecular level. This hybrid metal-graphene structure provides a novel path to generate high sensitivity in nanoscale molecular recognition for numerous applications.

  9. Surface plasmon resonance based optical fiber riboflavin sensor by using molecularly imprinted gel

    Science.gov (United States)

    Verma, Roli; Gupta, Banshi D.

    2013-05-01

    We report the fabrication and characterization of surface plasmon resonance (SPR) based optical fiber riboflavin/vitamin B2 sensor using combination of colloidal crystal templating and molecularly imprinted gel. The sensor works on spectral interrogation method. The operating range of the sensor lies from 0 μg/ml to 320 μg/ml, the suitable amount of intakes of riboflavin recommended for different age group. The SPR spectra show blue shift with increasing concentration of riboflavin, which is due to the interaction of riboflavin molecule over specific binding sites caused by molecular imprinting. The present sensor has many advantageous features such as fast response, small probe size, low cost and can be used for remote/online monitoring.

  10. Aqueous electrolyte surfaces in strong electric fields: molecular insight into nanoscale jets and bridges

    Science.gov (United States)

    Jirsák, Jan; Moučka, Filip; Škvor, Jiří; Nezbeda, Ivo

    2015-04-01

    Exposing aqueous surfaces to a strong electric field gives rise to interesting phenomena, such as formation of a floating water bridge or an eruption of a jet in electrospinning. In an effort to account for the phenomena at the molecular level, we performed molecular dynamics simulations using several protocols on both pure water and aqueous solutions of sodium chloride subjected to an electrostatic field. All simulations consistently point to the same mechanisms which govern the rearrangement of the originally planar surface. The results show that the phenomena are primarily governed by an orientational reordering of the water molecules driven by the applied field. It is demonstrated that, for pure water, a sufficiently strong field yields a columnar structure parallel to the field with an anisotropic arrangement of the water molecules with their dipole moments aligned along the applied field not only in the surface layer but over the entire cross section of the column. Nonetheless, the number of hydrogen bonds per molecule does not seem to be affected by the field regardless of its strength and molecule's orientation. In the electrolyte solutions, the ionic charge is able to overcome the effect of the external field tending to arrange the water molecules radially in the first coordination shell of an ion. The ion-water interaction interferes thus with the water-electric field interaction, and the competition between these two forces (i.e., strength of the field versus concentration) provides the key mechanism determining the stability of the observed structures.

  11. Assessing the cleanliness of surfaces: Innovative molecular approaches vs. standard spore assays

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, M.; Duc, M.T. La; Probst, A.; Vaishampayan, P.; Stam, C.; Benardini, J.N.; Piceno, Y.M.; Andersen, G.L.; Venkateswaran, K.

    2011-04-01

    A bacterial spore assay and a molecular DNA microarray method were compared for their ability to assess relative cleanliness in the context of bacterial abundance and diversity on spacecraft surfaces. Colony counts derived from the NASA standard spore assay were extremely low for spacecraft surfaces. However, the PhyloChip generation 3 (G3) DNA microarray resolved the genetic signatures of a highly diverse suite of microorganisms in the very same sample set. Samples completely devoid of cultivable spores were shown to harbor the DNA of more than 100 distinct microbial phylotypes. Furthermore, samples with higher numbers of cultivable spores did not necessarily give rise to a greater microbial diversity upon analysis with the DNA microarray. The findings of this study clearly demonstrated that there is not a statistically significant correlation between the cultivable spore counts obtained from a sample and the degree of bacterial diversity present. Based on these results, it can be stated that validated state-of-the-art molecular techniques, such as DNA microarrays, can be utilized in parallel with classical culture-based methods to further describe the cleanliness of spacecraft surfaces.

  12. Strain effect on the adsorption, diffusion, and molecular dissociation of hydrogen on Mg (0001) surface

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Huaping; Wang, Caizhuang; Yao, Yongxin; Hupalo, Myron [Ames Laboratory, USDOE, Ames, Iowa 50011 (United States); Wang, Yangang [Ames Laboratory, USDOE, Ames, Iowa 50011 (United States); Supercomputing Center of Computer Network Information Center, CAS, Beijing 100190 (China); McDougall, Dan; Tringides, Michael; Ho, Kaiming [Ames Laboratory, USDOE, Ames, Iowa 50011 (United States); Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011 (United States)

    2013-12-14

    The adsorption, diffusion, and molecular dissociation of hydrogen on the biaxially strained Mg (0001) surface have been systematically investigated by the first principle calculations based on density functional theory. When the strain changes from the compressive to tensile state, the adsorption energy of H atom linearly increases while its diffusion barrier linearly decreases oppositely. The dissociation barrier of H{sub 2} molecule linearly reduces in the tensile strain region. Through the chemical bonding analysis including the charge density difference, the projected density of states and the Mulliken population, the mechanism of the strain effect on the adsorption of H atom and the dissociation of H{sub 2} molecule has been elucidated by an s-p charge transfer model. With the reduction of the orbital overlap between the surface Mg atoms upon the lattice expansion, the charge transfers from p to s states of Mg atoms, which enhances the hybridization of H s and Mg s orbitals. Therefore, the bonding interaction of H with Mg surface is strengthened and then the atomic diffusion and molecular dissociation barriers of hydrogen decrease accordingly. Our works will be helpful to understand and to estimate the influence of the lattice deformation on the performance of Mg-containing hydrogen storage materials.

  13. Surface-directed molecular assembly of pentacene on monolayer graphene for high-performance organic transistors.

    Science.gov (United States)

    Lee, Wi Hyoung; Park, Jaesung; Sim, Sung Hyun; Lim, Soojin; Kim, Kwang S; Hong, Byung Hee; Cho, Kilwon

    2011-03-30

    Organic electronic devices that use graphene electrodes have received considerable attention because graphene is regarded as an ideal candidate electrode material. Transfer and lithographic processes during fabrication of patterned graphene electrodes typically leave polymer residues on the graphene surfaces. However, the impact of these residues on the organic semiconductor growth mechanism on graphene surface has not been reported yet. Here, we demonstrate that polymer residues remaining on graphene surfaces induce a stand-up orientation of pentacene, thereby controlling pentacene growth such that the molecular assembly is optimal for charge transport. Thus, pentacene field-effect transistors (FETs) using source/drain monolayer graphene electrodes with polymer residues show a high field-effect mobility of 1.2 cm(2)/V s. In contrast, epitaxial growth of pentacene having molecular assembly of lying-down structure is facilitated by π-π interaction between pentacene and the clean graphene electrode without polymer residues, which adversely affects lateral charge transport at the interface between electrode and channel. Our studies provide that the obtained high field-effect mobility in pentacene FETs using monolayer graphene electrodes arises from the extrinsic effects of polymer residues as well as the intrinsic characteristics of the highly conductive, ultrathin two-dimensional monolayer graphene electrodes.

  14. Atomic and molecular adsorption on transition-metal carbide (111) surfaces from density-functional theory: a trend study of surface electronic factors

    DEFF Research Database (Denmark)

    Vojvodic, Aleksandra; Ruberto, C.; Lundqvist, Bengt

    2010-01-01

    ) surfaces. The spatial extent and the dangling bond nature of these SRs are supported by real-space analyses of the calculated Kohn-Sham wavefunctions. Then, atomic and molecular adsorption energies, geometries, and charge transfers are presented. An analysis of the adsorbate-induced changes in surface DOSs...

  15. Challenging the Science Curriculum Paradigm: Teaching Primary Children Atomic-Molecular Theory

    Science.gov (United States)

    Haeusler, Carole; Donovan, Jennifer

    2017-11-01

    Solutions to global issues demand the involvement of scientists, yet concern exists about retention rates in science as students pass through school into University. Young children are curious about science, yet are considered incapable of grappling with abstract and microscopic concepts such as atoms, sub-atomic particles, molecules and DNA. School curricula for primary (elementary) aged children reflect this by their limitation to examining only what phenomena are without providing any explanatory frameworks for how or why they occur. This research challenges the assumption that atomic-molecular theory is too difficult for young children, examining new ways of introducing atomic theory to 9 year olds and seeks to verify their efficacy in producing genuine learning in the participants. Early results in three cases in different schools indicate these novel methods fostered further interest in science, allowed diverse children to engage and learn aspects of atomic theory, and satisfied the children's desire for intellectual challenge. Learning exceeded expectations as demonstrated in the post-interview findings. Learning was also remarkably robust, as demonstrated in two schools 8 weeks after the intervention and, in one school, 1 year after their first exposure to ideas about atoms, elements and molecules.

  16. Laser surface modification of ultra-high-molecular-weight polyethylene (UHMWPE) for biomedical applications

    International Nuclear Information System (INIS)

    Riveiro, A.; Soto, R.; Val, J. del; Comesaña, R.; Boutinguiza, M.; Quintero, F.; Lusquiños, F.; Pou, J.

    2014-01-01

    Ultra-high-molecular-weight polyethylene (UHMWPE) is a synthetic polymer used for biomedical applications because of its high impact resistance, ductility and stability in contact with physiological fluids. Therefore, this material is being used in human orthopedic implants such as total hip or knee replacements. Surface modification of this material relates to changes on its chemistry, microstructure, roughness, and topography, all influencing its biological response. Surface treatment of UHMWPE is very difficult due to its high melt viscosity. This work presents a systematic approach to discern the role of different laser wavelengths (λ = 1064, 532, and 355 nm) on the surface modification of carbon coated UHMWPE samples. Influence of laser processing conditions (irradiance, pulse frequency, scanning speed, and spot overlapping) on the surface properties of this material was determined using an advanced statistical planning of experiments. A full factorial design of experiments was used to find the main effects of the processing parameters. The obtained results indicate the way to maximize surface properties which largely influence cell–material interaction.

  17. Laser surface modification of ultra-high-molecular-weight polyethylene (UHMWPE) for biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Riveiro, A., E-mail: ariveiro@uvigo.es [Applied Physics Department, University of Vigo, ETSII, Lagoas-Marcosende, 9, Vigo 36310 (Spain); Centro Universitario de la Defensa, Escuela Naval Militar, Plaza de España 2, 36920 Marín (Spain); Soto, R.; Val, J. del; Comesaña, R.; Boutinguiza, M.; Quintero, F.; Lusquiños, F.; Pou, J. [Applied Physics Department, University of Vigo, ETSII, Lagoas-Marcosende, 9, Vigo 36310 (Spain)

    2014-05-01

    Ultra-high-molecular-weight polyethylene (UHMWPE) is a synthetic polymer used for biomedical applications because of its high impact resistance, ductility and stability in contact with physiological fluids. Therefore, this material is being used in human orthopedic implants such as total hip or knee replacements. Surface modification of this material relates to changes on its chemistry, microstructure, roughness, and topography, all influencing its biological response. Surface treatment of UHMWPE is very difficult due to its high melt viscosity. This work presents a systematic approach to discern the role of different laser wavelengths (λ = 1064, 532, and 355 nm) on the surface modification of carbon coated UHMWPE samples. Influence of laser processing conditions (irradiance, pulse frequency, scanning speed, and spot overlapping) on the surface properties of this material was determined using an advanced statistical planning of experiments. A full factorial design of experiments was used to find the main effects of the processing parameters. The obtained results indicate the way to maximize surface properties which largely influence cell–material interaction.

  18. Effects of surface proteins and lipids on molecular structure, thermal properties, and enzymatic hydrolysis of rice starch

    Directory of Open Access Journals (Sweden)

    Pan HU

    Full Text Available Abstract Rice starches with different amylose contents were treated with sodium dodecyl sulfate (SDS to deplete surface proteins and lipids, and the changes in molecular structure, thermal properties, and enzymatic hydrolysis were evaluated. SDS treatment did not significantly change the molecular weight distribution, crystalline structure, short-range ordered degree, and gelatinization properties of starch, but significantly altered the pasting properties and increased the swelling power of starch. The removal of surface proteins and lipids increased the enzymatic hydrolysis and in vitro digestion of starch. The influences of removing surface proteins and lipids from starch on swelling power, pasting properties, and enzymatic hydrolysis were different among the various starches because of the differences in molecular structures of different starch styles. The aforementioned results indicated that removing the surface proteins and lipids from starch did not change the molecular structure but had significant effects on some functional properties.

  19. Mapping the Diffusion Potential of a Reconstructed Au(111) Surface at Nanometer Scale with 2D Molecular Gas

    International Nuclear Information System (INIS)

    Yan Shi-Chao; Xie Nan; Gong Hui-Qi; Guo Yang; Shan Xin-Yan; Lu Xing-Hua; Sun Qian

    2012-01-01

    The adsorption and diffusion behaviors of benzene molecules on an Au(111) surface are investigated by low-temperature scanning tunneling microscopy. A herringbone surface reconstruction of the Au(111) surface is imaged with atomic resolution, and significantly different behaviors are observed for benzene molecules adsorbed on step edges and terraces. The electric field induced modification in the molecular diffusion potential is revealed with a 2D molecular gas model, and a new method is developed to map the diffusion potential over the reconstructed Au(111) surface at the nanometer scale. (condensed matter: structure, mechanical and thermal properties)

  20. Reaction probability of molecular deuterium with a disordered InSb (110) surface

    International Nuclear Information System (INIS)

    Wolf, B.; Zehe, A.

    1987-01-01

    A detailed experimental analysis of the interaction of molecular deuterium with sputter-damaged InSb surfaces by the aid of SIMS is given. The sticking probability of D 2 and its transformation to a chemisorbed state resulting in InD + signals in SIMS measurements can be determined by adsorption experimens both with and without a hot tungsten filament. The calculated sticking probability of D 2 = 2 x 10 -4 is at least three orders of magnitude higher than the known-value for a cleavage plane of InSb

  1. Pulsed melting of silicon (111) and (100) surfaces simulated by molecular dynamics

    International Nuclear Information System (INIS)

    Abraham, F.F.; Broughton, J.Q.

    1986-01-01

    The pulsed heating of Si (100) and (111) surfaces has been simulated by molecular dynamics. The (111) crystal-melt interface propagates by layer-by-layer growth whereas the (100) interface grows in a continuous fashion. The equilibrium crystal-melt interface is sharp for the (111) orientation and broad for the (100) orientation. These simulations are the first use of nonpairwise potentials to study interfaces between condensed phases, and the results support models of interfaces which heretofore had to be deduced from indirect experimental information

  2. Incipient plasticity and indentation response of MgO surfaces using molecular dynamics

    Science.gov (United States)

    Tran, Anh-Son; Hong, Zheng-Han; Chen, Ming-Yuan; Fang, Te-Hua

    2018-05-01

    The mechanical characteristics of magnesium oxide (MgO) based on nanoindentation are studied using molecular dynamics (MD) simulation. The effects of indenting speed and temperature on the structural deformation and loading-unloading curve are investigated. Results show that the strained surface of the MgO expands to produce a greater relaxation of atoms in the surroundings of the indent. The dislocation propagation and pile-up for MgO occur more significantly with the increasing temperature from 300 K to 973 K. In addition, with increasing temperature, the high strained atoms with a great perturbation appearing at the groove location.

  3. Wetting kinetics of nanodroplets on lyophilic nanopillar-arrayed surfaces: A molecular dynamics study

    Science.gov (United States)

    Zong, Diyuan; Yang, Zhen; Duan, Yuanyuan

    2017-10-01

    Wetting kinetics of water droplets on substrates with lyophilic nanopillars was investigated using molecular dynamics simulations. Early spreading of the droplet is hindered by the nanopillars because of the penetration of the liquid which induce an extra dissipation in the droplet. Droplet spreading is mainly controlled by liquid viscosity and surface tension and not dependent on solid wettability. Propagation of the fringe film is hindered by the enhanced solid wettability because of the energy barrier introduced by the interaction between water molecules and nanopillars which increase with solid wettability.

  4. Molecular pathological epidemiology: new developing frontiers of big data science to study etiologies and pathogenesis.

    Science.gov (United States)

    Hamada, Tsuyoshi; Keum, NaNa; Nishihara, Reiko; Ogino, Shuji

    2017-03-01

    Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality. This MPE approach can provide etiologic and pathogenic insights, potentially contributing to precision medicine for personalized prevention and treatment. Although breast, prostate, lung, and colorectal cancers have been among the most commonly studied diseases, the MPE approach can be used to study any disease. In addition to molecular features, host immune status and microbiome profile likely affect a disease process, and thus serve as informative biomarkers. As such, further integration of several disciplines into MPE has been achieved (e.g., pharmaco-MPE, immuno-MPE, and microbial MPE), to provide novel insights into underlying etiologic mechanisms. With the advent of high-throughput sequencing technologies, available genomic and epigenomic data have expanded dramatically. The MPE approach can also provide a specific risk estimate for each disease subgroup, thereby enhancing the impact of genome-wide association studies on public health. In this article, we present recent progress of MPE, and discuss the importance of accounting for the disease heterogeneity in the era of big-data health science and precision medicine.

  5. New Material Development for Surface Layer and Surface Technology in Tribology Science to Improve Energy Efficiency

    International Nuclear Information System (INIS)

    Ismail, R.; Tauviqirrahman, M.; Jamari; Schipper, D. J.

    2009-01-01

    This paper reviews the development of new material and surface technology in tribology and its contribution to energy efficiency. Two examples of the economic benefits, resulted from the optimum tribology in the transportation sector and the manufacturing industry are discussed. The new materials are proposed to modify the surface property by laminating the bulk material with thin layer/coating. Under a suitable condition, the thin layer on a surface can provide a combination of good wear, a low friction and corrosion resistance for the mechanical components. The innovation in layer technology results molybdenum disulfide (MoS2), diamond like carbon (DLC), cubic boron nitride (CBN) and diamond which perform satisfactory outcome. The application of the metallic coatings to carbon fibre reinforced polymer matrix composites (CFRP) has the capacity to provide considerable weight and power savings for many engineering components. The green material for lubricant and additives such as the use of sunflower oil which possesses good oxidation resistance and the use of mallee leaves as bio‐degradable solvent are used to answer the demand of the environmentally friendly material with good performance. The tribology research implementation for energy efficiency also touches the simple things around us such as: erasing the laser‐print in a paper with different abrasion techniques. For the technology in the engineering surface, the consideration for generating the suitable surface of the components in running‐in period has been discussed in order to prolong the components life and reduce the machine downtime. The conclusion, tribology can result in reducing manufacturing time, reducing the maintenance requirements, prolonging the service interval, improving durability, reliability and mechanical components life, and reducing harmful exhaust emission and waste. All of these advantages will increase the energy efficiency and the economic benefits.

  6. New Material Development for Surface Layer and Surface Technology in Tribology Science to Improve Energy Efficiency

    Science.gov (United States)

    Ismail, R.; Tauviqirrahman, M.; Jamari, Jamari; Schipper, D. J.

    2009-09-01

    This paper reviews the development of new material and surface technology in tribology and its contribution to energy efficiency. Two examples of the economic benefits, resulted from the optimum tribology in the transportation sector and the manufacturing industry are discussed. The new materials are proposed to modify the surface property by laminating the bulk material with thin layer/coating. Under a suitable condition, the thin layer on a surface can provide a combination of good wear, a low friction and corrosion resistance for the mechanical components. The innovation in layer technology results molybdenum disulfide (MoS2), diamond like carbon (DLC), cubic boron nitride (CBN) and diamond which perform satisfactory outcome. The application of the metallic coatings to carbon fibre reinforced polymer matrix composites (CFRP) has the capacity to provide considerable weight and power savings for many engineering components. The green material for lubricant and additives such as the use of sunflower oil which possesses good oxidation resistance and the use of mallee leaves as bio-degradable solvent are used to answer the demand of the environmentally friendly material with good performance. The tribology research implementation for energy efficiency also touches the simple things around us such as: erasing the laser-print in a paper with different abrasion techniques. For the technology in the engineering surface, the consideration for generating the suitable surface of the components in running-in period has been discussed in order to prolong the components life and reduce the machine downtime. The conclusion, tribology can result in reducing manufacturing time, reducing the maintenance requirements, prolonging the service interval, improving durability, reliability and mechanical components life, and reducing harmful exhaust emission and waste. All of these advantages will increase the energy efficiency and the economic benefits.

  7. Mars' surface radiation environment measured with the Mars science laboratory's curiosity rover

    NARCIS (Netherlands)

    Hassler, D.M.; Zeitlin, C.; Wimmer-Schweingruber, R.F.; Ehresmann, B.; Rafkin, S.; Eigenbrode, J.L.; Brinza, D.E.; Weigle, G.; Böttcher, S.; Böhm, E.; Burmeister, S.; Guo, J.; Köhler, J.; Martin, C.; Reitz, G.; Cucinotta, F.A.; Kim, M.-H.; Grinspoon, D.; Bullock, M.A.; Posner, A.; Gómez-Elvira, J.; Vasavada, A.; Grotzinger, J.P.; MSL Science Team, the|info:eu-repo/dai/nl/292012217

    2014-01-01

    The Radiation Assessment Detector (RAD) on the Mars Science Laboratory’s Curiosity rover began making detailed measurements of the cosmic ray and energetic particle radiation environment on the surface of Mars on 7 August 2012. We report and discuss measurements of the absorbed dose and dose

  8. Isolate extended state in the DNA molecular transistor with surface interaction

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Le, E-mail: wang_le917@gs.zzu.edu.cn; Qin, Zhi-Jie

    2016-02-01

    The field effect characteristic of a DNA molecular device is investigated in a tight binding model with binary disorder and side site correlation. Using the transfer-matrix method and Landauer–Büttiker theory, we find that the system has isolated extended state that is irrespective of the DNA sequence and can be modulated by the gate voltage. When the gate voltage reaches some proper value, the isolated extended state appears at the Fermi level of the system and the long range charge transport is greatly enhanced. We attribute this phenomenon to the combination of the external field, the surface interaction, and the intrinsic disorder of DNA. The result is a generic feature of the nanowire with binary disorder and surface interaction.

  9. Molecular dynamics study of Pb-substituted Cu(1 0 0) surface layers

    Energy Technology Data Exchange (ETDEWEB)

    Evangelakis, G.A. [Department of Physics, University of Ioannina, PO Box 1186, Ioannina 45110 (Greece); Pontikis, V., E-mail: Vassilis.pontikis@cea.f [Laboratoire des Solides Irradies, CEA-DRECAM, 91191 Gif-sur-Yvette Cedex (France)

    2009-08-26

    Using molecular dynamics (MD) and phenomenological n-body potentials from the literature, we have studied the structure of the uppermost layers of low-index surfaces in copper after partial substitution of copper by lead atoms at randomly selected sites. We found that lead atoms substituting copper strongly perturb the positions of nearest and of next-nearest neighbors thus triggering the setup of a disordered, nanometer-thick amorphous-like surface layer. Equilibrium atomic density profiles, computed along the [1 0 0] crystallographic direction, show that amorphous overlayers are largely metastable whereas the system displays a structured compositional profile of lead segregating at the interfaces. Similarities between our results and experimental findings are briefly discussed.

  10. Molecular dynamics study of Pb-substituted Cu(1 0 0) surface layers

    International Nuclear Information System (INIS)

    Evangelakis, G.A.; Pontikis, V.

    2009-01-01

    Using molecular dynamics (MD) and phenomenological n-body potentials from the literature, we have studied the structure of the uppermost layers of low-index surfaces in copper after partial substitution of copper by lead atoms at randomly selected sites. We found that lead atoms substituting copper strongly perturb the positions of nearest and of next-nearest neighbors thus triggering the setup of a disordered, nanometer-thick amorphous-like surface layer. Equilibrium atomic density profiles, computed along the [1 0 0] crystallographic direction, show that amorphous overlayers are largely metastable whereas the system displays a structured compositional profile of lead segregating at the interfaces. Similarities between our results and experimental findings are briefly discussed.

  11. Surface electronic structure and molecular orientation of poly(9-vinylcarbazole) thin film: ARUPS and NEXAFS

    CERN Document Server

    Okudaira, K K; Hasegawa, S; Ishii, H; Azuma, Y; Imamura, M; Shimada, H; Seki, K; Ueno, N

    2001-01-01

    The molecular orientation at the surfaces of poly(9-vinylcarbazole) (PvCz) thin films was studied by angle-resolved ultraviolet photoelectron spectroscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The observed take-off angle (theta) dependence of photoelectron intensities from top pi band peaks clearly at larger theta than the calculated one for the three-dimensional isotropic random orientation model. The results indicate that there are more pendant groups with large tilt angles than the three-dimensional isotropic random orientation model, which is in good agreement with the result obtained from NEXAFS spectroscopy. The surface electronic states of PvCz may be rather dominated by sigma(C-H) states at the pendant carbazole group than pi states

  12. Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.

    Science.gov (United States)

    Kihara, Daisuke; Sael, Lee; Chikhi, Rayan; Esquivel-Rodriguez, Juan

    2011-09-01

    The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions of protein structures. We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. The 3DZD is a series expansion of mathematical three-dimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series. A strong advantage of the 3DZD is that it is invariant to rotation of target object to be represented. These two characteristics of the 3DZD allow rapid comparison of surface shapes, which is sufficient for real-time structure database screening. In this article, we review various applications of the 3DZD, which have been recently proposed.

  13. Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research

    Directory of Open Access Journals (Sweden)

    Richard J. Gillams

    2018-05-01

    Full Text Available An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.

  14. Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research.

    Science.gov (United States)

    Gillams, Richard J; Jia, Tony Z

    2018-05-08

    An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.

  15. Molecular Environmental Science: An Assessment of Research Accomplishments, Available Synchrotron Radiation Facilities, and Needs

    International Nuclear Information System (INIS)

    Brown, G

    2004-01-01

    Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutants at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and their reactions with

  16. Molecular Environmental Science: An Assessment of Research Accomplishments, Available Synchrotron Radiation Facilities, and Needs

    Energy Technology Data Exchange (ETDEWEB)

    Brown, G

    2004-02-05

    Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutants at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and

  17. Molecular environmental science : an assessment of research accomplishments, available synchrotron radiation facilities, and needs.

    Energy Technology Data Exchange (ETDEWEB)

    Brown, G. E., Jr.; Sutton, S. R.; Bargar, J. R.; Shuh, D. K.; Fenter, P. A.; Kemner, K. M.

    2004-10-20

    Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutants at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and

  18. Surface force analysis of molecular interfacial interactions of proteins and lipids with polymeric biomaterials

    International Nuclear Information System (INIS)

    Hamilton-Brown, P.; Griesser, H.J.; Meagher, L.

    2001-01-01

    Full text: Adverse biological responses to biomedical devices are often caused by the irreversible accumulation of biological deposits onto the surfaces of devices. Such deposits cause blocking of artificial blood vessels, fibrous encapsulation of soft tissue regenerative devices, 'fouling' of contact lenses, secondary cataracts on intraocular lenses, and other undesirable events that interfere with the intended functions of biomedical devices. The formation of deposits is triggered by an initial stage in which various proteins and lipids rapidly adsorb onto the synthetic material surface; further biological molecules and ultimately cellular entities (e.g., host cells, bacteria) then settle onto the initial adsorbed layer. Hence, to avoid or control the accumulation of biological deposits, molecular understanding is required of the initial adsorption processes. Such adsorption is caused by attractive interfacial forces, which we are characterising by the use of a novel method. In the present study, polymeric thin film coatings, polyethylene oxide (PEO), and polysaccharide coatings have been analysed in terms of their surface forces and the ensuing propensity for protein and lipid adsorption. Interfacial forces are measured using atomic force microscopy (AFM) with a colloid-modified tip in a liquid cell using solutions of physiological pH and ionic strength. The chemical composition and uniformity of the coatings was characterised by X-ray Photon Spectroscopy (XPS). For a polymeric solid coating, repulsive forces have been measured against a silica colloid probe, and the dominant surface force is electrostatic. For the highly hydrated, 'soft' PEO and polysaccharide coatings, on the other hand, steric/entropic forces are also significant and contribute to interfacial interactions with proteins and lipids. In one system we have observed a time dependence of the electrostatic surface potential, which affects interaction with charged proteins. Force measurements were

  19. Earth System Science at NASA: Teleconnections Between Sea Surface Temperature and Epidemics in Africa

    Science.gov (United States)

    Meeson, Blanche W.

    2000-01-01

    The research carried out in the Earth Sciences in NASA and at NASA's Goddard Space Flight Center will be the focus of the presentations. In addition, one research project that links sea surface temperature to epidemics in Africa will be highlighted. At GSFC research interests span the full breath of disciplines in Earth Science. Branches and research groups focus on areas as diverse as planetary geomagnetics and atmospheric chemistry. These organizations focus on atmospheric sciences (atmospheric chemistry, climate and radiation, regional processes, atmospheric modeling), hydrological sciences (snow, ice, oceans, and seasonal-to-interannual prediction), terrestrial physics (geology, terrestrial biology, land-atmosphere interactions, geophysics), climate modeling (global warming, greenhouse gases, climate change), on sensor development especially using lidar and microwave technologies, and on information technologies, that enable support of scientific and technical research.

  20. Molecular analysis of petroleum derived compounds that adsorb onto gas hydrate surfaces

    International Nuclear Information System (INIS)

    Borgund, Anna E.; Hoiland, Sylvi; Barth, Tanja; Fotland, Per; Askvik, Kjell M.

    2009-01-01

    Field observations have shown that some streams of water, gas and crude oil do not form gas hydrate plugs during petroleum production even when operating within thermodynamic conditions for hydrate formation. Also, when studied under controlled laboratory conditions, some oils are found to form hydrate dispersed systems whereas others form plugs. Oils with low tendency to form hydrate plugs are believed to contain natural hydrate plug inhibiting components (NICs) that adsorb onto the hydrate surface, making them less water-wet and preventing the particles from agglomerating into large hydrate clusters. The molecular structure of the NICs is currently unknown. In this work, hydrate adsorbing components were extracted from crude oils using freon hydrates as an extraction phase. The fractions were found to be enriched in polar material, and more polar material is associated with hydrates generated in biodegraded crude oils than in non-biodegraded oils. Various fractionation schemes and analytical techniques have been applied in the search for molecular characterisation. The average molecular weights were found to be approximately 500 g/mole. GC-MS chromatograms show a large UCM (Unresolved Complex Mixture). Thus, GC-MS has a limited potential for identification of compounds. A commercial biosurfactant was used as a model compound in the search for similar structures in the extracts. The results from analysis of the hydrate adsorbing components suggest that the type and structure are more important for hydrate morphology than the amount of material adsorbed.

  1. Molecular self-assembly in substituted alanine derivatives: XRD, Hirshfeld surfaces and DFT studies

    Science.gov (United States)

    Rajalakshmi, Periasamy; Srinivasan, Navaneethakrishnan; Sivaraman, Gandhi; Razak, Ibrahim Abdul; Rosli, Mohd Mustaqim; Krishnakumar, Rajaputi Venkatraman

    2014-06-01

    The molecular assemblage in the crystal structures of three modified chiral amino acids, two of which are isomeric D- and L-pairs boc-L-benzothienylalanine (BLA), boc-D-benzothienylalanine (BDA) and the other boc-D-naphthylalanine (NDA) differing from this pair very slightly in the chemical modification introduced, is accurately described. The aggregation of amino acid molecules is similar in all the crystals and may be described as a twisted double helical ladder in which two complementary long helical chains formed through O-H⋯O hydrogen bonds are interconnected through the characteristic head-to-tail N-H⋯O hydrogen bonds. Thus the molecular aggregation enabled through classical hydrogen bonds may be regarded as a mimic of the characteristic double helical structure of DNA. Also, precise structural information involving these amino acid molecules with lower symmetry exhibiting higher trigonal symmetry in their self-assembly is expected to throw light on the nature and strength of intermolecular interactions and their role in self-assembly of molecular aggregates, which are crucial in developing new or at least supplement existing crystal engineering strategies. Single crystal X-ray analysis and their electronic structures were calculated at the DFT level with a detailed analysis of Hirshfeld surfaces and fingerprint plots facilitating a comparison of intermolecular interactions in building different supramolecular architectures.

  2. Photoresponsive surface molecularly imprinted polymer on ZnO nanorods for uric acid detection in physiological fluids

    International Nuclear Information System (INIS)

    Tang, Qian; Li, Zai-yong; Wei, Yu-bo; Yang, Xia; Liu, Lan-tao; Gong, Cheng-bin; Ma, Xue-bing; Lam, Michael Hon-wah; Chow, Cheuk-fai

    2016-01-01

    A photoresponsive surface molecularly imprinted polymer for uric acid in physiological fluids was fabricated through a facile and effective method using bio-safe and biocompatible ZnO nanorods as a support. The strategy was carried out by introducing double bonds on the surface of the ZnO nanorods with 3-methacryloxypropyltrimethoxysilane. The surface molecularly imprinted polymer on ZnO nanorods was then prepared by surface polymerization using uric acid as template, water-soluble 5-[(4-(methacryloyloxy)phenyl)diazenyl]isophthalic acid as functional monomer, and triethanolamine trimethacryl ester as cross-linker. The surface molecularly imprinted polymer on ZnO nanorods showed good photoresponsive properties, high recognition ability, and fast binding kinetics toward uric acid, with a dissociation constant of 3.22 × 10"−"5 M in aqueous NaH_2PO_4 buffer at pH = 7.0 and a maximal adsorption capacity of 1.45 μmol g"−"1. Upon alternate irradiation at 365 and 440 nm, the surface molecularly imprinted polymer on ZnO nanorods can quantitatively uptake and release uric acid. - Highlights: • Novel surface molecularly imprinted polymer on ZnO nanorods was synthesized. • ZnO-SMIP showed good selectivity toward uric acid in physiological fluids. • ZnO-SMIP displayed good photoresponsive properties.

  3. Photoresponsive surface molecularly imprinted polymer on ZnO nanorods for uric acid detection in physiological fluids

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Qian [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Department of Science and Environmental Studies, The Hong Kong Institute of Education (Hong Kong); Li, Zai-yong; Wei, Yu-bo; Yang, Xia; Liu, Lan-tao [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Gong, Cheng-bin, E-mail: gongcbtq@swu.edu.cn [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Ma, Xue-bing [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Lam, Michael Hon-wah [Department of Biology and Chemistry, City University of Hong Kong (Hong Kong); Chow, Cheuk-fai, E-mail: cfchow@ied.edu.hk [Department of Science and Environmental Studies, The Hong Kong Institute of Education (Hong Kong)

    2016-09-01

    A photoresponsive surface molecularly imprinted polymer for uric acid in physiological fluids was fabricated through a facile and effective method using bio-safe and biocompatible ZnO nanorods as a support. The strategy was carried out by introducing double bonds on the surface of the ZnO nanorods with 3-methacryloxypropyltrimethoxysilane. The surface molecularly imprinted polymer on ZnO nanorods was then prepared by surface polymerization using uric acid as template, water-soluble 5-[(4-(methacryloyloxy)phenyl)diazenyl]isophthalic acid as functional monomer, and triethanolamine trimethacryl ester as cross-linker. The surface molecularly imprinted polymer on ZnO nanorods showed good photoresponsive properties, high recognition ability, and fast binding kinetics toward uric acid, with a dissociation constant of 3.22 × 10{sup −5} M in aqueous NaH{sub 2}PO{sub 4} buffer at pH = 7.0 and a maximal adsorption capacity of 1.45 μmol g{sup −1}. Upon alternate irradiation at 365 and 440 nm, the surface molecularly imprinted polymer on ZnO nanorods can quantitatively uptake and release uric acid. - Highlights: • Novel surface molecularly imprinted polymer on ZnO nanorods was synthesized. • ZnO-SMIP showed good selectivity toward uric acid in physiological fluids. • ZnO-SMIP displayed good photoresponsive properties.

  4. Preparation and recognition of surface molecularly imprinted core-shell microbeads for protein in aqueous solutions

    International Nuclear Information System (INIS)

    Lu Yan; Yan Changling; Gao Shuyan

    2009-01-01

    In this paper, a surface molecular imprinting technique was reported for preparing core-shell microbeads of protein imprinting, and bovine hemoglobin or bovine serum albumin were used as model proteins for studying the imprinted core-shell microbeads. 3-Aminophenylboronic acid (APBA) was polymerized onto the surface of polystyrene microbead in the presence of the protein templates to create protein-imprinted core-shell microbeads. The various samples were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) methods. The effect of pH on rebinding of the template hemoglobin, the specific binding and selective recognition were studied for the imprinted microbeads. The results show that the bovine hemoglobin-imprinted core-shell microbeads were successfully created. The shell was a sort of imprinted thin films with porous structure and larger surface areas. The imprinted microbeads have good selectivity for templates and high stability. Due to the recognition sites locating at or closing to the surface, these imprinted microbeads have good property of mass-transport. Unfortunately, the imprint technology was not successfully applied to imprinting bovine serum albumin (BSA).

  5. Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

    International Nuclear Information System (INIS)

    Imran, Muhammad; Hussain, Fayyaz; Ullah, Hafeez; Ahmad, Ejaz; Rashid, Muhammad; Ismail, Muhammad; Cai, Yongqing; Javid, M Arshad; Ahmad, S A

    2016-01-01

    Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results. (paper)

  6. State-to-state inelastic and reactive molecular beam scattering from surfaces

    International Nuclear Information System (INIS)

    Lykke, K.R.; Kay, B.D.

    1990-01-01

    Resonantly enhanced multiphoton ionization (REMPI) laser spectroscopic and molecular beam-surface scattering techniques are coupled to study inelastic and reactive gas-surface scattering with state-to-state specificity. Rotational, vibrational, translational and angular distributions have been measured for the inelastic scattering of HCI and N 2 from Au(111). In both cases the scattering is direct-inelastic in nature and exhibits interesting dynamical features such as rotational rainbow scattering. In an effort to elucidate the dynamics of chemical reactions occurring on surfaces we have extended our quantum-resolved scattering studies to include the reactive scattering of a beam of gas phase H-atoms from a chlorinated metal surface M-CI. The nascent rotational and vibrational distributions of the HCI product are determined using REMPI. The thermochemistry for this reaction on Au indicates that the product formation proceeding through chemisorbed H-atoms is slightly endothermic while direct reaction of a has phase H-atom with M-CI is highly exothermic (ca. 50 kcal/mole). Details of the experimental techniques, results and implications regarding the scattering dynamics are discussed. 55 ref., 8 fig

  7. Arrays of Molecular Rotors with Triptycene Stoppers: Surface Inclusion in Hexagonal Tris(o-phenylenedioxy)cyclotriphosphazene.

    Science.gov (United States)

    Kaleta, Jiří; Dron, Paul I; Zhao, Ke; Shen, Yongqiang; Císařová, Ivana; Rogers, Charles T; Michl, Josef

    2015-06-19

    A new generation of rod-shaped dipolar molecular rotors designed for controlled insertion into channel arrays in the surface of hexagonal tris(o-phenylenedioxy)cyclotriphosphazene (TPP) has been designed and synthesized. Triptycene is used as a stopper intended to prevent complete insertion, forcing the formation of a surface inclusion. Two widely separated (13)C NMR markers are present in the shaft for monitoring the degree of insertion. The structure of the two-dimensional rotor arrays contained in these surface inclusions was examined by solid-state NMR and X-ray powder diffraction. The NMR markers and the triptycene stopper functioned as designed, but half of the guest molecules were not inserted as deeply into the TPP channels as the other half. As a result, the dipolar rotators were distributed equally in two planes parallel to the crystal surface instead of being located in a single plane as would be required for ferroelectricity. Dielectric spectroscopy revealed rotational barriers of ∼4 kcal/mol but no ferroelectric behavior.

  8. Preparation and recognition of surface molecularly imprinted core-shell microbeads for protein in aqueous solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lu Yan, E-mail: yanlu2001@sohu.com [College of Chemistry and Environmental Science, Henan Normal University, 46 Jlanshe Road, Xinxiang 453007 (China); Yan Changling; Gao Shuyan [College of Chemistry and Environmental Science, Henan Normal University, 46 Jlanshe Road, Xinxiang 453007 (China)

    2009-04-01

    In this paper, a surface molecular imprinting technique was reported for preparing core-shell microbeads of protein imprinting, and bovine hemoglobin or bovine serum albumin were used as model proteins for studying the imprinted core-shell microbeads. 3-Aminophenylboronic acid (APBA) was polymerized onto the surface of polystyrene microbead in the presence of the protein templates to create protein-imprinted core-shell microbeads. The various samples were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) methods. The effect of pH on rebinding of the template hemoglobin, the specific binding and selective recognition were studied for the imprinted microbeads. The results show that the bovine hemoglobin-imprinted core-shell microbeads were successfully created. The shell was a sort of imprinted thin films with porous structure and larger surface areas. The imprinted microbeads have good selectivity for templates and high stability. Due to the recognition sites locating at or closing to the surface, these imprinted microbeads have good property of mass-transport. Unfortunately, the imprint technology was not successfully applied to imprinting bovine serum albumin (BSA).

  9. Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

    Energy Technology Data Exchange (ETDEWEB)

    Ylikantola, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Linnanto, J., E-mail: juha.m.linnanto@gmail.com [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); University of Tartu, Institute of Physics, Riia 142, EE-51014 Tartu (Estonia); Knuutinen, J.; Oravilahti, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Toivakka, M. [Åbo Akademi University, Laboratory of Paper Coating and Converting and Center for Functional Materials, FI-20500 Turku/Åbo (Finland)

    2013-07-01

    The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree–Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree–Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree–Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

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

    International Nuclear Information System (INIS)

    Huang Guoliang; Yang Xiaoyong; Ma Li; Yang Xu

    2011-01-01

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

  11. A Nanosensor for TNT Detection Based on Molecularly Imprinted Polymers and Surface Enhanced Raman Scattering

    Directory of Open Access Journals (Sweden)

    Mikella E. Hankus

    2011-03-01

    Full Text Available We report on a new sensor strategy that integrates molecularly imprinted polymers (MIPs with surface enhanced Raman scattering (SERS. The sensor was developed to detect the explosive, 2,4,6-trinitrotoluene (TNT. Micron thick films of sol gel-derived xerogels were deposited on a SERS-active surface as the sensing layer. Xerogels were molecularly imprinted for TNT using non-covalent interactions with the polymer matrix. Binding of the TNT within the polymer matrix results in unique SERS bands, which allow for detection and identification of the molecule in the MIP. This MIP-SERS sensor exhibits an apparent dissociation constant of (2.3 ± 0.3 × 10−5 M for TNT and a 3 µM detection limit. The response to TNT is reversible and the sensor is stable for at least 6 months. Key challenges, including developing a MIP formulation that is stable and integrated with the SERS substrate, and ensuring the MIP does not mask the spectral features of the target analyte through SERS polymer background, were successfully met. The results also suggest the MIP-SERS protocol can be extended to other target analytes of interest.

  12. A surface acoustic wave sensor functionalized with a polypyrrole molecularly imprinted polymer for selective dopamine detection.

    Science.gov (United States)

    Maouche, Naima; Ktari, Nadia; Bakas, Idriss; Fourati, Najla; Zerrouki, Chouki; Seydou, Mahamadou; Maurel, François; Chehimi, Mohammed Mehdi

    2015-11-01

    A surface acoustic wave sensor operating at 104 MHz and functionalized with a polypyrrole molecularly imprinted polymer has been designed for selective detection of dopamine (DA). Optimization of pyrrole/DA ratio, polymerization and immersion times permitted to obtain a highly selective sensor, which has a sensitivity of 0.55°/mM (≈ 550 Hz/mM) and a detection limit of ≈ 10 nM. Morphology and related roughness parameters of molecularly imprinted polymer surfaces, before and after extraction of DA, as well as that of the non imprinted polymer were characterized by atomic force microscopy. The developed chemosensor selectively recognized dopamine over the structurally similar compound 4-hydroxyphenethylamine (referred as tyramine), or ascorbic acid,which co-exists with DA in body fluids at a much higher concentration. Selectivity tests were also carried out with dihydroxybenzene, for which an unexpected phase variation of order of 75% of the DA one was observed. Quantum chemical calculations, based on the density functional theory, were carried out to determine the nature of interactions between each analyte and the PPy matrix and the DA imprinted PPy polypyrrole sensing layer in order to account for the important phase variation observed during dihydroxybenzene injection. Copyright © 2015 John Wiley & Sons, Ltd.

  13. Enhancing the magnetic anisotropy of maghemite nanoparticles via the surface coordination of molecular complexes

    Science.gov (United States)

    Prado, Yoann; Daffé, Niéli; Michel, Aude; Georgelin, Thomas; Yaacoub, Nader; Grenèche, Jean-Marc; Choueikani, Fadi; Otero, Edwige; Ohresser, Philippe; Arrio, Marie-Anne; Cartier-dit-Moulin, Christophe; Sainctavit, Philippe; Fleury, Benoit; Dupuis, Vincent; Lisnard, Laurent; Fresnais, Jérôme

    2015-01-01

    Superparamagnetic nanoparticles are promising objects for data storage or medical applications. In the smallest—and more attractive—systems, the properties are governed by the magnetic anisotropy. Here we report a molecule-based synthetic strategy to enhance this anisotropy in sub-10-nm nanoparticles. It consists of the fabrication of composite materials where anisotropic molecular complexes are coordinated to the surface of the nanoparticles. Reacting 5 nm γ-Fe2O3 nanoparticles with the [CoII(TPMA)Cl2] complex (TPMA: tris(2-pyridylmethyl)amine) leads to the desired composite materials and the characterization of the functionalized nanoparticles evidences the successful coordination—without nanoparticle aggregation and without complex dissociation—of the molecular complexes to the nanoparticles surface. Magnetic measurements indicate the significant enhancement of the anisotropy in the final objects. Indeed, the functionalized nanoparticles show a threefold increase of the blocking temperature and a coercive field increased by one order of magnitude. PMID:26634987

  14. Acidic deposition: State of science and technology. Report 15. Liming acidic surface waters. Final report

    International Nuclear Information System (INIS)

    Olem, H.; Thornelof, E.; Sandoy, S.; Schreiber, R.K.

    1990-09-01

    The document describes the science and technology of aquatic liming--a method for improving the water quality of acidic surface waters to restore or enhance fisheries. The report is a comprehensive compilation of years of research in North America and Europe by dozens of scientists. Several mitigation technologies--including those that have only been proposed--are critically evaluated along with the effects of liming on water chemistry and aquatic biota. Through these evaluations, the state of the science and technology of aquatic liming is identified for the reader. Whole-lake liming is now recognized as a valuable management tool for acidic surface waters and their fisheries. However, some liming technologies are considered experimental and will need further evaluation. Distinctions between technologies are included--as is the distinction between liming acidic surface waters and reducing acidifying emissions

  15. Monte Carlo and molecular dynamics simulations of near-surface phenomena. Quarterly report 3. quarter 1987

    International Nuclear Information System (INIS)

    Valkealahti, Seppo.

    1987-10-01

    Monte Carlo simulation is used to investigate positron and electron slowing down in solid matter. The description of elastic scattering is based on accurate cross sections of effective crystalline atom potentials. Inelastic processes are described separately for each energby level y Gryzinski's excitation function. Various materials are studied and several electron and positron slowing down parameters and distributions are extracted. The results are used to analyze and interprete a number of recent experiments utilizing keV electron and positron beams. Molecular dynamics simulation methods are used to study (i) damage production in aluminum (110) surfaces due to low-energy argon ion bombardment and (ii) the premelting effects of solid noble gas surfaces. Appropriately constructed pair potentials were assigned between the particles and an electronic friction term proportional to the velocity was used for energetic ions. Of particular interest in (i) are the defect and implanted atom distributions, which are compared against recent experiments. In (ii) the simulations show the equilibrium existence of liquid-like layers on the densely packed surfaces well below the bulk melting temperature. In (i) the mean vacancy concentration depth depends only slightly on the incident angle. The total number of vacancies is almost independent of the incident ion dose for very oblique angles of incidence (0>45 deg C). Vancancy profile is found to have a clear peak in the topmost atomic layers and a broader tail deep in the material. The interstitial and Ar + ion profiles are clearly deeper in the material than the vacancy profile. In (ii), a layer-by-layer premelting of Lennard-Jones (111) surfaces is observed. Also the (100) surfaces premelt, but the disordering mechanism for the loosely packed (110) surfaces is roughening. Furthermore, a general rule seems to be that melting proceeds along the directions of high packing densities

  16. Significant improvement in the electrical characteristics of Schottky barrier diodes on molecularly modified Gallium Nitride surfaces

    Science.gov (United States)

    Garg, Manjari; Naik, Tejas R.; Pathak, C. S.; Nagarajan, S.; Rao, V. Ramgopal; Singh, R.

    2018-04-01

    III-Nitride semiconductors face the issue of localized surface states, which causes fermi level pinning and large leakage current at the metal semiconductor interface, thereby degrading the device performance. In this work, we have demonstrated the use of a Self-Assembled Monolayer (SAM) of organic molecules to improve the electrical characteristics of Schottky barrier diodes (SBDs) on n-type Gallium Nitride (n-GaN) epitaxial films. The electrical characteristics of diodes were improved by adsorption of SAM of hydroxyl-phenyl metallated porphyrin organic molecules (Zn-TPPOH) onto the surface of n-GaN. SAM-semiconductor bonding via native oxide on the n-GaN surface was confirmed using X-ray photoelectron spectroscopy measurements. Surface morphology and surface electronic properties were characterized using atomic force microscopy and Kelvin probe force microscopy. Current-voltage characteristics of different metal (Cu, Ni) SBDs on bare n-GaN were compared with those of Cu/Zn-TPPOH/n-GaN and Ni/Zn-TPPOH/n-GaN SBDs. It was found that due to the molecular monolayer, the surface potential of n-GaN was decreased by ˜350 mV. This caused an increase in the Schottky barrier height of Cu and Ni SBDs from 1.13 eV to 1.38 eV and 1.07 eV to 1.22 eV, respectively. In addition to this, the reverse bias leakage current was reduced by 3-4 orders of magnitude for both Cu and Ni SBDs. Such a significant improvement in the electrical performance of the diodes can be very useful for better device functioning.

  17. Behind adhesion of uranyl onto montmorillonite surface: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Yang, W.; Zaoui, A., E-mail: azaoui@polytech-lille.fr

    2013-10-15

    Highlights: • We investigated the adsorption of uranyl onto Montmorillonite surface. • We studied the surface energy between layered Montmorillonite sheets. • We studied the work of adhesion between radionuclide and charged Montmorillonite. -- Abstract: We have performed molecular dynamics simulations to investigate the adsorption of radionuclide elements species onto substituted Montmorillonite (001) surface in the presence of different counterions. The structure and the dynamics of uranyl ion as well as its aquo, chloride ion, and carbonate complexes are analyzed. In addition, we have studied the surface energy between layered Montmorillonite sheets and the work of adhesion between radionuclide and charged Montmorillonite. The clay model used here is a Wyoming-type Montmorillonite with 0.75e negative charge per unit cell resulting from substitutions in Octahedral and Tetrahedral sheets. The system model was constructed based on CLAYFF force field potential model. To evaluate the thermodynamic work of adhesion, each surface and clay layer regions are converted to a thin film model. One and two species of radionuclide elements (UO{sub 2}(H{sub 2}O){sub 5},UO{sub 2}CO{sub 3}(H{sub 2}O){sub 5}, and UO{sub 2}Cl{sub 2}(H{sub 2}O){sub 5}) were deposited near the clay surface in a pseudo-two-dimensional periodic cell. Analysis shows that the uranyl ion structure is preserved with two axial oxygen atoms detected at 1.8 Å. Radial distribution functions results indicate that average U-O{sub w} distances are 2.45–2.61 Å, and 2.29–2.40 Å for U-O{sub c} distance. Average U-Cl distances are 2.78–3.08 Å, which is relatively larger than that of Uranium atom-Oxygen atom because of electrostatic factors.

  18. Sulfur amino acids and alanine on pyrite (100) by X-ray photoemission spectroscopy: Surface or molecular role?

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Arenillas, M.; Galvez-Martinez, S.; Mateo-Marti, E., E-mail: mateome@cab.inta-csic.es

    2017-08-31

    Highlights: • Surface annealing pretreatment on pyrite surfaces can select molecular adsorption. • Enriched monosulfide species on pyrite (100) surface favors NH{sub 2} adsorption form. • Enriching disulfide species on pyrite (100) surface promotes NH{sub 3}{sup +} adsorption form. • Unique structure of each aminoacid provides a particular fingerprint in the process. • Spectroscopy evidence, pretreatment surface processes drives molecular adsorption. - Abstract: This paper describes the first successful adsorption of the cysteine, cystine, methionine and alanine amino acids on the pyrite (100) surface under ultra-high vacuum conditions with crucial chemical adsorption parameters driving the process. We have demonstrated by X-ray photoemission spectroscopy (XPS) that the surface pretreatment annealing process on pyrite surfaces is a critical parameter driving surface reactivity. The presence of enriched monosulfide species on the pyrite (100) surface favours the amino acid NH{sub 2} chemical form, whereas a longer annealing surface pretreatment of over 3 h repairs the sulfur vacancies in the pyrite, enriching disulfide species on the pyrite surface, which promotes NH{sub 3}{sup +} adsorption due to the sulfur vacancies in the pyrite being replaced by sulfur atom dimers (S{sub 2}{sup 2−}) on the surface. Furthermore, even if the surface chemistry (monosulfide or disulfide species enrichment) is the main factor promoting a partial conversion from NH{sub 2} to NH{sub 3}{sup +} species, the unique chemical structure of each amino acid provides a particular fingerprint in the process.

  19. Molecular Nutrition Research—The Modern Way Of Performing Nutritional Science

    Science.gov (United States)

    Norheim, Frode; Gjelstad, Ingrid M. F.; Hjorth, Marit; Vinknes, Kathrine J.; Langleite, Torgrim M.; Holen, Torgeir; Jensen, Jørgen; Dalen, Knut Tomas; Karlsen, Anette S.; Kielland, Anders; Rustan, Arild C.; Drevon, Christian A.

    2012-01-01

    In spite of amazing progress in food supply and nutritional science, and a striking increase in life expectancy of approximately 2.5 months per year in many countries during the previous 150 years, modern nutritional research has a great potential of still contributing to improved health for future generations, granted that the revolutions in molecular and systems technologies are applied to nutritional questions. Descriptive and mechanistic studies using state of the art epidemiology, food intake registration, genomics with single nucleotide polymorphisms (SNPs) and epigenomics, transcriptomics, proteomics, metabolomics, advanced biostatistics, imaging, calorimetry, cell biology, challenge tests (meals, exercise, etc.), and integration of all data by systems biology, will provide insight on a much higher level than today in a field we may name molecular nutrition research. To take advantage of all the new technologies scientists should develop international collaboration and gather data in large open access databases like the suggested Nutritional Phenotype database (dbNP). This collaboration will promote standardization of procedures (SOP), and provide a possibility to use collected data in future research projects. The ultimate goals of future nutritional research are to understand the detailed mechanisms of action for how nutrients/foods interact with the body and thereby enhance health and treat diet-related diseases. PMID:23208524

  20. Molecular Nutrition Research—The Modern Way Of Performing Nutritional Science

    Directory of Open Access Journals (Sweden)

    Arild C. Rustan

    2012-12-01

    Full Text Available In spite of amazing progress in food supply and nutritional science, and a striking increase in life expectancy of approximately 2.5 months per year in many countries during the previous 150 years, modern nutritional research has a great potential of still contributing to improved health for future generations, granted that the revolutions in molecular and systems technologies are applied to nutritional questions. Descriptive and mechanistic studies using state of the art epidemiology, food intake registration, genomics with single nucleotide polymorphisms (SNPs and epigenomics, transcriptomics, proteomics, metabolomics, advanced biostatistics, imaging, calorimetry, cell biology, challenge tests (meals, exercise, etc., and integration of all data by systems biology, will provide insight on a much higher level than today in a field we may name molecular nutrition research. To take advantage of all the new technologies scientists should develop international collaboration and gather data in large open access databases like the suggested Nutritional Phenotype database (dbNP. This collaboration will promote standardization of procedures (SOP, and provide a possibility to use collected data in future research projects. The ultimate goals of future nutritional research are to understand the detailed mechanisms of action for how nutrients/foods interact with the body and thereby enhance health and treat diet-related diseases.

  1. Thermodynamical and structural properties of solid surfaces in the high temperature range by molecular dynamics solution: evidence for a roughening transition on the F.C.C. {110} surface

    International Nuclear Information System (INIS)

    Rosato, Vittorio

    1986-01-01

    We have studied by Molecular Dynamics simulation the thermodynamical and structural properties of the {110} solid Argon surface as a function of temperature up to T m . The following results have been obtained: 1) the Arrhenius plot indicates that for T> 0.7 T m the defect creation becomes a nearly athermal process. The measured surface diffusion coefficients are very high and are comparable with those observed in the liquid state. 2) the long range order is preserved at least up to T= 0.94 T m . The thermal disorder is related to the onset of a roughening transition on that surface at T ≅ 0.7 T m . Surface layers are not melted in the whole range of temperature we have studied. Furthermore we have investigated the influence of constraints on the surface structure for the same model system previously used at T = 0.48 T m . We have shown that both temperature and constraints induce disorder on surface: for constraints corresponding to elastic deformations of -5 pc applied along the dense axis {110}, the surface structure results to be very similar to that obtained, without constraints, at a higher temperature (T = 0.68 T m ). The implications of our bindings in several areas of Materials Science are briefly discussed. (author) [fr

  2. Integration of pharmacology, molecular pathology, and population data science to support precision gastrointestinal oncology.

    Science.gov (United States)

    Ogino, Shuji; Jhun, Iny; Mata, Douglas A; Soong, Thing Rinda; Hamada, Tsuyoshi; Liu, Li; Nishihara, Reiko; Giannakis, Marios; Cao, Yin; Manson, JoAnn E; Nowak, Jonathan A; Chan, Andrew T

    2017-01-01

    Precision medicine has a goal of customizing disease prevention and treatment strategies. Under the precision medicine paradigm, each patient has unique pathologic processes resulting from cellular genomic, epigenomic, proteomic, and metabolomic alterations, which are influenced by pharmacological, environmental, microbial, dietary, and lifestyle factors. Hence, to realize the promise of precision medicine, multi-level research methods that can comprehensively analyze many of these variables are needed. In order to address this gap, the integrative field of molecular pathology and population data science (i.e., molecular pathological epidemiology) has been developed to enable such multi-level analyses, especially in gastrointestinal cancer research. Further integration of pharmacology can improve our understanding of drug effects, and inform decision-making of drug use at both the individual and population levels. Such integrative research demonstrated potential benefits of aspirin in colorectal carcinoma with PIK3CA mutations, providing the basis for new clinical trials. Evidence also suggests that HPGD (15-PDGH) expression levels in normal colon and the germline rs6983267 polymorphism that relates to tumor CTNNB1 (β-catenin)/ WNT signaling status may predict the efficacy of aspirin for cancer chemoprevention. As immune checkpoint blockade targeting the CD274 (PD-L1)/ PDCD1 (PD-1) pathway for microsatellite instability-high (or mismatch repair-deficient) metastatic gastrointestinal or other tumors has become standard of care, potential modifying effects of dietary, lifestyle, microbial, and environmental factors on immunotherapy need to be studied to further optimize treatment strategies. With its broad applicability, our integrative approach can provide insights into the interactive role of medications, exposures, and molecular pathology, and guide the development of precision medicine.

  3. Molecular adsorption of alkanes on platinum surfaces: A predictive theoretical model

    International Nuclear Information System (INIS)

    Stinnett, J.A.; Madix, R.J.

    1996-01-01

    The adsorption probabilities of methane and propane on Pt(111), and propane on Pt(110)-(1x2) have been successfully predicted for a wide range of incident energies and angles with classical stochastic trajectory simulations, using a pairwise additive Morse methyl endash platinum potential previously developed from the measured trapping probabilities of ethane on Pt(111). These predictions, along with those for ethane adsorption on Pt(110)endash(1x2), comprise a unified model for the molecular adsorption of alkanes on platinum surfaces. The simulations show the initial trapping probabilities of methane and propane on Pt(111) are determined to within approximately 10% by the fate of the first bounce. They also indicate that at normal incidence on Pt(111) energy conversions from perpendicular translational motion to both cartwheeling rotation and lattice phonons play increasingly important roles in increasing the trapping probability as the alkane increases in size and molecular weight. For methane itself excitation of parallel translational momentum after the first bounce serves as the most effective energy storage mechanism which facilitates trapping, whereas for propane cartwheel rotational motion plays the dominant role. Excessive excitation of these modes of motion, however, can cause scattering on subsequent bounces by reconversion of the energy into perpendicular translational energy. Collisions of methane with the hollow and bridge sites on the Pt(111) surface appear less effective in trapping than do atop sites. The simulations also suggest excitation of the C endash C endash C bending mode of propane has little effect on the trapping of propane on platinum surfaces for beam energies below 55 kJ/mol. copyright 1996 American Institute of Physics

  4. Surface properties of heat-induced soluble soy protein aggregates of different molecular masses.

    Science.gov (United States)

    Guo, Fengxian; Xiong, Youling L; Qin, Fang; Jian, Huajun; Huang, Xiaolin; Chen, Jie

    2015-02-01

    Suspensions (2% and 5%, w/v) of soy protein isolate (SPI) were heated at 80, 90, or 100 °C for different time periods to produce soluble aggregates of different molecular sizes to investigate the relationship between particle size and surface properties (emulsions and foams). Soluble aggregates generated in these model systems were characterized by gel permeation chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Heat treatment increased surface hydrophobicity, induced SPI aggregation via hydrophobic interaction and disulfide bonds, and formed soluble aggregates of different sizes. Heating of 5% SPI always promoted large-size aggregate (LA; >1000 kDa) formation irrespective of temperature, whereas the aggregate size distribution in 2% SPI was temperature dependent: the LA fraction progressively rose with temperature (80→90→100 °C), corresponding to the attenuation of medium-size aggregates (MA; 670 to 1000 kDa) initially abundant at 80 °C. Heated SPI with abundant LA (>50%) promoted foam stability. LA also exhibited excellent emulsifying activity and stabilized emulsions by promoting the formation of small oil droplets covered with a thick interfacial protein layer. However, despite a similar influence on emulsion stability, MA enhanced foaming capacity but were less capable of stabilizing emulsions than LA. The functionality variation between heated SPI samples is clearly related to the distribution of aggregates that differ in molecular size and surface activity. The findings may encourage further research to develop functional SPI aggregates for various commercial applications. © 2015 Institute of Food Technologists®

  5. Landscape of Innovation for Cardiovascular Pharmaceuticals: From Basic Science to New Molecular Entities.

    Science.gov (United States)

    Beierlein, Jennifer M; McNamee, Laura M; Walsh, Michael J; Kaitin, Kenneth I; DiMasi, Joseph A; Ledley, Fred D

    2017-07-01

    This study examines the complete timelines of translational science for new cardiovascular therapeutics from the initiation of basic research leading to identification of new drug targets through clinical development and US Food and Drug Administration (FDA) approval of new molecular entities (NMEs) based on this research. This work extends previous studies by examining the association between the growth of research on drug targets and approval of NMEs associated with these targets. Drawing on research on innovation in other technology sectors, where technological maturity is an important determinant in the success or failure of new product development, an analytical model was used to characterize the growth of research related to the known targets for all 168 approved cardiovascular therapeutics. Categorizing and mapping the technological maturity of cardiovascular therapeutics reveal that (1) there has been a distinct transition from phenotypic to targeted methods for drug discovery, (2) the durations of clinical and regulatory processes were significantly influenced by changes in FDA practice, and (3) the longest phase of the translational process was the time required for technology to advance from initiation of research to a statistically defined established point of technology maturation (mean, 30.8 years). This work reveals a normative association between metrics of research maturation and approval of new cardiovascular therapeutics and suggests strategies for advancing translational science by accelerating basic and applied research and improving the synchrony between the maturation of this research and drug development initiatives. Copyright © 2017 Elsevier HS Journals, Inc. All rights reserved.

  6. Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

    Energy Technology Data Exchange (ETDEWEB)

    Doughty, Benjamin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Goverapet Srinivasan, Sriram [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Indian Inst. of Technology (IIT), Rajasthan (India); Bryantsev, Vyacheslav S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Dongkyu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Ho Nyung [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ma, Ying-Zhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lutterman, Daniel A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-06-12

    The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments, and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.

  7. Atomistic modeling of metal surfaces under electric fields: direct coupling of electric fields to a molecular dynamics algorithm

    CERN Document Server

    Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

    2011-01-01

    The effect of electric fields on metal surfaces is fairly well studied, resulting in numerous analytical models developed to understand the mechanisms of ionization of surface atoms observed at very high electric fields, as well as the general behavior of a metal surface in this condition. However, the derivation of analytical models does not include explicitly the structural properties of metals, missing the link between the instantaneous effects owing to the applied field and the consequent response observed in the metal surface as a result of an extended application of an electric field. In the present work, we have developed a concurrent electrodynamic–molecular dynamic model for the dynamical simulation of an electric-field effect and subsequent modification of a metal surface in the framework of an atomistic molecular dynamics (MD) approach. The partial charge induced on the surface atoms by the electric field is assessed by applying the classical Gauss law. The electric forces acting on the partially...

  8. A parametric study of surface roughness and bonding mechanisms of aluminum alloys with epoxies: a molecular dynamics simulation

    Science.gov (United States)

    Timilsina, Rajendra; Termaath, Stephanie

    The marine environment is highly aggressive towards most materials. However, aluminium-magnesium alloys (Al-Mg, specifically, 5xxx series) have exceptionally long service life in such aggressive marine environments. For instance, an Al-Mg alloy, AA5083, is extensively used in naval structures because of its good mechanical strength, formability, seawater corrosion resistance and weldability. However, bonding mechanisms of these alloys with epoxies in a rough surface environment are not fully understood yet. It requires a rigorous investigation at molecular or atomic levels. We performed a molecular dynamics simulation to study an adherend surface preparation and surface bonding mechanisms of Al-Mg alloy (AA5083) with different epoxies by developing several computer models. Various distributions of surface roughness are introduced in the models and performed molecular dynamics simulations. Formation of a beta phase (Al3Mg2) , microstructures, bonding energies at the interface, bonding strengths and durability are investigated. Office of Naval Research.

  9. Surface chemistry and growth mechanisms studies of homo epitaxial (1 0 0) GaAs by laser molecular beam epitaxy

    International Nuclear Information System (INIS)

    Yan Dawei; Wu Weidong; Zhang Hong; Wang Xuemin; Zhang Hongliang; Zhang Weibin; Xiong Zhengwei; Wang Yuying; Shen Changle; Peng Liping; Han Shangjun; Zhou Minjie

    2011-01-01

    In this paper, GaAs thin film has been deposited on thermally desorbed (1 0 0) GaAs substrate using laser molecular beam epitaxy. Scanning electron microscopy, in situ reflection high energy electron diffraction and in situ X-ray photoelectron spectroscopy are applied for evaluation of the surface morphology and chemistry during growth process. The results show that a high density of pits is formed on the surface of GaAs substrate after thermal treatment and the epitaxial thin film heals itself by a step flow growth, resulting in a smoother surface morphology. Moreover, it is found that the incorporation of As species into GaAs epilayer is more efficient in laser molecular beam epitaxy than conventional molecular beam epitaxy. We suggest the growth process is impacted by surface chemistry and morphology of GaAs substrate after thermal treatment and the growth mechanisms are discussed in details.

  10. Surface engineering on mesoporous silica chips for enriching low molecular weight phosphorylated proteins

    Science.gov (United States)

    Hu, Ye; Peng, Yang; Lin, Kevin; Shen, Haifa; Brousseau, Louis C., III; Sakamoto, Jason; Sun, Tong; Ferrari, Mauro

    2011-02-01

    Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV = 18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications.Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous

  11. Thermal grafting of fluorinated molecular monolayers on doped amorphous silicon surfaces

    International Nuclear Information System (INIS)

    Sabbah, H.; Zebda, A.; Ababou-Girard, S.; Solal, F.; Godet, C.; Conde, J. P.; Chu, V.

    2009-01-01

    Thermally induced (160-300 deg. C) gas phase grafting of linear alkene molecules (perfluorodecene) was performed on hydrogenated amorphous silicon (a-Si:H) films, either nominally undoped or doped with different boron and phosphorus concentrations. Dense and smooth a-Si:H films were grown using plasma decomposition of silane. Quantitative analysis of in situ x-ray photoelectron spectroscopy indicates the grafting of a single layer of organic molecules. The hydrophobic properties of perfluorodecene-modified surfaces were studied as a function of surface coverage. Annealing experiments in ultrahigh vacuum show the covalent binding and the thermal stability of these immobilized layers up to 370 deg. C; this temperature corresponds to the Si-C bond cleavage temperature. In contrast with hydrogenated crystalline Si(111):H, no heavy wet chemistry surface preparation is required for thermal grafting of alkene molecules on a-Si:H films. A threshold grafting temperature is observed, with a strong dependence on the doping level which produces a large contrast in the molecular coverage for grafting performed at 230 deg. C

  12. Molecular dynamics simulation of boron implanted into diamond (0 0 1) 2 x 1 reconstruction surface

    International Nuclear Information System (INIS)

    Li Rongbin; Dai Yongbin; Hu Xiaojun; Sheng Heshen; He Xianchang

    2003-01-01

    Molecular dynamic simulations, utilizing the Tersoff many-body potential, are used to investigate the microscopic processes of a single boron atom with energy of 500 eV implanted into the diamond (0 0 1) 2 x 1 reconstruction surface. The lifetime of thermal spike created by B bombardment is about 0.18 ps by calculating the variation of the mean coordination numbers with time. The formation of the split-interstitial composed of projectile and lattice atom (B-C) is observed. The total potential energy of the system decreases about 0.56 eV with a stable B split-interstitial in diamond. The lattice relaxations in the diamond (0 0 1) 2 x 1 reconstruction surface or near surface of simulated have been discussed. The outermost layer atoms tend to move inward, and the other atoms move outward. The interplanar distance between the outermost layer and the second layer has been shortened by 15% compared with its starting interplanar distance. Stress distribution in the calculated diamond configuration is inhomogeneous. After boron implanted into diamond with the energy of 500 eV, there is an excess of compressively stressed atoms in the lattice, which induces the total stress being compressive

  13. Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

    International Nuclear Information System (INIS)

    Kobayashi, Kazuya; Liang, Yunfeng; Matsuoka, Toshifumi; Sakka, Tetsuo

    2014-01-01

    The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules

  14. Molecular dynamics simulations of ejecta production from sinusoidal tin surfaces under supported and unsupported shocks

    Science.gov (United States)

    Wu, Bao; Wu, FengChao; Zhu, YinBo; Wang, Pei; He, AnMin; Wu, HengAn

    2018-04-01

    Micro-ejecta, an instability growth process, occurs at metal/vacuum or metal/gas interface when compressed shock wave releases from the free surface that contains surface defects. We present molecular dynamics (MD) simulations to investigate the ejecta production from tin surface shocked by supported and unsupported waves with pressures ranging from 8.5 to 60.8 GPa. It is found that the loading waveforms have little effect on spike velocity while remarkably affect the bubble velocity. The bubble velocity of unsupported shock loading remains nonzero constant value at late time as observed in experiments. Besides, the time evolution of ejected mass in the simulations is compared with the recently developed ejecta source model, indicating the suppressed ejection of unmelted or partial melted materials. Moreover, different reference positions are chosen to characterize the amount of ejecta under different loading waveforms. Compared with supported shock case, the ejected mass of unsupported shock case saturates at lower pressure. Through the analysis on unloading path, we find that the temperature of tin sample increases quickly from tensile stress state to zero pressure state, resulting in the melting of bulk tin under decaying shock. Thus, the unsupported wave loading exhibits a lower threshold pressure causing the solid-liquid phase transition on shock release than the supported shock loading.

  15. Molecular dynamics simulations of ejecta production from sinusoidal tin surfaces under supported and unsupported shocks

    Directory of Open Access Journals (Sweden)

    Bao Wu

    2018-04-01

    Full Text Available Micro-ejecta, an instability growth process, occurs at metal/vacuum or metal/gas interface when compressed shock wave releases from the free surface that contains surface defects. We present molecular dynamics (MD simulations to investigate the ejecta production from tin surface shocked by supported and unsupported waves with pressures ranging from 8.5 to 60.8 GPa. It is found that the loading waveforms have little effect on spike velocity while remarkably affect the bubble velocity. The bubble velocity of unsupported shock loading remains nonzero constant value at late time as observed in experiments. Besides, the time evolution of ejected mass in the simulations is compared with the recently developed ejecta source model, indicating the suppressed ejection of unmelted or partial melted materials. Moreover, different reference positions are chosen to characterize the amount of ejecta under different loading waveforms. Compared with supported shock case, the ejected mass of unsupported shock case saturates at lower pressure. Through the analysis on unloading path, we find that the temperature of tin sample increases quickly from tensile stress state to zero pressure state, resulting in the melting of bulk tin under decaying shock. Thus, the unsupported wave loading exhibits a lower threshold pressure causing the solid-liquid phase transition on shock release than the supported shock loading.

  16. Molecular dynamic simulations of the high-speed copper nanoparticles collision with the aluminum surface

    Science.gov (United States)

    Pogorelko, V. V.; Mayer, A. E.

    2016-11-01

    With the use of the molecular dynamic simulations, we investigated the effect of the high-speed (500 m/s, 1000 m/s) copper nanoparticle impact on the mechanical properties of an aluminum surface. Dislocation analysis shows that a large number of dislocations are formed in the impact area; the total length of dislocations is determined not only by the speed and size of the incoming copper nanoparticle (kinetic energy of the nanoparticle), but by a temperature of the system as well. The dislocations occupy the whole area of the aluminum single crystal at high kinetic energy of the nanoparticle. With the decrease of the nanoparticle kinetic energy, the dislocation structures are formed in the near-surface layer; formation of the dislocation loops takes place. Temperature rise of the system (aluminum substrate + nanoparticle) reduces the total dislocation length in the single crystal of aluminum; there is deeper penetration of the copper atoms in the aluminum at high temperatures. Average energy of the nanoparticles and room temperature of the system are optimal for production of high-quality layers of copper on the aluminum surface.

  17. Committee on Atomic, Molecular, and Optical Sciences (CAMOS). Technical progress report ampersand continuation proposal, February 1, 1993--January 31, 1994

    International Nuclear Information System (INIS)

    Taylor, R.D.

    1997-01-01

    The Committee on Atomic, Molecular and Optical Sciences (CAMOS) of the National Research Council (NRC) is charged with monitoring the health of the field of atomic, molecular, and optical (AMO) science in the United States. Accordingly, the Committee identifies and examines both broad and specific issues affecting the field. Regular meetings, teleconferences, briefings from agencies and the scientific community, the formation of study panels to prepare reports, and special symposia are among the mechanisms used by the CAMOS to meet its charge. This progress report presents a review of CAMOS activities from February 1, 1993 to January 31, 1994. The details of prior activities are discussed in earlier progress reports. This report also includes the status of activities associated with the CAMOS study on the field that is being conducted by the Panel on the Future of Atomic, Molecular, and Optical Sciences (FAMOS). During the above period, CAMOS has continued to track and participate in, when requested, discussions on the health of the field. Much of the perspective of CAMOS has been presented in the recently-published report Research Briefing on Selected Opportunities in Atomic, Molecular, and Optical Sciences. That report has served as the basis for briefings to representatives of the federal government as well as the community-at-large. In keeping with its charge to monitor the health of the field, CAMOS launched a study designed to highlight future directions of the field

  18. Single NdPc{sub 2} molecules on surfaces. Adsorption, interaction, and molecular magnetism

    Energy Technology Data Exchange (ETDEWEB)

    Fahrendorf, Sarah

    2013-01-24

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc{sub 2}) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc{sub 2}) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc{sub 2} molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the

  19. Single NdPc2 molecules on surfaces. Adsorption, interaction, and molecular magnetism

    International Nuclear Information System (INIS)

    Fahrendorf, Sarah

    2013-01-01

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc 2 ) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc 2 ) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc 2 molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the spin

  20. Surface-enhanced Raman scattering: a new optical probe in molecular biophysics and biomedicine

    DEFF Research Database (Denmark)

    Kneipp, J.; Wittig, B.; Bohr, Henrik

    2010-01-01

    Sensitive and detailed molecular structural information plays an increasing role in molecular biophysics and molecular medicine. Therefore, vibrational spectroscopic techniques, such as Raman scattering, which provide high structural information content are of growing interest in biophysical and ...

  1. Improved Fab presentation on phage surface with the use of molecular chaperone coplasmid system.

    Science.gov (United States)

    Loh, Qiuting; Leong, Siew Wen; Tye, Gee Jun; Choong, Yee Siew; Lim, Theam Soon

    2015-05-15

    The low presentation efficiency of Fab (fragment antigen binding) fragments during phage display is largely due to the complexity of disulphide bond formation. This can result in the presentation of Fab fragments devoid of a light chain during phage display. Here we propose the use of a coplasmid system encoding several molecular chaperones (DsbA, DsbC, FkpA, and SurA) to improve Fab packaging. A comparison was done using the Fab fragment from IgG and IgD. We found that the use of the coplasmid during phage packaging was able to improve the presentation efficiency of the Fab fragment on phage surfaces. A modified version of panning using the coplasmid system was evaluated and was successful at enriching Fab binders. Therefore, the coplasmid system would be an attractive alternative for improved Fab presentation for phage display. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution

    KAUST Repository

    Yu, Weili

    2014-08-19

    A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution

    KAUST Repository

    Yu, Weili; Isimjan, Tayirjan T.; Del Gobbo, Silvano; Anjum, Dalaver Hussain; Abdel-Azeim, Safwat; Cavallo, Luigi; Garcia Esparza, Angel T.; Domen, Kazunari; Xu, Wei; Takanabe, Kazuhiro

    2014-01-01

    A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. NATO Advanced Research Workshop on Geometrical Derivatives of Energy Surfaces and Molecular Properties

    CERN Document Server

    Simons, Jack

    1986-01-01

    The development and computational implementation of analytical expres­ sions for the low-order derivatives of electronic energy surfaces and other molecular properties has undergone rapid growth in recent years. It is now fairly routine for chemists to make use of energy gradient information in locating and identifying stable geometries and transition states. The use of second analytical derivative (Hessian or curvature) expressions is not yet routine, and third and higher energy derivatives as well as property (e.g., dipole moment, polarizability) derivatives are just beginning to be applied to chemical problems. This NATO Advanced Research Workshop focused on analyzing the re­ lative merits of various strategies for deriving the requisite analyti­ cal expressions, for computing necessary integral derivatives and wave­ function parameter derivatives, and for efficiently coding these expres­ sions on conventional scalar machines and vector-oriented computers. The participant list contained many scientist...

  5. Synthesis and analytical applications of molecularly imprinted polymers on the surface of carbon nanotubes: a review

    International Nuclear Information System (INIS)

    Dai, Hao; Xiao, Deli; Li, Hui; Yuan, Danhua; Zhang, Chan; He, Hua

    2015-01-01

    This review (with 142 references) summarize the state of the art in molecularly imprinting technology as applied to the surface of carbon nanotubes (CNTs) which result in so-called CNTs-MIPs. These nanomaterials offer a remedy to the flaws of traditional MIPs, such as poor site accessibility for templates, slow mass transfer and template leakage. They also are flexible in that different materials can be integrated with CNTs. Given the advantages of using CNT-MIPs, this technology has experienced rapid expansion, not the least because CNT-MIPs can be produced at low cost and by a variety of synthetic approaches. We summarize methods of, and recent advances in the synthesis of CNT-MIPs, and then highlight some representative applications. We also comment on their potential future developments and research directions. (author)

  6. A saliva molecular imprinted localized surface plasmon resonance biosensor for wine astringency estimation.

    Science.gov (United States)

    Guerreiro, J Rafaela L; Teixeira, Natércia; De Freitas, Victor; Sales, M Goreti F; Sutherland, Duncan S

    2017-10-15

    Wine astringency was evaluated based on the interaction of two complex matrices (red wine and saliva) by combining localized surface plasmon resonance (LSPR) and molecular imprinted polymers (MIP) at gold nanodisks as an alternative to sensorial analysis. The main objective of the work was to simulate wine astringency inside the mouth by mimicking this biological system. The LSPR/MIP sensor provided a linear response for astringency expressed in pentagalloyl glucose (PGG) units in concentrations ranging from 1 to 140μmol/L. The sensor was also applied to wine samples correlating well with sensorial analysis obtained by a trained panel. The correlation of astringency and wine composition was also evaluated showing that anthocyanins may have an important role, not only for pigmentation but also in astringency. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Beam line 4: A dedicated surface science facility at Daresbury Laboratory

    International Nuclear Information System (INIS)

    Dhanak, V.R.; Robinson, A.W.; van der Laan, G.; Thornton, G.

    1992-01-01

    We describe a beam line currently under construction at the Daresbury Laboratory which forms part of a surface science research facility for the Interdisciplinary Research Centre in Surface Science. The beam line has three branches, two of which are described here. The first branch covers the high-energy range 640 eV≤hν≤10 keV, being equipped with a double-crystal monochromator and a novel multicoated premirror system. The second branch line is optimized for the energy range 15≤hν≤250 eV, using cylindrical focusing mirrors, a spherical diffraction grating and an ellipsoidal refocusing mirror to achieve high resolution with a small spot size

  8. Structural and molecular insights into novel surface-exposed mucus adhesins from Lactobacillus reuteri human strains.

    Science.gov (United States)

    Etzold, Sabrina; MacKenzie, Donald A; Jeffers, Faye; Walshaw, John; Roos, Stefan; Hemmings, Andrew M; Juge, Nathalie

    2014-05-01

    The mucus layer covering the gastrointestinal tract is the first point of contact of the intestinal microbiota with the host. Cell surface macromolecules are critical for adherence of commensal bacteria to mucus but structural information is scarce. Here we report the first molecular and structural characterization of a novel cell-surface protein, Lar_0958 from Lactobacillus reuteri JCM 1112(T) , mediating adhesion of L. reuteri human strains to mucus. Lar_0958 is a modular protein of 133 kDa containing six repeat domains, an N-terminal signal sequence and a C-terminal anchoring motif (LPXTG). Lar_0958 homologues are expressed on the cell-surface of L. reuteri human strains, as shown by flow-cytometry and immunogold microscopy. Adhesion of human L. reuteri strains to mucus in vitro was significantly reduced in the presence of an anti-Lar_0958 antibody and Lar_0958 contribution to adhesion was further confirmed using a L. reuteri ATCC PTA 6475 lar_0958 KO mutant (6475-KO). The X-ray crystal structure of a single Lar_0958 repeat, determined at 1.5 Å resolution, revealed a divergent immunoglobulin (Ig)-like β-sandwich fold, sharing structural homology with the Ig-like inter-repeat domain of internalins of the food borne pathogen Listeria monocytogenes. These findings provide unique structural insights into cell-surface protein repeats involved in adhesion of Gram-positive bacteria to the intestine. © 2014 John Wiley & Sons Ltd.

  9. Low energy Cu clusters slow deposition on a Fe (001) surface investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shixu [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gong, Hengfeng [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Division of Nuclear Materials Science and Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Chen, Xuanzhi [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Li, Gongping, E-mail: ligp@lzu.edu.cn [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Wang, Zhiguang, E-mail: zhgwang@impcas.ac.cn [Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2014-09-30

    Highlights: • We study the deposition of low energy Cu clusters on Fe (001) surface by molecular dynamics. • The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. • The phenomenon of contact epitaxy of cluster occurred. • The thermal diffusion of cluster atoms was analyzed. - Abstract: The slow deposition of low energy Cu clusters on a Fe (001) surface was investigated by molecular dynamics simulation. A many-body potential based on Finnis–Sinclair model was used to describe the interactions among atoms. Three clusters comprising of 13, 55 and 147 atoms, respectively, were deposited with incident energies ranging from 0.0 to 1.0 eV/atom at various substrate temperatures (0, 300 and 800 K). The rearrangement and the diffusion of cluster can occur, only when the cluster atoms are activated and obtained enough migration energy. The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. In the former, the migration energy originates from the latent heat of binding energy for the soft deposition regime and primarily comes from the incident energy of cluster for the energetic cluster deposition regime. In the latter, the thermal vibration would result in some cluster atoms activated again at medium and high substrate temperatures. Also, the effects of incident energy, cluster size and substrate temperature on the interaction potential energy between cluster and substrate, the final deposition morphology of cluster, the spreading index and the structure parameter of cluster are analyzed.

  10. High-speed collision of copper nanoparticle with aluminum surface: Molecular dynamics simulation

    Science.gov (United States)

    Pogorelko, Victor V.; Mayer, Alexander E.; Krasnikov, Vasiliy S.

    2016-12-01

    We investigate the effect of the high-speed collision of copper nanoparticles with aluminum surface by means of molecular dynamic simulations. Studied diameter of nanoparticles is varied within the range 7.2-22 nm and the velocity of impact is equal to 500 or 1000 m/s. Dislocation analysis shows that a large quantity of dislocations is formed within the impact area. Overall length of dislocations is determined, first of all, by the impact velocity and by the size of incident copper nanoparticle, in other words, by the kinetic energy of the nanoparticle. Dislocations occupy the total volume of the impacted aluminum single crystal layer (40.5 nm in thickness) in the form of intertwined structure in the case of large kinetic energy of the incident nanoparticle. Decrease in the initial kinetic energy or increase in the layer thickness lead to restriction of the penetration depth of the dislocation net; formation of separate dislocation loops is observed in this case. Increase in the initial system temperature slightly raises the dislocation density inside the bombarded layer and considerably decreases the dislocation density inside the nanoparticle. The temperature increase also leads to a deeper penetration of the copper atoms inside the aluminum. Additional molecular dynamic simulations show that the deposited particles demonstrate a very good adhesion even in the case of the considered relatively large nanoparticles. Medium energy of the nanoparticles corresponding to velocity of about 500 m/s and elevated temperature of the system about 700-900 K are optimal parameters for production of high-quality layers of copper on the aluminum surface. These conditions provide both a good adhesion and a less degree of the plastic deformation. At the same time, higher impact velocities can be used for combined treatment consisting of both the plastic deformation and the coating.

  11. European analytical column No. 36 from the Division of Analytical Chemistry (DAC) of the European Association for Chemical and Molecular Sciences (EuCheMS)

    DEFF Research Database (Denmark)

    Karlberg, Bo; Emons, Hendrik; Andersen, Jens Enevold Thaulov

    2008-01-01

    European analytical column no. 36 from the division of analytical chemistry (DAC) of the European association for chemical and molecular sciences (EuCheMS)......European analytical column no. 36 from the division of analytical chemistry (DAC) of the European association for chemical and molecular sciences (EuCheMS)...

  12. Associateship | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Fellowship; Associateship. Associate Profile. Period: 2016–2019. Bhattacharya, Dr Atanu Ph.D. (Colorado State). Date of birth: 2 March 1983. Specialization: Ultrafast Science, Surface Science, Molecular Beam Experiments Address: IPC Department, Indian Institute of Science, Bengaluru 560 012, Karnataka Contact:

  13. Interplay of adsorbate-adsorbate and adsorbate-substrate interactions in self-assembled molecular surface nanostructures

    DEFF Research Database (Denmark)

    Schnadt, Joachim; Xu, Wei; Vang, Ronnie Thorbjørn

    2010-01-01

    a large tolerance to monatomic surface steps on the Ag(110) surface. The observed behaviour is explained in terms of strong intermolecular hydrogen bonding and a strong surface-mediated directionality, assisted by a sufficient degree of molecular backbone flexibility. In contrast, the same kind of step......-edge crossing is not observed when the molecules are adsorbed on the isotropic Ag(111) or more reactive Cu(110) surfaces. On Ag(111), similar 1-D assemblies are formed to those on Ag(110), but they are oriented along the step edges. On Cu(110), the carboxylic groups of NDCA are deprotonated and form covalent...... bonds to the surface, a situation which is also achieved on Ag(110) by annealing to 200 degrees C. These results show that the formation of particular self-assembled molecular nanostructures depends significantly on a subtle balance between the adsorbate-adsorbate and adsorbate-substrate interactions...

  14. A post-genomic surprise. The molecular reinscription of race in science, law and medicine.

    Science.gov (United States)

    Duster, Troy

    2015-03-01

    The completion of the first draft of the Human Genome Map in 2000 was widely heralded as the promise and future of genetics-based medicines and therapies - so much so that pundits began referring to the new century as 'The Century of Genetics'. Moreover, definitive assertions about the overwhelming similarities of all humans' DNA (99.9 per cent) by the leaders of the Human Genome Project were trumpeted as the end of racial thinking about racial taxonomies of human genetic differences. But the first decade of the new century brought unwelcomed surprises. First, gene therapies turned out to be far more complicated than any had anticipated - and instead the pharmaceutical industry turned to a focus on drugs that might be 'related' to population differences based upon genetic markers. While the language of 'personalized medicine' dominated this frame, research on racially and ethnically designated populations differential responsiveness to drugs dominated the empirical work in the field. Ancestry testing and 'admixture research' would play an important role in a new kind of molecular reification of racial categories. Moreover, the capacity of the super-computer to map differences reverberated into personal identification that would affect both the criminal justice system and forensic science, and generate new levels of concern about personal privacy. Social scientists in general, and sociologists in particular, have been caught short by these developments - relying mainly on assertions that racial categories are socially constructed, regionally and historically contingent, and politically arbitrary. While these assertions are true, the imprimatur of scientific legitimacy has shifted the burden, since now 'admixture research' can claim that its results get at the 'reality' of human differentiation, not the admittedly flawed social constructions of racial categories. Yet what was missing from this framing of the problem: 'admixture research' is itself based upon socially

  15. Surface Effect on Oil Transportation in Nanochannel: a Molecular Dynamics Study.

    Science.gov (United States)

    Zheng, Haixia; Du, Yonggang; Xue, Qingzhong; Zhu, Lei; Li, Xiaofang; Lu, Shuangfang; Jin, Yakang

    2017-12-01

    In this work, we investigate the dynamics mechanism of oil transportation in nanochannel using molecular dynamics simulations. It is demonstrated that the interaction between oil molecules and nanochannel has a great effect on the transportation properties of oil in nanochannel. Because of different interactions between oil molecules and channel, the center of mass (COM) displacement of oil in a 6-nm channel is over 30 times larger than that in a 2-nm channel, and the diffusion coefficient of oil molecules at the center of a 6-nm channel is almost two times more than that near the channel surface. Besides, it is found that polarity of oil molecules has the effect on impeding oil transportation, because the electrostatic interaction between polar oil molecules and channel is far larger than that between nonpolar oil molecules and channel. In addition, channel component is found to play an important role in oil transportation in nanochannel, for example, the COM displacement of oil in gold channel is very few due to great interaction between oil and gold substrate. It is also found that nano-sized roughness of channel surface greatly influences the speed and flow pattern of oil. Our findings would contribute to revealing the mechanism of oil transportation in nanochannels and therefore are very important for design of oil extraction in nanochannels.

  16. Adsorption of 1-naphthyl methyl carbamate in water by utilizing a surface molecularly imprinted polymer

    Science.gov (United States)

    So, Juhyok; Pang, Cholho; Dong, Hongxing; Jang, Paeksan; U, Juhyok; Ri, Kumchol; Yun, Cholyong

    2018-05-01

    Surface molecularly imprinting polymer (SMIP) was utilized in the removal of a residual pesticide (carbaryl (CBL)) in water and simulated fruit juice. Being the crosslinking agent, ethylene glycol dimethacrylate (EGDMA) was copolymerized with the monomer, methacrylic acid (MAA) and CBL as the template molecules on the surface of the silica gel particles to produce the SMIP adsorbents. The SMIP adsorbents showed good selectivity and good adsorption capacity for CBL in the competitive adsorptions with two structurally related carbamate pesticides. The effect of the pretreatment solvents on the adsorption capacity of the SMIP adsorbent was investigated with the results of the numerical simulations. The adsorption isotherms and the adsorption kinetics were well described by the Freundlich equilibrium model and the pseudo-second-order kinetic model, respectively. Scatchard plot analysis revealed that there were two classes of binding sites populated in the SMIP adsorbents. In addition, the good selective adsorption of CBL by the SMIP adsorbent in a simulated fruit juice containing vitamin C and fructose indicated the great potential of the SMIP adsorbents to remove residual pesticide in food industry and processing industry for agricultural products.

  17. Molecular insight into nanoscale water films dewetting on modified silica surfaces.

    Science.gov (United States)

    Zhang, Jun; Li, Wen; Yan, Youguo; Wang, Yefei; Liu, Bing; Shen, Yue; Chen, Haixiang; Liu, Liang

    2015-01-07

    In this work, molecular dynamics simulations are adopted to investigate the microscopic dewetting mechanism of nanoscale water films on methylated silica surfaces. The simulation results show that the dewetting process is divided into two stages: the appearance of dry patches and the quick contraction of the water film. First, the appearance of dry patches is due to the fluctuation in the film thickness originating from capillary wave instability. Second, for the fast contraction of water film, the unsaturated electrostatic and hydrogen bond interactions among water molecules are the driving forces, which induce the quick contraction of the water film. Finally, the effect of film thickness on water films dewetting is studied. Research results suggest that upon increasing the water film thickness from 6 to 8 Å, the final dewetting patterns experience separate droplets and striation-shaped structures, respectively. But upon further increasing the water film thickness, the water film is stable and there are no dry patches. The microscopic dewetting behaviors of water films on methylated silica surfaces discussed here are helpful in understanding many phenomena in scientific and industrial processes better.

  18. Surface functionalization of solid state ultra-high molecular weight polyethylene through chemical grafting

    Science.gov (United States)

    Sherazi, Tauqir A.; Rehman, Tayyiba; Naqvi, Syed Ali Raza; Shaikh, Ahson Jabbar; Shahzad, Sohail Anjum; Abbas, Ghazanfar; Raza, Rizwan; Waseem, Amir

    2015-12-01

    The surface of ultra-high molecular weight polyethylene (UHMWPE) powder was functionalized with styrene using chemical grafting technique. The grafting process was initiated through radical generation on base polymer matrix in the solid state by sodium thiosulfate, while peroxides formed at radical sites during this process were dissociated by ceric ammonium nitrate. Various factors were optimized and reasonably high level of monomer grafting was achieved, i.e., 15.6%. The effect of different acids as additive and divinyl benzene (DVB) as a cross-linking agent was also studied. Post-grafting sulfonation was conducted to introduce the ionic moieties to the grafted polymer. Ion-exchange capacity (IEC) was measured experimentally and is found to be 1.04 meq g-1, which is in close agreement with the theoretical IEC values. The chemical structure of grafted and functionalized polymer was characterized by attenuated total reflection infrared spectroscopy (ATR-FTIR) and thermal properties were investigated by thermo gravimetric analysis (TGA) and differential scanning calorimetry (DSC). Thermal analysis depicts that the presence of radicals on the polymer chain accelerates the thermal decomposition process. The results signify that the chemical grafting is an effective tool for substantial surface modification and subsequent functionalization of polyethylene.

  19. Fellowship | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Specialization: Solid State Chemistry, Surface Science, Spectroscopy and Molecular Structure Address: Linus Pauling Research Professor, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, Karnataka Contact: Office: (080) 2365 3075, (080) 2208 2761. Residence: (080) 2360 1410

  20. The New Horizons Radio Science Experiment: Expected Performance in Measurements of Pluto's Atmospheric Structure, Surface Pressure, and Surface Temperature

    Science.gov (United States)

    Hinson, D. P.; Linscott, I.; Woods, W. W.; Tyler, G. L.; Bird, M. K.; Paetzold, M.; Strobel, D. F.

    2014-12-01

    The New Horizons (NH) payload includes a Radio Science Experiment (REX) for investigating key characteristics of Pluto and Charon during the upcoming flyby in July 2015. REX flight equipment augments the NH radio transceiver used for spacecraft communications and tracking. The REX hardware implementation requires 1.6 W and 160 g. This presentation will focus on the final design and the predicted performance of two high-priority observations. First, REX will receive signals from a pair of 70-m antennas on Earth - each transmitting 20 kW at 4.2-cm wavelength - during a diametric radio occultation by Pluto. The data recorded by REX will reveal the surface pressure, the temperature structure of the lower atmosphere, and the surface radius. Second, REX will measure the thermal emission from Pluto at 4.2-cm wavelength during two linear scans across the disk at close range when both the dayside and the nightside are visible, allowing the surface temperature and its spatial variations to be determined. Both scans extend from limb to limb with a resolution of about 10 pixels; one bisects Pluto whereas the second crosses the winter pole. We will illustrate the capabilities of REX by reviewing the method of analysis and the precision achieved in a lunar occultation observed by New Horizons in May 2011. Re-analysis of radio occultation measurements by Voyager 2 at Triton is also under way. More generally, REX objectives include a radio occultation search for Pluto's ionosphere; examination of Charon through both radio occultation and radiometry; a search for a radar echo from Pluto's surface; and improved knowledge of the Pluto system mass and the Pluto-Charon mass ratio from a combination of two-way and one-way Doppler frequency measurements.

  1. Determining risk for severe leptospirosis by molecular analysis of environmental surface waters for pathogenic Leptospira.

    Directory of Open Access Journals (Sweden)

    Christian A Ganoza

    2006-08-01

    Full Text Available Although previous data indicate that the overall incidence of human leptospirosis in the Peruvian Amazon is similar in urban and rural sites, severe leptospirosis has been observed only in the urban context. As a potential explanation for this epidemiological observation, we tested the hypothesis that concentrations of more virulent Leptospira would be higher in urban than in rural environmental surface waters.A quantitative real-time PCR assay was used to compare levels of Leptospira in urban and rural environmental surface waters in sites in the Peruvian Amazon region of Iquitos. Molecular taxonomic analysis of a 1,200-bp segment of the leptospiral 16S ribosomal RNA gene was used to identify Leptospira to the species level. Pathogenic Leptospira species were found only in urban slum water sources (Fisher's exact test; p = 0.013. The concentration of pathogen-related Leptospira was higher in urban than rural water sources (approximately 10(3 leptospires/ml versus 0.5 x 10(2 leptospires/ml; F = 8.406, p < 0.05. Identical 16S rRNA gene sequences from Leptospira interrogans serovar Icterohaemorrhagiae were found in urban slum market area gutter water and in human isolates, suggesting a specific mode of transmission from rats to humans. In a prospective, population-based study of patients presenting with acute febrile illness, isolation of L. interrogans-related leptospires from humans was significantly associated with urban acquisition (75% of urban isolates; human isolates of other leptospiral species were associated with rural acquisition (78% of rural isolates (chi-square analysis; p < 0.01. This distribution of human leptospiral isolates mirrored the distribution of leptospiral 16S ribosomal gene sequences in urban and rural water sources.Our findings data support the hypothesis that urban severe leptospirosis in the Peruvian Amazon is associated with higher concentrations of more pathogenic leptospires at sites of exposure and transmission

  2. Assessment of environments for Mars Science Laboratory entry, descent, and surface operations

    Science.gov (United States)

    Vasavada, Ashwin R.; Chen, Allen; Barnes, Jeffrey R.; Burkhart, P. Daniel; Cantor, Bruce A.; Dwyer-Cianciolo, Alicia M.; Fergason, Robini L.; Hinson, David P.; Justh, Hilary L.; Kass, David M.; Lewis, Stephen R.; Mischna, Michael A.; Murphy, James R.; Rafkin, Scot C.R.; Tyler, Daniel; Withers, Paul G.

    2012-01-01

    The Mars Science Laboratory mission aims to land a car-sized rover on Mars' surface and operate it for at least one Mars year in order to assess whether its field area was ever capable of supporting microbial life. Here we describe the approach used to identify, characterize, and assess environmental risks to the landing and rover surface operations. Novel entry, descent, and landing approaches will be used to accurately deliver the 900-kg rover, including the ability to sense and "fly out" deviations from a best-estimate atmospheric state. A joint engineering and science team developed methods to estimate the range of potential atmospheric states at the time of arrival and to quantitatively assess the spacecraft's performance and risk given its particular sensitivities to atmospheric conditions. Numerical models are used to calculate the atmospheric parameters, with observations used to define model cases, tune model parameters, and validate results. This joint program has resulted in a spacecraft capable of accessing, with minimal risk, the four finalist sites chosen for their scientific merit. The capability to operate the landed rover over the latitude range of candidate landing sites, and for all seasons, was verified against an analysis of surface environmental conditions described here. These results, from orbital and model data sets, also drive engineering simulations of the rover's thermal state that are used to plan surface operations.

  3. Energy harvesting through gas dynamics in the free molecular flow regime between structured surfaces at different temperatures

    DEFF Research Database (Denmark)

    Baier, Tobias; Dölger, Julia; Hardt, Steffen

    2014-01-01

    For a gas confined between surfaces held at different temperatures the velocity distribution shows a significant deviation from the Maxwell distribution when the mean free path of the molecules is comparable to or larger than the channel dimensions. If one of the surfaces is suitably structured...... from the thermal creep flow that has gained more attention so far. This situation is studied in the limit of free-molecular flow for the case that an unstructured surface is allowed to move tangentially with respect to a structured surface. Parameter studies are conducted, and configurations...

  4. Mars' Surface Radiation Environment Measured with the Mars Science Laboratory's Curiosity Rover

    Science.gov (United States)

    Hassler, Donald M.; Zeitlin, Cary; Wimmer-Schweingruber, Robert F.; Ehresmann, Bent; Rafkin, Scot; Eigenbrode, Jennifer L.; Brinza, David E.; Weigle, Gerald; Böttcher, Stephan; Böhm, Eckart; Burmeister, Soenke; Guo, Jingnan; Köhler, Jan; Martin, Cesar; Reitz, Guenther; Cucinotta, Francis A.; Kim, Myung-Hee; Grinspoon, David; Bullock, Mark A.; Posner, Arik; Gómez-Elvira, Javier; Vasavada, Ashwin; Grotzinger, John P.; MSL Science Team; Kemppinen, Osku; Cremers, David; Bell, James F.; Edgar, Lauren; Farmer, Jack; Godber, Austin; Wadhwa, Meenakshi; Wellington, Danika; McEwan, Ian; Newman, Claire; Richardson, Mark; Charpentier, Antoine; Peret, Laurent; King, Penelope; Blank, Jennifer; Schmidt, Mariek; Li, Shuai; Milliken, Ralph; Robertson, Kevin; Sun, Vivian; Baker, Michael; Edwards, Christopher; Ehlmann, Bethany; Farley, Kenneth; Griffes, Jennifer; Miller, Hayden; Newcombe, Megan; Pilorget, Cedric; Rice, Melissa; Siebach, Kirsten; Stack, Katie; Stolper, Edward; Brunet, Claude; Hipkin, Victoria; Léveillé, Richard; Marchand, Geneviève; Sánchez, Pablo Sobrón; Favot, Laurent; Cody, George; Steele, Andrew; Flückiger, Lorenzo; Lees, David; Nefian, Ara; Martin, Mildred; Gailhanou, Marc; Westall, Frances; Israël, Guy; Agard, Christophe; Baroukh, Julien; Donny, Christophe; Gaboriaud, Alain; Guillemot, Philippe; Lafaille, Vivian; Lorigny, Eric; Paillet, Alexis; Pérez, René; Saccoccio, Muriel; Yana, Charles; Armiens-Aparicio, Carlos; Rodríguez, Javier Caride; Blázquez, Isaías Carrasco; Gómez, Felipe Gómez; Hettrich, Sebastian; Malvitte, Alain Lepinette; Jiménez, Mercedes Marín; Martínez-Frías, Jesús; Martín-Soler, Javier; Martín-Torres, F. Javier; Jurado, Antonio Molina; Mora-Sotomayor, Luis; Caro, Guillermo Muñoz; López, Sara Navarro; Peinado-González, Verónica; Pla-García, Jorge; Manfredi, José Antonio Rodriguez; Romeral-Planelló, Julio José; Fuentes, Sara Alejandra Sans; Martinez, Eduardo Sebastian; Redondo, Josefina Torres; Urqui-O'Callaghan, Roser; Mier, María-Paz Zorzano; Chipera, Steve; Lacour, Jean-Luc; Mauchien, Patrick; Sirven, Jean-Baptiste; Manning, Heidi; Fairén, Alberto; Hayes, Alexander; Joseph, Jonathan; Squyres, Steven; Sullivan, Robert; Thomas, Peter; Dupont, Audrey; Lundberg, Angela; Melikechi, Noureddine; Mezzacappa, Alissa; Berger, Thomas; Matthia, Daniel; Prats, Benito; Atlaskin, Evgeny; Genzer, Maria; Harri, Ari-Matti; Haukka, Harri; Kahanpää, Henrik; Kauhanen, Janne; Kemppinen, Osku; Paton, Mark; Polkko, Jouni; Schmidt, Walter; Siili, Tero; Fabre, Cécile; Wray, James; Wilhelm, Mary Beth; Poitrasson, Franck; Patel, Kiran; Gorevan, Stephen; Indyk, Stephen; Paulsen, Gale; Gupta, Sanjeev; Bish, David; Schieber, Juergen; Gondet, Brigitte; Langevin, Yves; Geffroy, Claude; Baratoux, David; Berger, Gilles; Cros, Alain; d'Uston, Claude; Forni, Olivier; Gasnault, Olivier; Lasue, Jérémie; Lee, Qiu-Mei; Maurice, Sylvestre; Meslin, Pierre-Yves; Pallier, Etienne; Parot, Yann; Pinet, Patrick; Schröder, Susanne; Toplis, Mike; Lewin, Éric; Brunner, Will; Heydari, Ezat; Achilles, Cherie; Oehler, Dorothy; Sutter, Brad; Cabane, Michel; Coscia, David; Israël, Guy; Szopa, Cyril; Dromart, Gilles; Robert, François; Sautter, Violaine; Le Mouélic, Stéphane; Mangold, Nicolas; Nachon, Marion; Buch, Arnaud; Stalport, Fabien; Coll, Patrice; François, Pascaline; Raulin, François; Teinturier, Samuel; Cameron, James; Clegg, Sam; Cousin, Agnès; DeLapp, Dorothea; Dingler, Robert; Jackson, Ryan Steele; Johnstone, Stephen; Lanza, Nina; Little, Cynthia; Nelson, Tony; Wiens, Roger C.; Williams, Richard B.; Jones, Andrea; Kirkland, Laurel; Treiman, Allan; Baker, Burt; Cantor, Bruce; Caplinger, Michael; Davis, Scott; Duston, Brian; Edgett, Kenneth; Fay, Donald; Hardgrove, Craig; Harker, David; Herrera, Paul; Jensen, Elsa; Kennedy, Megan R.; Krezoski, Gillian; Krysak, Daniel; Lipkaman, Leslie; Malin, Michael; McCartney, Elaina; McNair, Sean; Nixon, Brian; Posiolova, Liliya; Ravine, Michael; Salamon, Andrew; Saper, Lee; Stoiber, Kevin; Supulver, Kimberley; Van Beek, Jason; Van Beek, Tessa; Zimdar, Robert; French, Katherine Louise; Iagnemma, Karl; Miller, Kristen; Summons, Roger; Goesmann, Fred; Goetz, Walter; Hviid, Stubbe; Johnson, Micah; Lefavor, Matthew; Lyness, Eric; Breves, Elly; Dyar, M. Darby; Fassett, Caleb; Blake, David F.; Bristow, Thomas; DesMarais, David; Edwards, Laurence; Haberle, Robert; Hoehler, Tori; Hollingsworth, Jeff; Kahre, Melinda; Keely, Leslie; McKay, Christopher; Wilhelm, Mary Beth; Bleacher, Lora; Brinckerhoff, William; Choi, David; Conrad, Pamela; Dworkin, Jason P.; Floyd, Melissa; Freissinet, Caroline; Garvin, James; Glavin, Daniel; Harpold, Daniel; Jones, Andrea; Mahaffy, Paul; Martin, David K.; McAdam, Amy; Pavlov, Alexander; Raaen, Eric; Smith, Michael D.; Stern, Jennifer; Tan, Florence; Trainer, Melissa; Meyer, Michael; Voytek, Mary; Anderson, Robert C.; Aubrey, Andrew; Beegle, Luther W.; Behar, Alberto; Blaney, Diana; Calef, Fred; Christensen, Lance; Crisp, Joy A.; DeFlores, Lauren; Ehlmann, Bethany; Feldman, Jason; Feldman, Sabrina; Flesch, Gregory; Hurowitz, Joel; Jun, Insoo; Keymeulen, Didier; Maki, Justin; Mischna, Michael; Morookian, John Michael; Parker, Timothy; Pavri, Betina; Schoppers, Marcel; Sengstacken, Aaron; Simmonds, John J.; Spanovich, Nicole; Juarez, Manuel de la Torre; Webster, Christopher R.; Yen, Albert; Archer, Paul Douglas; Jones, John H.; Ming, Douglas; Morris, Richard V.; Niles, Paul; Rampe, Elizabeth; Nolan, Thomas; Fisk, Martin; Radziemski, Leon; Barraclough, Bruce; Bender, Steve; Berman, Daniel; Dobrea, Eldar Noe; Tokar, Robert; Vaniman, David; Williams, Rebecca M. E.; Yingst, Aileen; Lewis, Kevin; Leshin, Laurie; Cleghorn, Timothy; Huntress, Wesley; Manhès, Gérard; Hudgins, Judy; Olson, Timothy; Stewart, Noel; Sarrazin, Philippe; Grant, John; Vicenzi, Edward; Wilson, Sharon A.; Hamilton, Victoria; Peterson, Joseph; Fedosov, Fedor; Golovin, Dmitry; Karpushkina, Natalya; Kozyrev, Alexander; Litvak, Maxim; Malakhov, Alexey; Mitrofanov, Igor; Mokrousov, Maxim; Nikiforov, Sergey; Prokhorov, Vasily; Sanin, Anton; Tretyakov, Vladislav; Varenikov, Alexey; Vostrukhin, Andrey; Kuzmin, Ruslan; Clark, Benton; Wolff, Michael; McLennan, Scott; Botta, Oliver; Drake, Darrell; Bean, Keri; Lemmon, Mark; Schwenzer, Susanne P.; Anderson, Ryan B.; Herkenhoff, Kenneth; Lee, Ella Mae; Sucharski, Robert; Hernández, Miguel Ángel de Pablo; Ávalos, Juan José Blanco; Ramos, Miguel; Malespin, Charles; Plante, Ianik; Muller, Jan-Peter; Navarro-González, Rafael; Ewing, Ryan; Boynton, William; Downs, Robert; Fitzgibbon, Mike; Harshman, Karl; Morrison, Shaunna; Dietrich, William; Kortmann, Onno; Palucis, Marisa; Sumner, Dawn Y.; Williams, Amy; Lugmair, Günter; Wilson, Michael A.; Rubin, David; Jakosky, Bruce; Balic-Zunic, Tonci; Frydenvang, Jens; Jensen, Jaqueline Kløvgaard; Kinch, Kjartan; Koefoed, Asmus; Madsen, Morten Bo; Stipp, Susan Louise Svane; Boyd, Nick; Campbell, John L.; Gellert, Ralf; Perrett, Glynis; Pradler, Irina; VanBommel, Scott; Jacob, Samantha; Owen, Tobias; Rowland, Scott; Atlaskin, Evgeny; Savijärvi, Hannu; García, César Martín; Mueller-Mellin, Reinhold; Bridges, John C.; McConnochie, Timothy; Benna, Mehdi; Franz, Heather; Bower, Hannah; Brunner, Anna; Blau, Hannah; Boucher, Thomas; Carmosino, Marco; Atreya, Sushil; Elliott, Harvey; Halleaux, Douglas; Rennó, Nilton; Wong, Michael; Pepin, Robert; Elliott, Beverley; Spray, John; Thompson, Lucy; Gordon, Suzanne; Newsom, Horton; Ollila, Ann; Williams, Joshua; Vasconcelos, Paulo; Bentz, Jennifer; Nealson, Kenneth; Popa, Radu; Kah, Linda C.; Moersch, Jeffrey; Tate, Christopher; Day, Mackenzie; Kocurek, Gary; Hallet, Bernard; Sletten, Ronald; Francis, Raymond; McCullough, Emily; Cloutis, Ed; ten Kate, Inge Loes; Kuzmin, Ruslan; Arvidson, Raymond; Fraeman, Abigail; Scholes, Daniel; Slavney, Susan; Stein, Thomas; Ward, Jennifer; Berger, Jeffrey; Moores, John E.

    2014-01-01

    The Radiation Assessment Detector (RAD) on the Mars Science Laboratory's Curiosity rover began making detailed measurements of the cosmic ray and energetic particle radiation environment on the surface of Mars on 7 August 2012. We report and discuss measurements of the absorbed dose and dose equivalent from galactic cosmic rays and solar energetic particles on the martian surface for ~300 days of observations during the current solar maximum. These measurements provide insight into the radiation hazards associated with a human mission to the surface of Mars and provide an anchor point with which to model the subsurface radiation environment, with implications for microbial survival times of any possible extant or past life, as well as for the preservation of potential organic biosignatures of the ancient martian environment.

  5. Mars' surface radiation environment measured with the Mars Science Laboratory's Curiosity rover.

    Science.gov (United States)

    Hassler, Donald M; Zeitlin, Cary; Wimmer-Schweingruber, Robert F; Ehresmann, Bent; Rafkin, Scot; Eigenbrode, Jennifer L; Brinza, David E; Weigle, Gerald; Böttcher, Stephan; Böhm, Eckart; Burmeister, Soenke; Guo, Jingnan; Köhler, Jan; Martin, Cesar; Reitz, Guenther; Cucinotta, Francis A; Kim, Myung-Hee; Grinspoon, David; Bullock, Mark A; Posner, Arik; Gómez-Elvira, Javier; Vasavada, Ashwin; Grotzinger, John P

    2014-01-24

    The Radiation Assessment Detector (RAD) on the Mars Science Laboratory's Curiosity rover began making detailed measurements of the cosmic ray and energetic particle radiation environment on the surface of Mars on 7 August 2012. We report and discuss measurements of the absorbed dose and dose equivalent from galactic cosmic rays and solar energetic particles on the martian surface for ~300 days of observations during the current solar maximum. These measurements provide insight into the radiation hazards associated with a human mission to the surface of Mars and provide an anchor point with which to model the subsurface radiation environment, with implications for microbial survival times of any possible extant or past life, as well as for the preservation of potential organic biosignatures of the ancient martian environment.

  6. Interfacially enhancement of PBO/epoxy composites by grafting MWCNTs onto PBO surface through melamine as molecular bridge

    Science.gov (United States)

    Lv, Junwei; Wang, Bin; Ma, Qi; Wang, Wenjing; Xiang, Dong; Li, Mengyao; Zeng, Lan; Li, Hui; Li, Yuntao; Zhao, Chunxia

    2018-06-01

    Melamine and multi-walled carbon nanotubes (MWCNTs) were grafted onto Poly-p-phenylene benzobisoxazole (PBO) fiber surface effectively via layer-by-layer method. Both of them have been chemically bonded as fourier transform infrared spectroscopy (FTIR) confirmed. Grafting melamine overcame the inertness of PBO surface. Ammoniation was processed on PBO surface through grafting melamine so that the MWCNTs could be grafted onto PBO surface. Scanning electron microscopy (SEM) images indicated that melamine used as molecular bridge could increase MWCNTs’ quantity on PBO surface. X-ray photoelectron spectroscopy (XPS) results revealed the variation of chemical composition of PBO surface. Test of interfacial shear strength (IFSS) and tensile strength indicated the great mechanical properties of modified PBO fibers when combining with epoxy resin. Furthermore, whole reaction was processed under a simple condition. Results in this research also promised a potential method to modify PBO surface.

  7. Potential applications of luminescent molecular rotors in food science and engineering.

    Science.gov (United States)

    Alhassawi, Fatemah M; Corradini, Maria G; Rogers, Michael A; Ludescher, Richard D

    2017-06-29

    Fluorescent molecular rotors (MRs) are compounds whose emission is modulated by segmental mobility; photoexcitation generates a locally excited (LE), planar state that can relax either by radiative decay (emission of a photon) or by formation of a twisted intramolecular charge transfer (TICT) state that can relax nonradiatively due to internal rotation. If the local environment around the probe allows for rapid internal rotation in the excited state, fast non-radiative decay can either effectively quench the fluorescence or generate a second, red-shifted emission band. Conversely, any environmental restriction to twisting in the excited state due to free volume, crowding or viscosity, slows rotational relaxation and promotes fluorescence emission from the LE state. The environmental sensitivity of MRs has been exploited extensively in biological applications to sense microviscosity in biofluids, the stability and physical state of biomembranes, and conformational changes in macromolecules. The application of MRs in food research, however, has been only marginally explored. In this review, we summarize the main characteristics of fluorescent MRs, their current applications in biological research and their current and potential applications as sensors of physical properties in food science and engineering.

  8. Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

    Science.gov (United States)

    Oliver, David M; Hanley, Nick D; van Niekerk, Melanie; Kay, David; Heathwaite, A Louise; Rabinovici, Sharyl J M; Kinzelman, Julie L; Fleming, Lora E; Porter, Jonathan; Shaikh, Sabina; Fish, Rob; Chilton, Sue; Hewitt, Julie; Connolly, Elaine; Cummins, Andy; Glenk, Klaus; McPhail, Calum; McRory, Eric; McVittie, Alistair; Giles, Amanna; Roberts, Suzanne; Simpson, Katherine; Tinch, Dugald; Thairs, Ted; Avery, Lisa M; Vinten, Andy J A; Watts, Bill D; Quilliam, Richard S

    2016-02-01

    The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

  9. Molecular Mechanistic Reasoning: Toward Bridging the Gap between the Molecular and Cellular Levels in Life Science Education

    Science.gov (United States)

    van Mil, Marc H. W.; Postma, Paulien A.; Boerwinkel, Dirk Jan; Klaassen, Kees; Waarlo, Arend Jan

    2016-01-01

    Although learning about DNA, RNA, and proteins is part of the upper secondary biology curriculum in most countries, many studies report that students fail to connect molecular knowledge to phenomena at the higher level of cells, organs, and organisms. As a result, many students use memorization and rote learning as a coping strategy when presented…

  10. The New Horizons Radio Science Experiment: Performance and Measurements of Pluto's Atmospheric Structure, Surface Pressure, and Surface Temperature

    Science.gov (United States)

    Linscott, I.; Hinson, D. P.; Bird, M. K.; Stern, A.; Weaver, H. A., Jr.; Olkin, C.; Young, L. A.; Ennico Smith, K.

    2015-12-01

    The New Horizons (NH) spacecraft payload contained the Radio Science Experiment (REX) for determining key characteristics of Pluto and Charon during the July 14, 2015, flyby of the Pluto/Charon system. The REX flight equipment augments the NH X-band radio transceiver by providing a high precision, narrow band recording of high power uplink transmissions from Earth stations, as well as a record of broadband radiometric power. This presentation will review the performance and initial results of two high- priority observations. First, REX received two pair of 20-kW signals, one pair per polarization, transmitted from the DSN at 4.2-cm wavelength during a diametric radio occultation by Pluto. REX recorded these uplink signals and determined precise measurement of the surface pressure, the temperature structure of the lower atmosphere, and the surface radius of Pluto. The ingress portion of one polarization was played back from the spacecraft in July and processed to obtain the pressure and temperature structure of Pluto's atmosphere. Second, REX measured the thermal emission from Pluto at 4.2- cm wavelength during two linear scans across the disk at close range when both the dayside and the night side are visible. Both scans extend from limb to limb with a resolution of one-tenth Pluto's disk and temperature resolution of 0.1 K. Occultation and radiometric temperature results presented here will encompass additional data scheduled for playback in September.

  11. Molecular dynamics simulations of the calcite/solution interface as a means to explore surface modifications induced by nitrate

    Energy Technology Data Exchange (ETDEWEB)

    Hofmann, Sascha; Schmidt, Moritz [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Surface Processes; Spijker, P. [Aalto Univ., Helsinki (Finland). Dept. of Applied Physics; Voitchovsky, K. [Durham Univ. (United Kingdom). Physics Dept.

    2016-07-01

    The reactivity of calcite, one of the most abundant minerals in the earth's crust, is determined by the molecular details of its interface with the contacting solution. Recently, it has been found that trace concentrations of NaNO{sub 3} severely affect calcite's (104) surface and its reactivity. Molecular dynamics (MD) simulations reveal density profiles of different ions near calcite's surface, with NO{sub 3}{sup -} able to reach closer to the surface than CO{sub 3}{sup 2-} and in higher concentrations. Additionally, incorporation of NO{sub 3}{sup -} into the surface significantly disturbs the water structure at the interface.

  12. Surface properties of poly(acrylonitrile) (PAN) precipitation polymerized in supercritical CO2 and the influence of the molecular weight.

    Science.gov (United States)

    Shen, Qing; Gu, Qing-Feng; Hu, Jian-Feng; Teng, Xin-Rong; Zhu, Yun-Feng

    2003-11-15

    In this paper, the surface properties, e.g., the total surface free energy and the related Lifshitz-van der Waals and Lewis acid-base components, of polyacrylonitrile (PAN) precipitation polymerized in supercritical CO(2) have been characterized. Moreover, the influence of molecular weight varying has been also investigated. Results show that the surface properties of PAN resulting from supercritical CO(2) are different from those obtained by the conventional method. Of these data, one important finding is that the supercritical CO(2) PAN seems to decrease the surface free energy with the increased molecular weight. Based on previous recorded NMR spectra of this PAN and especially compared to commercial PAN, such phenomena are discussed and ascribed to an increase of the H-bonds and a reduction of the isotacticity in the supercritical CO(2) condition for PAN.

  13. Adhesion between a rutile surface and a polyimide: a coarse grained molecular dynamics study

    Science.gov (United States)

    Kumar, Arun; Sudarkodi, V.; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Nair, Nisanth N.; Basu, Sumit

    2018-04-01

    Titanium, due to its high strength to weight ratio and polyimides, due to their excellent thermal stability are being increasingly used in aerospace applications. We investigate the bonding between a (110) rutile substrate and a popular commercial polyimide, PMR-15, starting from the known atomic structure of the rutile substrate and the architecture of the polymer. First, the long PMR-15 molecule is divided into four fragments and an all-atom non-bonded forcefield governing the interaction between PMR-15 and a rutile substrate is developed. To this end, parameters of Buckingham potential for interaction between each atom in the fragments and the rutile surface are fitted, so as to ensure that the sum of non-bonded and electrostatic interaction energy between the substrate and a large number of configurations of each fragment, calculated by the quantum mechanical route and obtained from the fitted potential, is closely matched. Further, two coarse grained models of PMR-15 are developed—one for interaction between two coarse grained PMR-15 molecules and another for that between a coarse grained PMR-15 and the rutile substrate. Molecular dynamics simulations with the coarse grained models yields a traction separation law—a very useful tool for conducting continuum level finite element simulations of rutile-PMR-15 joints—governing the normal separation of a PMR-15 block from a flat rutile substrate. Moreover, detailed information about the affinity of various fragments to the substrate are also obtained. In fact, though the separation energy between rutile and PMR-15 turns out to be rather low, our analysis—with merely the molecular architecture of the polyimide as the starting point—provides a scheme for in-silico prediction of adhesion energies for new polyimide formulations.

  14. Atomic molecular and optical physics

    International Nuclear Information System (INIS)

    Anon.

    1986-01-01

    Laser-assisted manufacturing and fiber-optics communications are but two of the products of atomic, molecular, and optical physics, (AMO) research. AMO physics provides theoretical and experimental methods and essential data to neighboring areas of science such as chemistry, astrophysics, condensed-matter physics, plasma physics, surface science, biology, and medicine. This book addresses advances in atomic, molecular, and optical fields and provides recommendations for further research. It also looks at scientific applications in national security, manufacturing, medicine, and other fields

  15. THE SURFACE-MEDIATED UNFOLDING KINETICS OF GLOBULAR PROTEINS IS DEPENDENT ON MOLECULAR WEIGHT AND TEMPERATURE

    Energy Technology Data Exchange (ETDEWEB)

    Patananan, A.N.; Goheen, S.C.

    2008-01-01

    The adsorption and unfolding pathways of proteins on rigid surfaces are essential in numerous complex processes associated with biomedical engineering, nanotechnology, and chromatography. It is now well accepted that the kinetics of unfolding are characterized by chemical and physical interactions dependent on protein deformability and structure, as well as environmental pH, temperature, and surface chemistry. Although this fundamental process has broad implications in medicine and industry, little is known about the mechanism because of the atomic lengths and rapid time scales involved. Therefore, the unfolding kinetics of myoglobin, β-glucosidase, and ovalbumin were investigated by adsorbing the globular proteins to non-porous cationic polymer beads. The protein fractions were adsorbed at different residence times (0, 9, 10, 20, and 30 min) at near-physiological conditions using a gradient elution system similar to that in high-performance liquid chromatography. The elution profi les and retention times were obtained by ultraviolet/visible spectrophotometry. A decrease in recovery was observed with time for almost all proteins and was attributed to irreversible protein unfolding on the non-porous surfaces. These data, and those of previous studies, fi t a positively increasing linear trend between percent unfolding after a fi xed (9 min) residence time (71.8%, 31.1%, and 32.1% of myoglobin, β-glucosidase, and ovalbumin, respectively) and molecular weight. Of all the proteins examined so far, only myoglobin deviated from this trend with higher than predicted unfolding rates. Myoglobin also exhibited an increase in retention time over a wide temperature range (0°C and 55°C, 4.39 min and 5.74 min, respectively) whereas ovalbumin and β-glucosidase did not. Further studies using a larger set of proteins are required to better understand the physiological and physiochemical implications of protein unfolding kinetics. This study confi rms that surface

  16. Dependence of surface morphology on molecular structure and its influence on the properties of OLEDs

    Energy Technology Data Exchange (ETDEWEB)

    Lim, S.H. [Department of Chemical Engineering, Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of); Ryu, G.Y. [Department of Electric Information and Control Engineering, Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of); Seo, J.H.; Park, J.H. [Center for Organic Materials and Information Devices (COMID), Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of); Department of Information Display, Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of); Youn, S.W. [Department of Chemical Engineering, Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of); Kim, Y.K. [Center for Organic Materials and Information Devices (COMID), Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of); Department of Information Display, Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of); Shin, D.M. [Department of Chemical Engineering, Hongik University, 72-1, Sangsu-Dong, Mapo-Gu, Seoul 121-791 (Korea, Republic of)], E-mail: shindm@wow.hongik.ac.kr

    2008-09-15

    Most organic light-emitting diodes (OLEDs) have a multilayer structure composed of organic layers such as a hole injection layer (HIL), a hole transport layer (HTL), an emission layer (EML), an electron transport layer (ETL) and an electron injection layer (EIL) sandwiched between two electrodes. The organic layers are thin solid films with a thickness from a few nano meters to a few tenths nano meter, respectively. Surface morphology of an organic thin solid film in OLEDs depends on the molecular structure of the organic material and has an affect on device performance. To analyze the effect of surface morphology of an organic thin solid film on fluorescence and electroluminescence (EL) properties, thin solid films of 4-(dicyanomethylene)-2-methyl-6-(julolidin-4-yl-vinyl)-4H-pyran (DCM2) and new red fluorophores, (2E,2'E)-3,3'-[4,4''-bis(dimethylamino)-1,1':4',1''-terphenyl-2',5'-diyl] bis[2= -(2-thienyl)acrylonitrile] (ABCV-Th) and (2Z,2'Z)-3,3'-[4,4''-bis(dimethylamino)-1,1':4',1''-terphenyl-2',5'-diyl] bis(2-phenylacrylonitrile) (ABCV-P) were investigated by atomic force microscopy (AFM). The samples for EL and AFM measurement were fabricated by the high-vacuum thermal deposition (8x10{sup -7} Torr) of organic materials onto the surface of indium tin oxide (ITO)-coated glass substrate, in which the layer structures of samples for AFM measurement and those for EL measurement were ITO/NPB (40 nm)/red emitters (80 nm) and ITO/NPB (40 nm)/red emitters (80 nm)/BCP (30 nm)/Liq (2 nm)/Al (100 nm), respectively. The analysis based on AFM measurements well supported that the photoluminescence properties and the device performance were very much dependent upon surface morphology of an organic thin layer.

  17. Contact Angle and Adhesion Dynamics and Hysteresis on Molecularly Smooth Chemically Homogeneous Surfaces.

    Science.gov (United States)

    Chen, Szu-Ying; Kaufman, Yair; Schrader, Alex M; Seo, Dongjin; Lee, Dong Woog; Page, Steven H; Koenig, Peter H; Isaacs, Sandra; Gizaw, Yonas; Israelachvili, Jacob N

    2017-09-26

    Measuring truly equilibrium adhesion energies or contact angles to obtain the thermodynamic values is experimentally difficult because it requires loading/unloading or advancing/receding boundaries to be measured at rates that can be slower than 1 nm/s. We have measured advancing-receding contact angles and loading-unloading adhesion energies for various systems and geometries involving molecularly smooth and chemically homogeneous surfaces moving at different but steady velocities in both directions, ±V, focusing on the thermodynamic limit of ±V → 0. We have used the Bell Theory (1978) to derive expressions for the dynamic (velocity-dependent) adhesion energies and contact angles suitable for both (i) dynamic adhesion measurements using the classic Johnson-Kendall-Roberts (JKR, 1971) theory of "contact mechanics" and (ii) dynamic contact angle hysteresis measurements of both rolling droplets and syringe-controlled (sessile) droplets on various surfaces. We present our results for systems that exhibited both steady and varying velocities from V ≈ 10 mm/s to 1 nm/s, where in all cases but one, the advancing (V > 0) and receding (V contact angles converged toward the same theoretical (thermodynamic) values as V → 0. Our equations for the dynamic contact angles are similar to the classic equations of Blake & Haynes (1969) and fitted the experimental adhesion data equally well over the range of velocities studied, although with somewhat different fitting parameters for the characteristic molecular length/dimension or area and characteristic bond formation/rupture lifetime or velocity. Our theoretical and experimental methods and results unify previous kinetic theories of adhesion and contact angle hysteresis and offer new experimental methods for testing kinetic models in the thermodynamic, quasi-static, limit. Our analyses are limited to kinetic effects only, and we conclude that hydrodynamic, i.e., viscous, and inertial effects do not play a role at the

  18. High-speed collision of copper nanoparticle with aluminum surface: Molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Pogorelko, Victor V., E-mail: vik_ko83@mail.ru [Chelyabinsk State University, Bratiev Kashirinykh 129, 454001 Chelyabinsk (Russian Federation); South Ural State University (National Research University), Lenin Prospect 76, 454080 Chelyabinsk (Russian Federation); Mayer, Alexander E., E-mail: mayer@csu.ru [Chelyabinsk State University, Bratiev Kashirinykh 129, 454001 Chelyabinsk (Russian Federation); South Ural State University (National Research University), Lenin Prospect 76, 454080 Chelyabinsk (Russian Federation); Krasnikov, Vasiliy S., E-mail: vas.krasnikov@gmail.com [Chelyabinsk State University, Bratiev Kashirinykh 129, 454001 Chelyabinsk (Russian Federation); South Ural State University (National Research University), Lenin Prospect 76, 454080 Chelyabinsk (Russian Federation)

    2016-12-30

    Highlights: • High-speed nanoparticle impact induces shock waves and intensive plastic deformation. • Lattice orientation strongly influences on the deformation degree. • Plastic deformation goes through nucleation, growth and separation of semi-loops. • Medium impact energy and elevated temperature are optimal for high-quality coating. • High impact velocity and room temperature lead to plastic deformation and coating. - Abstract: We investigate the effect of the high-speed collision of copper nanoparticles with aluminum surface by means of molecular dynamic simulations. Studied diameter of nanoparticles is varied within the range 7.2–22 nm and the velocity of impact is equal to 500 or 1000 m/s. Dislocation analysis shows that a large quantity of dislocations is formed within the impact area. Overall length of dislocations is determined, first of all, by the impact velocity and by the size of incident copper nanoparticle, in other words, by the kinetic energy of the nanoparticle. Dislocations occupy the total volume of the impacted aluminum single crystal layer (40.5 nm in thickness) in the form of intertwined structure in the case of large kinetic energy of the incident nanoparticle. Decrease in the initial kinetic energy or increase in the layer thickness lead to restriction of the penetration depth of the dislocation net; formation of separate dislocation loops is observed in this case. Increase in the initial system temperature slightly raises the dislocation density inside the bombarded layer and considerably decreases the dislocation density inside the nanoparticle. The temperature increase also leads to a deeper penetration of the copper atoms inside the aluminum. Additional molecular dynamic simulations show that the deposited particles demonstrate a very good adhesion even in the case of the considered relatively large nanoparticles. Medium energy of the nanoparticles corresponding to velocity of about 500 m/s and elevated temperature of the

  19. High-speed collision of copper nanoparticle with aluminum surface: Molecular dynamics simulation

    International Nuclear Information System (INIS)

    Pogorelko, Victor V.; Mayer, Alexander E.; Krasnikov, Vasiliy S.

    2016-01-01

    Highlights: • High-speed nanoparticle impact induces shock waves and intensive plastic deformation. • Lattice orientation strongly influences on the deformation degree. • Plastic deformation goes through nucleation, growth and separation of semi-loops. • Medium impact energy and elevated temperature are optimal for high-quality coating. • High impact velocity and room temperature lead to plastic deformation and coating. - Abstract: We investigate the effect of the high-speed collision of copper nanoparticles with aluminum surface by means of molecular dynamic simulations. Studied diameter of nanoparticles is varied within the range 7.2–22 nm and the velocity of impact is equal to 500 or 1000 m/s. Dislocation analysis shows that a large quantity of dislocations is formed within the impact area. Overall length of dislocations is determined, first of all, by the impact velocity and by the size of incident copper nanoparticle, in other words, by the kinetic energy of the nanoparticle. Dislocations occupy the total volume of the impacted aluminum single crystal layer (40.5 nm in thickness) in the form of intertwined structure in the case of large kinetic energy of the incident nanoparticle. Decrease in the initial kinetic energy or increase in the layer thickness lead to restriction of the penetration depth of the dislocation net; formation of separate dislocation loops is observed in this case. Increase in the initial system temperature slightly raises the dislocation density inside the bombarded layer and considerably decreases the dislocation density inside the nanoparticle. The temperature increase also leads to a deeper penetration of the copper atoms inside the aluminum. Additional molecular dynamic simulations show that the deposited particles demonstrate a very good adhesion even in the case of the considered relatively large nanoparticles. Medium energy of the nanoparticles corresponding to velocity of about 500 m/s and elevated temperature of the

  20. Molecular dynamics for reactions of heterogeneous catalysis

    NARCIS (Netherlands)

    Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

    1991-01-01

    An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

  1. Understanding the influence of buckwheat bran on wheat dough baking performance: Mechanistic insights from molecular and material science approaches.

    Science.gov (United States)

    Zanoletti, Miriam; Marti, Alessandra; Marengo, Mauro; Iametti, Stefania; Pagani, M Ambrogina; Renzetti, Stefano

    2017-12-01

    A molecular and material science approach is used to describe the influence of coarse and fine buckwheat bran on wheat dough properties and bread textural quality. Focus is given on (i) gluten solvation and structural arrangements in presence of bran as studied by front-face fluorescence; (ii) thermo-mechanical behavior of dough during heating studied by dynamic mechanical thermal analysis and (iii) texture of bread crumb analyzed in terms of a cellular solid. The thermo-mechanical behavior of dough was found to be largely related to starch phase transitions during heating. The use of thermodynamic approaches to biopolymer melting revealed that key transitions such as the onset of starch gelatinization were function of the interplay of water and bran volume fractions in the dough. Front-face fluorescence studies in wheat dough revealed that gluten solvation and structural arrangements were delayed by increasing bran addition level and reduction in particle size, as indicated by the drastic decrease in the protein surface hydrophobicity index. Variations in gluten structure could be strongly related to dough baking performance, i.e. specific volume. With regards to texture, the approach revealed that crumb texture was controlled by variations in density, moisture and bran volume fractions. Overall, this study elucidates a number of physical mechanisms describing the influence of buckwheat bran addition to dough and bread quality. These mechanisms strongly pointed at the influence of bran on water partitioning among the main polymeric components. In the future, these mechanisms should be investigated with bran material of varying source, composition and structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Quantitative relationships for the prediction of the vapor pressure of some hydrocarbons from the van der Waals molecular surface

    Directory of Open Access Journals (Sweden)

    Olariu Tudor

    2015-01-01

    Full Text Available A quantitative structure - property relationship (QSPR modeling of vapor pressure at 298.15 K, expressed as log (VP / Pa was performed for a series of 84 hydrocarbons (63 alkanes and 21 cycloalkanes using the van der Waals (vdW surface area, SW/Å2, calculated by the Monte Carlo method, as the molecular descriptor. The QSPR model developed from the subset of 63 alkanes (C1-C16, deemed as the training set, was successfully used for the prediction of the log (VP / Pa values of the 21 cycloalkanes, which was the external prediction (test subset. A QSPR model was also developed for a series composed of all 84 hydrocarbons. Both QSPR models were statistically tested for their ability to fit the data and for prediction. The results showed that the vdW molecular surface used as molecular descriptor (MD explains the variance of the majority of the log (VP / Pa values in this series of 84 hydrocarbons. This MD describes very well the intermolecular forces that hold neutral molecules together. The clear physical meaning of the molecular surface values, SW/Å2, could explain the success of the QSPR models obtained with a single structural molecular descriptor.

  3. Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hua; Carney, Paul J.; Mishin, Vasiliy P.; Guo, Zhu; Chang, Jessie C.; Wentworth, David E.; Gubareva, Larisa V.; Stevens, James; Schultz-Cherry, S.

    2016-04-06

    ABSTRACT

    During 2014, a subclade 2.3.4.4 highly pathogenic avian influenza (HPAI) A(H5N8) virus caused poultry outbreaks around the world. In late 2014/early 2015, the virus was detected in wild birds in Canada and the United States, and these viruses also gave rise to reassortant progeny, composed of viral RNA segments (vRNAs) from both Eurasian and North American lineages. In particular, viruses were found with N1, N2, and N8 neuraminidase vRNAs, and these are collectively referred to as H5Nx viruses. In the United States, more than 48 million domestic birds have been affected. Here we present a detailed structural and biochemical analysis of the surface antigens of H5N1, H5N2, and H5N8 viruses in addition to those of a recent human H5N6 virus. Our results with recombinant hemagglutinin reveal that these viruses have a strict avian receptor binding preference, while recombinantly expressed neuraminidases are sensitive to FDA-approved and investigational antivirals. Although H5Nx viruses currently pose a low risk to humans, it is important to maintain surveillance of these circulating viruses and to continually assess future changes that may increase their pandemic potential.

    IMPORTANCEThe H5Nx viruses emerging in North America, Europe, and Asia pose a great public health concern. Here we report a molecular and structural study of the major surface proteins of several H5Nx influenza viruses. Our results improve the understanding of these new viruses and provide important information on their receptor preferences and susceptibilities to antivirals, which are central to pandemic risk assessment.

  4. Selective cell-surface labeling of the molecular motor protein prestin

    International Nuclear Information System (INIS)

    McGuire, Ryan M.; Silberg, Jonathan J.; Pereira, Fred A.; Raphael, Robert M.

    2011-01-01

    Highlights: → Trafficking to the plasma membrane is required for prestin function. → Biotin acceptor peptide (BAP) was fused to prestin through a transmembrane domain. → BAP-prestin can be metabolically labeled with biotin in HEK293 cells. → Biotin-BAP-prestin allows for selective imaging of fully trafficked prestin. → The biotin-BAP-prestin displays voltage-sensitive activity. -- Abstract: Prestin, a multipass transmembrane protein whose N- and C-termini are localized to the cytoplasm, must be trafficked to the plasma membrane to fulfill its cellular function as a molecular motor. One challenge in studying prestin sequence-function relationships within living cells is separating the effects of amino acid substitutions on prestin trafficking, plasma membrane localization and function. To develop an approach for directly assessing prestin levels at the plasma membrane, we have investigated whether fusion of prestin to a single pass transmembrane protein results in a functional fusion protein with a surface-exposed N-terminal tag that can be detected in living cells. We find that fusion of the biotin-acceptor peptide (BAP) and transmembrane domain of the platelet-derived growth factor receptor (PDGFR) to the N-terminus of prestin-GFP yields a membrane protein that can be metabolically-labeled with biotin, trafficked to the plasma membrane, and selectively detected at the plasma membrane using fluorescently-tagged streptavidin. Furthermore, we show that the addition of a surface detectable tag and a single-pass transmembrane domain to prestin does not disrupt its voltage-sensitive activity.

  5. Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications.

    Science.gov (United States)

    Tavtigian, Sean V; Byrnes, Graham B; Goldgar, David E; Thomas, Alun

    2008-11-01

    Many individually rare missense substitutions are encountered during deep resequencing of candidate susceptibility genes and clinical mutation screening of known susceptibility genes. BRCA1 and BRCA2 are among the most resequenced of all genes, and clinical mutation screening of these genes provides an extensive data set for analysis of rare missense substitutions. Align-GVGD is a mathematically simple missense substitution analysis algorithm, based on the Grantham difference, which has already contributed to classification of missense substitutions in BRCA1, BRCA2, and CHEK2. However, the distribution of genetic risk as a function of Align-GVGD's output variables Grantham variation (GV) and Grantham deviation (GD) has not been well characterized. Here, we used data from the Myriad Genetic Laboratories database of nearly 70,000 full-sequence tests plus two risk estimates, one approximating the odds ratio and the other reflecting strength of selection, to display the distribution of risk in the GV-GD plane as a series of surfaces. We abstracted contours from the surfaces and used the contours to define a sequence of missense substitution grades ordered from greatest risk to least risk. The grades were validated internally using a third, personal and family history-based, measure of risk. The Align-GVGD grades defined here are applicable to both the genetic epidemiology problem of classifying rare missense substitutions observed in known susceptibility genes and the molecular epidemiology problem of analyzing rare missense substitutions observed during case-control mutation screening studies of candidate susceptibility genes. (c) 2008 Wiley-Liss, Inc.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    The rapid collapse of intrinsic single-walled carbon nanotube (SWNT) on the aluminum surface is observed using molecular dynamics simulation. The collapsing threshold is similar to 10 angstrom, and the length has no influence on its collapse. Furthermore, we report that the structural stability o...

  7. Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling

    NARCIS (Netherlands)

    Wolthers, M.; Di Tommaso, D.; Du, Zhimei; de Leeuw, Nora H.

    2013-01-01

    It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two

  8. Molecular Beam Epitaxy on Gas Cluster Ion Beam Prepared GaSb Substrates: Towards Improved Surfaces and Interfaces

    National Research Council Canada - National Science Library

    Krishnaswami, Kannan; Vangala, Shivashankar R; Dauplaise, Helen M; Allen, Lisa P; Dallas, Gordon; Bakken, Daniel; Bliss, David F; Goodhue, WIlliam D

    2007-01-01

    ... at temperatures ranging 530 degrees C to 560 degrees C. Cross-sectional transmission electron microscopy of molecular beam epitaxy grown GaSb/AlGaSb layers showed that the HBr-GCIB surface produced a smooth dislocation-free substrate-to-epi transition...

  9. HIGHLY SELECTIVE SENSORS FOR CHEMICAL AND BIOLOGICAL WARFARE AGENTS, INSECTICIDES AND VOCS BASED ON A MOLECULAR SURFACE IMPRINTING TECHNIQUE

    Science.gov (United States)

    Abstract was given as an oral platform presentation at the Pittsburgh Conference, Orlando FL (March 5-9, 2006). Research described is the development of sensors based on molecular surface imprinting. Applications include the monitoring of chemical and biological agents and inse...

  10. Adsorption of molecular brushes with polyelectrolyte backbones onto oppositely charged surfaces: A self-consistent field theory

    NARCIS (Netherlands)

    Feuz, L.; Leermakers, F.A.M.; Textor, M.; Borisov, O.V.

    2008-01-01

    The two-gradient version of the Scheutjens¿Fleer self-consistent field (SF-SCF) theory is employed to model the interaction between a molecular bottle brush with a polyelectrolyte backbone and neutral hydrophilic side chains and an oppositely charged surface. Our system mimics graft-copolymers with

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  12. Three-dimensional hybrid silicon nanostructures for surface enhanced Raman spectroscopy based molecular detection

    Science.gov (United States)

    Vendamani, V. S.; Nageswara Rao, S. V. S.; Venugopal Rao, S.; Kanjilal, D.; Pathak, A. P.

    2018-01-01

    Three-dimensional silver nanoparticles decorated vertically aligned Si nanowires (Si NWs) are effective surface-enhanced Raman spectroscopy (SERS) substrates for molecular detection at low concentration levels. The length of Si NWs prepared by silver assisted electroless etching is increased with an increase in etching time, which resulted in the reduced optical reflection in the visible region. These substrates were tested and optimized by measuring the Raman spectrum of standard dye Rhodamine 6G (R6G) of 10 nM concentration. Further, effective SERS enhancements of ˜105 and ˜104 were observed for the cytosine protein (concentration of 50 μM) and ammonium perchlorate (oxidizer used in explosives composition with a concentration of 10 μM), respectively. It is established that these three-dimensional SERS substrates yielded considerably higher enhancement factors for the detection of R6G when compared to previous reports. The sensitivity can further be increased and optimized since the Raman enhancement was found to increase with an increase in the density of silver nanoparticles decorated on the walls of Si NWs.

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

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Haining; Kim, Seungchul; Lee, Kwang-Ryeol, E-mail: krlee@kist.re.kr [Computational Science Research Center, Korea Institute of Science and Technology, 5, Hwarangno 14-gil, Seongbuk-gu, Seoul 02792 (Korea, Republic of); Department of Nanomaterial Science and Technology, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113 (Korea, Republic of); Srivastava, Pooja; Choi, Keunsu [Computational Science Research Center, Korea Institute of Science and Technology, 5, Hwarangno 14-gil, Seongbuk-gu, Seoul 02792 (Korea, Republic of)

    2016-03-28

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

  14. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation.

  15. On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yi, E-mail: yig057@ucsd.edu; Galperin, Michael, E-mail: migalperin@ucsd.edu [Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 (United States); Nitzan, Abraham, E-mail: nitzan@post.tau.ac.il [Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and School of Chemistry, Tel Aviv University, Tel Aviv 69978 (Israel)

    2016-06-28

    Within a generic model we analyze the Stokes linewidth in surface enhanced Raman scattering (SERS) from molecules embedded as bridges in molecular junctions. We identify four main contributions to the off-resonant Stokes signal and show that under zero voltage bias (a situation pertaining also to standard SERS experiments) and at low bias junctions only one of these contributions is pronounced. The linewidth of this component is determined by the molecular vibrational relaxation rate, which is dominated by interactions with the essentially bosonic thermal environment when the relevant molecular electronic energy is far from the metal(s) Fermi energy(ies). It increases when the molecular electronic level is close to the metal Fermi level so that an additional vibrational relaxation channel due to electron-hole (eh) exciton in the molecule opens. Other contributions to the Raman signal, of considerably broader linewidths, can become important at larger junction bias.

  16. Fundamental properties of molecules on surfaces. Molecular switching and interaction of magnetic molecules with superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hatter, Nino

    2016-12-14

    In this thesis, we investigate individual molecular switches and metal-organic complexes on surfaces with scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperatures. One focus addresses the switching ability and mechanism of diarylethene on Ag(111). The other focus lies on resolving and tuning magnetic interactions of individual molecules with superconductors. 4,4'-(4,4'-(perfluorocyclopent-1-ene-1,2-diyl)bis (5-methylthiophene-4,2-diyl)dip yridine (PDTE) is a prototypical photochromic switch. We can induce a structural change of individual PDTE molecules on Ag(111) with the STM tip. This change is accompanied by a reduction of the energy gap between the occupied and unoccupied molecular orbitals. Density functional theory (DFT) calculations reveal that the induced switching corresponds to a ring-closing reaction from an open isomer in a flat adsorption configuration to a ring-closed isomer with its methyl groups in a cis configuration. The final product is thermodynamically stabilized by strong dispersion interactions with the surface. A linear dependence of the switching threshold with the tip-sample distance with a minimal threshold of 1.4 V is found, which we assign to a combination of an electric-field induced process and a tunneling-electron contribution. DFT calculations suggest a large activation barrier for a ring-closing reaction from the open flat configuration into the closed cis configuration. The interaction of magnetic molecules with superconductors is studied on manganese phthalocyanine (MnPc) adsorbed on Pb(111). We find triplets of Shiba states inside the superconducting gap. Different adsorption sites of MnPc provide a large variety of exchange coupling strengths, which lead to a collective energy shift of the Shiba triplets. We can assign the splitting of the Shiba states to be an effect of magnetic anisotropy in the system. A quantum phase transition from a ''Kondo screened'' to a &apos

  17. Super-Resolution Molecular and Functional Imaging of Nanoscale Architectures in Life and Materials Science

    KAUST Repository

    Habuchi, Satoshi

    2014-01-01

    fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative

  18. Density functionals for surface science: Exchange-correlation model development with Bayesian error estimation

    DEFF Research Database (Denmark)

    Wellendorff, Jess; Lundgård, Keld Troen; Møgelhøj, Andreas

    2012-01-01

    A methodology for semiempirical density functional optimization, using regularization and cross-validation methods from machine learning, is developed. We demonstrate that such methods enable well-behaved exchange-correlation approximations in very flexible model spaces, thus avoiding the overfit......A methodology for semiempirical density functional optimization, using regularization and cross-validation methods from machine learning, is developed. We demonstrate that such methods enable well-behaved exchange-correlation approximations in very flexible model spaces, thus avoiding...... the energetics of intramolecular and intermolecular, bulk solid, and surface chemical bonding, and the developed optimization method explicitly handles making the compromise based on the directions in model space favored by different materials properties. The approach is applied to designing the Bayesian error...... sets validates the applicability of BEEF-vdW to studies in chemistry and condensed matter physics. Applications of the approximation and its Bayesian ensemble error estimate to two intricate surface science problems support this....

  19. Initial oxidation processes of Si(001) surfaces by supersonic O2 molecular beams. Different oxidation mechanisms for clean and partially-oxidized surfaces

    International Nuclear Information System (INIS)

    Teraoka, Yuden; Yoshigoe, Akitaka

    2002-01-01

    Potential energy barriers for dissociative chemisorption of O 2 molecules on Si(001) clean surfaces were investigated using supersonic O 2 molecular beams and photoemission spectroscopy. Relative initial sticking probabilities of O 2 molecules and the saturated oxygen amount on the Si(001) surface were measured as a function of incident energy of O 2 molecules. Although the probability was independent on the incident energy in the region larger than 1 eV, the saturated oxygen amount was dependent on the incident energy without energy thresholds. An Si-2p photoemission spectrum of the Si(001) surface oxidized by thermal O 2 gas revealed the oxygen insertion into dimer backbond sites. These facts indicate that a reaction path of the oxygen insertion into dimer backbonds through bridge sites is open for the clean surface oxidation, and the direct chemisorption probability at the backbonds is negligibly small comparing with that at the bridge sites. (author)

  20. Calcite surface structure and reactivity: molecular dynamics simulations and macroscopic surface modelling of the calcite-water interface

    NARCIS (Netherlands)

    Wolthers, M.; Di Tommaso, D.; Du, Z.; de Leeuw, N.H.

    2012-01-01

    Calcite–water interactions are important not only in carbon sequestration and the global carbon cycle, but also in contaminant behaviour in calcite-bearing host rock and in many industrial applications. Here we quantify the effect of variations in surface structure on calcite surface reactivity.

  1. Towards an atomic level understanding of niobia based catalysts and catalysis by combining the science of catalysis with surface science

    Directory of Open Access Journals (Sweden)

    Martin Schmal

    2009-06-01

    Full Text Available The science of catalysis and surface science have developed, independently, key information for understanding catalytic processes. One might argue: is there anything fundamental to be discovered through the interplay between catalysis and surface science? Real catalysts of monometallic and bimetallic Co/Nb2O5 and Pd-Co/Nb2O5 catalysts showed interesting selectivity results on the Fischer-Tropsch synthesis (Noronha et al. 1996, Rosenir et al. 1993. The presence of a noble metal increased the C+5 selectivity and decreased the methane formation depending of the reduction temperature. Model catalyst of Co-Pd supported on niobia and alumina were prepared and characterized at the atomic level, thus forming the basis for a comparison with "real" support materials. Growth, morphology and structure of both pure metal and alloy particles were studied. It is possible to support the strong metal support interaction suggested by studies on real catalysts via the investigation of model systems for niobia in comparison to alumina support in which this effect does not occur. Formation of Co2+ penetration into the niobia lattice was suggested on the basis of powder studies and can be fully supported on the basis of model studies. It is shown for both real catalysts and model systems that oxidation state of Co plays a key role in controlling the reactivity in Fischer-Tropsch reactions systems and that the addition of Pd is a determining factor for the stability of the catalyst. It is demonstrated that the interaction with unsaturated hydrocarbons depends strongly on the state of oxidation.As ciências da catálise e da superfície têm desenvolvido independentemente temas básicos para o entendimento de processos catalíticos. Pode-se até questionar se há ainda algo fundamental para ser descoberto através da interface entre catálise eciência da superfície? Catalisadores mono e bimetálicos de Co/Nb2O5 e Pd-Co/ Nb2O5 apresentaram resultados interessantes de

  2. Surface 3D nanostructuring by tightly focused laser pulse: simulations by Lagrangian code and molecular dynamics

    Science.gov (United States)

    Inogamov, Nail A.; Zhakhovsky, Vasily V.

    2016-02-01

    There are many important applications in which the ultrashort diffraction-limited and therefore tightly focused laser pulses irradiates metal films mounted on dielectric substrate. Here we present the detailed picture of laser peeling and 3D structure formation of the thin (relative to a depth of a heat affected zone in the bulk targets) gold films on glass substrate. The underlying physics of such diffraction-limited laser peeling was not well understood previously. Our approach is based on a physical model which takes into consideration the new calculations of the two-temperature (2T) equation of state (2T EoS) and the two-temperature transport coefficients together with the coupling parameter between electron and ion subsystems. The usage of the 2T EoS and the kinetic coefficients is required because absorption of an ultrashort pulse with duration of 10-1000 fs excites electron subsystem of metal and transfers substance into the 2T state with hot electrons (typical electron temperatures 1-3 eV) and much colder ions. It is shown that formation of submicrometer-sized 3D structures is a result of the electron-ion energy transfer, melting, and delamination of film from substrate under combined action of electron and ion pressures, capillary deceleration of the delaminated liquid metal or semiconductor, and ultrafast freezing of molten material. We found that the freezing is going in non-equilibrium regime with strongly overcooled liquid phase. In this case the Stefan approximation is non-applicable because the solidification front speed is limited by the diffusion rate of atoms in the molten material. To solve the problem we have developed the 2T Lagrangian code including all this reach physics in. We also used the high-performance combined Monte- Carlo and molecular dynamics code for simulation of surface 3D nanostructuring at later times after completion of electron-ion relaxation.

  3. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  4. Adsorption of human serum albumin: Dependence on molecular architecture of the oppositely charged surface

    Science.gov (United States)

    Sukhishvili, Svetlana A.; Granick, Steve

    1999-05-01

    We contrast the adsorption of human serum albumin (HSA) onto two solid substrates previously primed with the same polyelectrolyte of net opposite charge to form one of two alternative structures: randomly adsorbed polymer and the "brush" configuration. These structures were formed either by the adsorption of quaternized poly-4-vinylpyridine (QPVP) or by end-grafting QPVP chains of the same chemical makeup and the same molecular weight to surfaces onto which QPVP segments did not adsorb. The adsorption of HSA was quantified by using Fourier transform infrared spectroscopy in attenuated total reflection (FTIR-ATR). The two substrates showed striking differences with regard to HSA adsorption. First, the brush substrate induced lesser perturbations in the secondary structure of the adsorbed HSA, reflecting easier conformational adjustment for longer free segments of polyelectrolyte upon binding with the protein. Second, the penetration of HSA into the brush substrate was kinetically retarded relative to the randomly adsorbed polymer, probably due to both pore size restriction and electrostatic sticking between charged groups of HSA and QPVP molecules. Third, release of HSA from the adsorbed layer, as the ionic strength was increased from a low level up to the high level of 1 M NaCl, was largely inhibited for the brush substrate, but occurred easily and rapidly for the substrate with statistically adsorbed QPVP chains. Finally, even after addition of a strong polymeric adsorption competitor (sodium polystyrene sulfonate), HSA remained trapped within a brush substrate though it desorbed slowly from the preadsorbed QPVP layer. This method to produce irreversible trapping of the protein within a brush substrate without major conformational change may find application in biosensor design.

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

    Science.gov (United States)

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

    2010-11-01

    Established methods for cleaning and sterilising biomedical devices may achieve removal of bioburden only at the macroscopic level while leaving behind molecular levels of contamination (mainly proteinaceous). This is of particular concern if the residue might contain prions. We investigated at the molecular level the removal of model and real-life proteinaceous contamination from model and practical surfaces by air plasma (ionised air) treatment. The surface-sensitive technique of X-ray photoelectron spectroscopy (XPS) was used to assess the removal of proteinaceous contamination, with the nitrogen (N1s) photoelectron signal as its marker. Model proteinaceous contamination (bovine serum albumin) adsorbed on to a model surface (silicon wafer) and the residual proteinaceous contamination resulting from incubating surgical stainless steel (a practical biomaterial) in whole human blood exhibited strong N1s signals [16.8 and 18.5 atomic percent (at.%), respectively] after thorough washing. After 5min air plasma treatment, XPS detected no nitrogen on the sample surfaces, indicating complete removal of proteinaceous contamination, down to the estimated XPS detection limit 10ng/cm(2). Applying the same plasma treatment, the 7.7at.% nitrogen observed on a clinically cleaned dental bur was reduced to a level reflective of new, as-received burs. Contact angle measurements and atomic force microscopy also indicated complete molecular-level removal of the proteinaceous contamination upon air plasma treatment. This study demonstrates the effectiveness of air plasma treatment for removing proteinaceous contamination from both model and practical surfaces and offers a method for ensuring that no molecular residual contamination such as prions is transferred upon re-use of surgical and dental instruments. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

  6. Effect of the selective adsorption on the reactive scattering process of molecular beams from stepped surfaces

    International Nuclear Information System (INIS)

    Garcia, N.

    1977-01-01

    An indicative proposal which may explain the diffusion of incident atomic beams scattered by a crystal surface is made in terms of the selective adsorption mechanism. In this sense, the stepped metallic surfaces present characteristics which enhance the displacements and the lifetimes of the beams on the surface. This may be important for increasing the exchange reactive scattering of molecules from crystal surfaces

  7. Control of Surface Wettability Using Tripodal Light-Activated Molecular Motors

    NARCIS (Netherlands)

    Chen, Kuang-Yen; Ivashenko, Oleksii; Carroll, Gregory T.; Robertus, Jort; Kistemaker, Jos C. M.; London, Gabor; Browne, Wesley R.; Rudolf, Petra; Feringa, Ben L.

    2014-01-01

    Monolayers of fluorinated light-driven molecular motors were synthesized and immobilized on gold films in an altitudinal orientation via tripodal stators. In this design the fimctionalized molecular motors are not interfering and preserve their rotary function on gold. The wettability of the

  8. Self-assembled diacetylene molecular wire polymerization on an insulating hexagonal boron nitride (0001) surface

    Czech Academy of Sciences Publication Activity Database

    Makarova, Marina; Okawa, Y.; Verveniotis, E.; Watanabe, K.; Taniguchi, T.; Joachim, Ch.; Aono, M.

    2016-01-01

    Roč. 27, č. 39 (2016), 1-8, č. článku 395303. ISSN 0957-4484 Institutional support: RVO:68378271 Keywords : molecular self-assembly * insulating substrate * molecular electronics * polydiacetylene Subject RIV: BJ - Thermodynamics Impact factor: 3.440, year: 2016

  9. Desert Research and Technology Studies (DRATS) 2010 Science Operations: Operational Approaches and Lessons Learned for Managing Science during Human Planetary Surface Missions

    Science.gov (United States)

    Eppler, Dean; Adams, Byron; Archer, Doug; Baiden, Greg; Brown, Adrian; Carey, William; Cohen, Barbara; Condit, Chris; Evans, Cindy; Fortezzo, Corey; hide

    2012-01-01

    Desert Research and Technology Studies (Desert RATS) is a multi-year series of hardware and operations tests carried out annually in the high desert of Arizona on the San Francisco Volcanic Field. These activities are designed to exercise planetary surface hardware and operations in conditions where long-distance, multi-day roving is achievable, and they allow NASA to evaluate different mission concepts and approaches in an environment less costly and more forgiving than space.The results from the RATS tests allows election of potential operational approaches to planetary surface exploration prior to making commitments to specific flight and mission hardware development. In previous RATS operations, the Science Support Room has operated largely in an advisory role, an approach that was driven by the need to provide a loose science mission framework that would underpin the engineering tests. However, the extensive nature of the traverse operations for 2010 expanded the role of the science operations and tested specific operational approaches. Science mission operations approaches from the Apollo and Mars-Phoenix missions were merged to become the baseline for this test. Six days of traverse operations were conducted during each week of the 2-week test, with three traverse days each week conducted with voice and data communications continuously available, and three traverse days conducted with only two 1-hour communications periods per day. Within this framework, the team evaluated integrated science operations management using real-time, tactical science operations to oversee daily crew activities, and strategic level evaluations of science data and daily traverse results during a post-traverse planning shift. During continuous communications, both tactical and strategic teams were employed. On days when communications were reduced to only two communications periods per day, only a strategic team was employed. The Science Operations Team found that, if

  10. Mars in Motion: An online Citizen Science platform looking for changes on the surface of Mars

    Science.gov (United States)

    Sprinks, James Christopher; Wardlaw, Jessica; Houghton, Robert; Bamford, Steven; Marsh, Stuart

    2016-10-01

    The European FP7 iMars project has developed tools and 3D models of the Martian surface through the co-registration of NASA and ESA mission data dating from the Viking missions of the 1970s to the present day, for a much more comprehensive interpretation of the geomorphological and climatic processes that have taken and do take place. We present the Citizen Science component of the project, 'Mars in Motion', created through the Zooniverse's Panoptes framework to allow volunteers to look for and identify changes on the surface of Mars over time. 'Mars in Motion', as with many other current citizen science platforms of a planetary or other disciplinary focus, has been developed to compliment the results of automated data mining analysis software, both by validation through the creation of training data and by adding context - gathering more in-depth data on the type and metrics of change initially detected.Through the analysis of initial volunteer results collected in the second half of 2016, the accuracy and ability of untrained participants to identify geomorphological changes is considered, as well as the impact of their position in the system. Volunteer contribution, either as a filter for poor quality imagery pre-algorithm, validation of algorithmic analysis, or adding context to pre-detected change, and their awareness and interpretation of its importance, can directly influence engagement with the platform and therefore ultimately its success. Understanding the effect of the volunteer and software's role in the system on both the results of and engagement with planetary science citizen science platforms will be an important lesson for the future, especially as the next generation of planetary missions will likely collect data orders of magnitude greater in volume. To deal with the data overload, it is likely that human or software solutions alone will not be sufficient, and that a combination of the two working together in a complimentary system that combines

  11. Molecular dynamics studies of the melting of butane and hexane monolayers adsorbed on the basal-plane surface of graphite

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Newton, J. C.; Taub, H.

    1993-01-01

    The effect of molecular steric properties on the melting of quasi-two-dimensional solids is investigated by comparing results of molecular dynamics simulations of the melting of butane and hexane monolayers adsorbed on the basal-plane surface of graphite. These molecules differ only in their length......, being members of the n-alkane series [CH3(CH2)n−2CH3] where n=4 for butane and n=6 for hexane. The simulations employ a skeletal model, which does not include the hydrogen atoms explicitly, to represent the intermolecular and molecule–substrate interactions. Nearest-neighbor intramolecular bonds...... are fixed in length, but the molecular flexibility is preserved by allowing the bend and dihedral torsion angles to vary. The simulations show a qualitatively different melting behavior for the butane and hexane monolayers consistent with neutron and x-ray scattering experiments. The melting of the low...

  12. Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

    International Nuclear Information System (INIS)

    Cernusca, S.; Winter, H.P.; Aumayr, F.; Diez Muino, R.; Juaristi, J.I.

    2003-01-01

    Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy <10 keV) on atomically clean surfaces of carbon-fiber inforced graphite used as first-wall armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to 'projectile molecular effects' (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials

  13. Off-Center Rotation of CuPc Molecular Rotor on a Bi(111) Surface and the Chiral Feature.

    Science.gov (United States)

    Sun, Kai; Tao, Min-Long; Tu, Yu-Bing; Wang, Jun-Zhong

    2017-05-04

    Molecular rotors with an off-center axis and the chiral feature of achiral CuPc molecules on a semi-metallic Bi(111) surface have been investigated by means of a scanning tunneling microscopy (STM) at liquid nitrogen (LN₂) temperature. The rotation axis of each CuPc molecular rotor is located at the end of a phthalocyanine group. As molecular coverage increases, the CuPc molecules are self-assembled into various nanoclusters and finally into two-dimensional (2D) domains, in which each CuPc molecule exhibits an apparent chiral feature. Such chiral features of the CuPc molecules can be attributed to the combined effect of asymmetric charge transfer between the CuPc and Bi(111) substrate, and the intermolecular van der Waals interactions.

  14. Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

    CERN Document Server

    Cernusca, S; Aumayr, F; Diez-Muino, R; Juaristi, J I

    2003-01-01

    Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy <10 keV) on atomically clean surfaces of carbon-fiber inforced graphite used as first-wall armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to 'projectile molecular effects' (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials.

  15. Atomic structure of screw dislocations intersecting the Au(111) surface: A combined scanning tunneling microscopy and molecular dynamics study

    DEFF Research Database (Denmark)

    Engbæk, Jakob; Schiøtz, Jakob; Dahl-Madsen, Bjarke

    2006-01-01

    The atomic-scale structure of naturally occurring screw dislocations intersecting a Au(111) surface has been investigated both experimentally by scanning tunneling microscopy (STM) and theoretically using molecular dynamics (MD) simulations. The step profiles of 166 dislocations were measured using...... STM. Many of them exhibit noninteger step-height plateaus with different widths. Clear evidence was found for the existence of two different populations at the surface with distinct (narrowed or widened) partial-splitting widths. All findings are fully confirmed by the MD simulations. The MD...... simulations extend the STM-, i.e., surface-, investigation to the subsurface region. Due to this additional insight, we can explain the different partial-splitting widths as the result of the interaction between the partial dislocations and the surface....

  16. Oxygen isotope evidence for sorption of molecular oxygen to pyrite surface sites and incorporation into sulfate in oxidation experiments

    International Nuclear Information System (INIS)

    Tichomirowa, Marion; Junghans, Manuela

    2009-01-01

    Experiments were conducted to investigate (i) the rate of O-isotope exchange between SO 4 and water molecules at low pH and surface temperatures typical for conditions of acid mine drainage (AMD) and (ii) the O- and S-isotope composition of sulfates produced by pyrite oxidation under closed and open conditions (limited and free access of atmospheric O 2 ) to identify the O source/s in sulfide oxidation (water or atmospheric molecular O 2 ) and to better understand the pyrite oxidation pathway. An O-isotope exchange between SO 4 and water was observed over a pH range of 0-2 only at 50 deg. C, whereas no exchange occurred at lower temperatures over a period of 8 a. The calculated half-time of the exchange rate for 50 deg. C (pH = 0 and 1) is in good agreement with former experimental data for higher and lower temperatures and excludes the possibility of isotope exchange for typical AMD conditions (T ≤ 25 deg. C, pH ≥ 3) for decades. Pyrite oxidation experiments revealed two dependencies of the O-isotope composition of dissolved sulfates: O-isotope values decreased with longer duration of experiments and increasing grain size of pyrite. Both changes are interpreted as evidence for chemisorption of molecular O 2 to pyrite surface sites. The sorption of molecular O 2 is important at initial oxidation stages and more abundant in finer grained pyrite fractions and leads to its incorporation in the produced SO 4 . The calculated bulk contribution of atmospheric O 2 in the dissolved SO 4 reached up to 50% during initial oxidation stages (first 5 days, pH 2, fine-grained pyrite fraction) and decreased to less than 20% after about 100 days. Based on the direct incorporation of molecular O 2 in the early-formed sulfates, chemisorption and electron transfer of molecular O 2 on S sites of the pyrite surface are proposed, in addition to chemisorption on Fe sites. After about 10 days, the O of all newly-formed sulfates originates only from water, indicating direct interaction

  17. Surface grafted chitosan gels. Part I. Molecular insight into the formation of chitosan and poly(acrylic acid) multilayers

    DEFF Research Database (Denmark)

    Liu, Chao; Thormann, Esben; Claesson, Per M.

    2014-01-01

    Composite polyelectrolyte multilayers of chitosan and low molecular weight poly(acrylic acid) (PAA) have been assembled by sequential adsorption as a first step toward building a surface anchored chitosan gel. Silane chemistry was used to graft the first chitosan layer to prevent film detachment...... and decomposition. The assembly process is characterized by nonlinear growth behavior, with different adsorption kinetics for chitosan and PAA. In situ analysis of the multilayer by means of surface sensitive total internal reflection Raman (TIRR) spectroscopy, combined with target factor analysis of the spectra...... molecular weight chitosan shows a similar behavior, although to a much lower extent. Our data demonstrate that the charged monomeric units of chitosan are mainly compensated by carboxylate ions from PAA. Furthermore, the morphology and mechanical properties of the multilayers were investigated in situ using...

  18. QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface

    Energy Technology Data Exchange (ETDEWEB)

    Yang Zhenyu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080(China); Zhao Yapu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080 (China)]. E-mail: yzhao@lnm.imech.ac.cn

    2006-05-15

    The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by 'GAMESS', and the rest atoms are treated as MM part calculated by 'TINKER'. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

  19. A study on EUV reticle surface molecular contamination under different storage conditions in a HVM foundry fab

    Science.gov (United States)

    Singh, SherJang; Yatzor, Brett; Taylor, Ron; Wood, Obert; Mangat, Pawitter

    2017-03-01

    The prospect of EUVL (Extreme Ultraviolet Lithography) insertion into HVM (High Volume Manufacturing) has never been this promising. As technology is prepared for "lab to fab" transition, it becomes important to comprehend challenges associated with integrating EUVL infrastructure within existing high volume chip fabrication processes in a foundry fab. The existing 193nm optical lithography process flow for reticle handling and storage in a fab atmosphere is well established and in-fab reticle contamination concerns are mitigated with the reticle pellicle. However EUVL reticle pellicle is still under development and if available, may only provide protection against particles but not molecular contamination. HVM fab atmosphere is known to be contaminated with trace amounts of AMC's (Atmospheric Molecular Contamination). If such contaminants are organic in nature and get absorbed on the reticle surface, EUV photon cause photo-dissociation resulting into carbon generation which is known to reduce multilayer reflectivity and also degrades exposure uniformity. Chemical diffusion and aggregation of other ions is also reported under the e-beam exposure of a EUV reticle which is known to cause haze issues in optical lithography. Therefore it becomes paramount to mitigate absorbed molecular contaminant concerns on EUVL reticle surface. In this paper, we have studied types of molecular contaminants that are absorbed on an EUVL reticle surface under HVM fab storage and handling conditions. Effect of storage conditions (gas purged vs atmospheric) in different storage pods (Dual pods, Reticle Clamshells) is evaluated. Absorption analysis is done both on ruthenium capping layer as well as TaBN absorber. Ru surface chemistry change as a result of storage is also studied. The efficacy of different reticle cleaning processes to remove absorbed contaminant is evaluated as well.

  20. Electroluminescence of a polythiophene molecular wire suspended between a metallic surface and the tip of a scanning tunneling microscope.

    Science.gov (United States)

    Reecht, Gaël; Scheurer, Fabrice; Speisser, Virginie; Dappe, Yannick J; Mathevet, Fabrice; Schull, Guillaume

    2014-01-31

    The electroluminescence of a polythiophene wire suspended between a metallic surface and the tip of a scanning tunneling microscope is reported. Under positive sample voltage, the spectral and voltage dependencies of the emitted light are consistent with the fluorescence of the wire junction mediated by localized plasmons. This emission is strongly attenuated for the opposite polarity. Both emission mechanism and polarity dependence are similar to what occurs in organic light emitting diodes (OLED) but at the level of a single molecular wire.

  1. Impact of molecular structure on the lubricant squeeze-out between curved surfaces with long range elasticity

    DEFF Research Database (Denmark)

    Tartaglino, Ugo; Sivebæk, Ion Marius; Persson, B N J

    2006-01-01

    layers develop in the lubricant film when the width is of the order of a few atomic diameters. The branched isobutane forms more disordered structures which permit it to stay liquidlike at smaller surface separations. During squeezing the solvation forces show oscillations corresponding to the width...... of a molecule. At low speeds (interfacial) squeezing velocity in most practical applications is very low when the lubricant layer has molecular thickness, one expects n-butane to be a better boundary lubricant than...

  2. Opportunities and limitations related to the application of plant-derived lipid molecular proxies in soil science

    Directory of Open Access Journals (Sweden)

    B. Jansen

    2017-11-01

    Full Text Available The application of lipids in soils as molecular proxies, also often referred to as biomarkers, has dramatically increased in the last decades. Applications range from inferring changes in past vegetation composition, climate, and/or human presence to unraveling the input and turnover of soil organic matter (SOM. The molecules used are extractable and non-extractable lipids, including ester-bound lipids. In addition, the carbon or hydrogen isotopic composition of such molecules is used. While holding great promise, the application of soil lipids as molecular proxies comes with several constraining factors, the most important of which are (i variability in the molecular composition of plant-derived organic matter both internally and between individual plants, (ii variability in (the relative contribution of input pathways into the soil, and (iii the transformation and/or (selective degradation of (some of the molecules once present in the soil. Unfortunately, the information about such constraining factors and their impact on the applicability of molecular proxies is fragmented and scattered. The purpose of this study is to provide a critical review of the current state of knowledge with respect to the applicability of molecular proxies in soil science, specifically focusing on the factors constraining such applicability. Variability in genetic, ontogenetic, and environmental factors influences plant n-alkane patterns in such a way that no unique compounds or specific molecular proxies pointing to, for example, plant community differences or environmental influences, exist. Other components, such as n-alcohols, n-fatty acids, and cutin- and suberin-derived monomers, have received far less attention in this respect. Furthermore, there is a high diversity of input pathways offering both opportunities and limitations for the use of molecular proxies at the same time. New modeling approaches might offer a possibility to unravel such mixed input

  3. An ab initio molecular

    Indian Academy of Sciences (India)

    mechanisms of two molecular crystals: An ab initio molecular dynamics ... for Computation in Molecular and Materials Science and Department of Chemistry, School of ..... NSAF Foundation of National Natural Science Foun- ... Matter 14 2717.

  4. Removal of cyanotoxins from surface water resources using reusable molecularly imprinted polymer adsorbents.

    Science.gov (United States)

    Krupadam, Reddithota J; Patel, Govind P; Balasubramanian, Rajasekhar

    2012-06-01

    Microcystins (MCs; cyclic heptapeptides) are produced by freshwater cyanobacteria and cause public health concern in potable water supplies. There are more than 60 types of MCs identified to date, of which MC-LR is the most common found worldwide. For MC-LR, the WHO has established a threshold value of 1 μg L(-1) for drinking water. The present MCs removal methods such as coagulation, flocculation, adsorption, and filtration showed low efficiency for removing dissolved MC fraction from surface waters to the stipulated limit prescribed by WHO based on MC health impacts. The search for cost-effective and efficient removal method is still warranted for remediation of dissolved MC-LR-contaminated water resources. Molecularly imprinted polymer (MIP) adsorbent has been prepared using non-covalent imprinting approach. Using MC-LR as a template, itaconic acid as a functional monomer, and ethylene glycol dimethacrylate as a cross-linking monomer, a MIP has been synthesized. Computer simulations were used to design effective binding sites for MC-LR binding in aqueous solutions. Batch binding adsorption assay was followed to determine binding capacity of MIP under the influence of environmental parameters such as total dissolved solids and pH. The adsorptive removal of MC-LR from lake water has been investigated using MIPs. The MIP showed excellent adsorption potential toward MC-LR in aqueous solutions with a binding capacity of 3.64 μg mg(-1) which is about 60% and 70% more than the commercially used powdered activated carbon (PAC) and resin XAD, respectively. Environmental parameters such as total organic carbon (represented as chemical oxygen demand (COD)) and total dissolved solids (TDS) showed no significant interference up to 300 mg L(-1) for MC-LR removal from lake water samples. It was found that the binding sites on PAC and XAD have more affinity toward COD and TDS than the MC-LR. Further, the adsorption capacity of the MIP was evaluated rigorously by its repeated

  5. 2D surface optical lattice formed by plasmon polaritons with application to nanometer-scale molecular deposition.

    Science.gov (United States)

    Yin, Yanning; Xu, Supeng; Li, Tao; Yin, Yaling; Xia, Yong; Yin, Jianping

    2017-08-10

    Surface plasmon polaritons, due to their tight spatial confinement and high local intensity, hold great promises in nanofabrication which is beyond the diffraction limit of conventional lithography. Here, we demonstrate theoretically the 2D surface optical lattices based on the surface plasmon polariton interference field, and the potential application to nanometer-scale molecular deposition. We present the different topologies of lattices generated by simple configurations on the substrate. By explicit theoretical derivations, we explain their formation and characteristics including field distribution, periodicity and phase dependence. We conclude that the topologies can not only possess a high stability, but also be dynamically manipulated via changing the polarization of the excitation laser. Nanometer-scale molecular deposition is simulated with these 2D lattices and discussed for improving the deposition resolution. The periodic lattice point with a width resolution of 33.2 nm can be obtained when the fullerene molecular beam is well-collimated. Our study can offer a superior alternative method to fabricate the spatially complicated 2D nanostructures, with the deposition array pitch serving as a reference standard for accurate and traceable metrology of the SI length standard.

  6. The Anomalies of Hyaluronan Structures in Presence of Surface Active Phospholipids—Molecular Mass Dependence

    Directory of Open Access Journals (Sweden)

    Piotr Bełdowski

    2018-03-01

    Full Text Available Interactions between hyaluronan (A- and phospholipids play a key role in many systems in the human body. One example is the articular cartilage system, where the synergistic effect of such interactions supports nanoscale lubrication. A molecular dynamics simulation has been performed to understand the process of formation of hydrogen bonds inside the hyaluronan network, both in the presence and absence of phospholipids. Additionally, the effect of the molecular mass of (A- was analyzed. The main finding of this work is a robust demonstration of the optimal parameters (H-bond energy, molecular mass influencing the facilitated lubrication mechanism of the articular cartilage system. Simulation results show that the presence of phospholipids has the greatest influence on hyaluronan at low molecular mass. We also show the specific sites of H-bonding between chains. Simulation results can help to understand how hyaluronan and phospholipids interact at several levels of articular cartilage system functioning.

  7. Aqueous Electrolyte Surfaces in Strong Electric Fields: Molecular Insight into Nanoscale Jets and Bridges.

    Czech Academy of Sciences Publication Activity Database

    Jirsák, J.; Moučka, F.; Škvor, J.; Nezbeda, Ivo

    2015-01-01

    Roč. 113, č. 8 (2015), s. 848-853 ISSN 0026-8976 Institutional support: RVO:67985858 Keywords : molecular dynamics * floating water bridge * electrospinning Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.837, year: 2015

  8. Molecular biology of Chlamydia pneumoniae surface proteins and their role in immunopathogenicity

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Boesen, Thomas; Hjernø, Karin

    1999-01-01

    present on the surface of the bacteria, we analyzed what components are present on the C pneumoniae surface. We identified a family of proteins, the GGAI or Omp4-15 proteins, of which at least 3 are present on the surface of C pneumoniae. We immunized rabbits with recombinant GGAI proteins and used...

  9. Nano- and Micro-sized Molecularly Imprinted Polymer Particles on Solid Surfaces

    OpenAIRE

    Kamra, Tripta

    2015-01-01

    Molecularly imprinted polymers (MIPs) are artificial receptors made by imprinting template molecules in a polymer matrix followed by their removal through washing to obtain a specific and selective template cavities. This property of the MIPs have made them a very efficient material for diverse applications such as chromatography, purification, drug sensing, etc. Recently, zero-dimensional polymer materials, in the present case molecularly imprinted polymer nanoparticles (MIP nanoparticles), ...

  10. Applications of neural networks to real-time data processing at the Environmental and Molecular Sciences Laboratory (EMSL)

    International Nuclear Information System (INIS)

    Keller, P.E.; Kouzes, R.T.; Kangas, L.J.

    1993-06-01

    Detailed design of the Environmental and Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory (PNL) is nearing completion and construction is scheduled to begin later this year. This facility will assist in the environmental restoration and waste management mission at the Hanford Site. This paper identifies several real-time data processing applications within the EMSL where neural networks can potentially be beneficial. These applications include real-time sensor data acquisition and analysis, spectral analysis, process control, theoretical modeling, and data compression

  11. Mechanisms of Zr surface corrosion determined via molecular dynamics simulations with charge-optimized many-body (COMB) potentials

    International Nuclear Information System (INIS)

    Noordhoek, Mark J.; Liang, Tao; Chiang, Tsu-Wu; Sinnott, Susan B.; Phillpot, Simon R.

    2014-01-01

    Highlights: • An interatomic potential for zirconium–zirconium oxide–zirconium hydride is presented. • Diffusion of oxygen and hydrogen into Zr (0 0 0 1). • Deposition of O 2 and H 2 O on low-index Zr surfaces. • Surface structure affects resulting corrosion behavior. - Abstract: A charge-optimized many-body (COMB) potential is proposed for the zirconium–zirconium oxide–zirconium hydride system. This potential is developed to describe the energetics of the interactions of oxygen and hydrogen with zirconium metal. We perform classical molecular dynamics simulations showing the initial corrosion behavior of three low-index zirconium surfaces via the deposition of O 2 and H 2 O molecules. The basal (0 0 0 1) surface shows greater resistance to oxygen diffusion than the prism (101 ¯ 0) and (112 ¯ 0) surfaces. We suggest ways in which the surface structure has a unique role in the experimentally observed enhanced corrosion of the prism surfaces

  12. Energy harvesting through gas dynamics in the free molecular flow regime between structured surfaces at different temperatures

    Science.gov (United States)

    Baier, Tobias; Dölger, Julia; Hardt, Steffen

    2014-05-01

    For a gas confined between surfaces held at different temperatures the velocity distribution shows a significant deviation from the Maxwell distribution when the mean free path of the molecules is comparable to or larger than the channel dimensions. If one of the surfaces is suitably structured, this nonequilibrium distribution can be exploited for momentum transfer in a tangential direction between the two surfaces. This opens up the possibility to extract work from the system which operates as a heat engine. Since both surfaces are held at constant temperatures, the mode of momentum transfer is different from the thermal creep flow that has gained more attention so far. This situation is studied in the limit of free-molecular flow for the case that an unstructured surface is allowed to move tangentially with respect to a structured surface. Parameter studies are conducted, and configurations with maximum thermodynamic efficiency are identified. Overall, it is shown that significant efficiencies can be obtained by tangential momentum transfer between structured surfaces.

  13. Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

    Science.gov (United States)

    Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

    2015-06-23

    We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

  14. Microfluidics' great promise for Biology - Microfluidics as a new engine for the molecular sciences

    KAUST Repository

    Kodzius, Rimantas

    2010-06-04

    History of the Life Sciences Origins of life Discoveries and instrumentation The power of genetic variation Diagnostics based on DNA/ protein variation Genomic scanning providers DNA sequencing companies Microfluidics story Commercial products available P

  15. Adhesion, friction, wear, and lubrication research by modern surface science techniques.

    Science.gov (United States)

    Keller, D. V., Jr.

    1972-01-01

    The field of surface science has undergone intense revitalization with the introduction of low-energy electron diffraction, Auger electron spectroscopy, ellipsometry, and other surface analytical techniques which have been sophisticated within the last decade. These developments have permitted submono- and monolayer structure analysis as well as chemical identification and quantitative analysis. The application of a number of these techniques to the solution of problems in the fields of friction, lubrication, and wear are examined in detail for the particular case of iron; and in general to illustrate how the accumulation of pure data will contribute toward the establishment of physiochemical concepts which are required to understand the mechanisms that are operational in friction systems. In the case of iron, LEED, Auger and microcontact studies have established that hydrogen and light-saturated organic vapors do not establish interfaces which prevent iron from welding, whereas oxygen and some oxygen and sulfur compounds do reduce welding as well as the coefficient of friction. Interpretation of these data suggests a mechanism of sulfur interaction in lubricating systems.

  16. Surface and interface sciences of Li-ion batteries. -Research progress in electrode-electrolyte interface-

    Science.gov (United States)

    Minato, Taketoshi; Abe, Takeshi

    2017-12-01

    The application potential of Li-ion batteries is growing as demand increases in different fields at various stages in energy systems, in addition to their conventional role as power sources for portable devices. In particular, applications in electric vehicles and renewable energy storage are increasing for Li-ion batteries. For these applications, improvements in battery performance are necessary. The Li-ion battery produces and stores electric power from the electrochemical redox reactions between the electrode materials. The interface between the electrodes and electrolyte strongly affects the battery performance because the charge transfer causing the electrode redox reaction begins at this interface. Understanding of the surface structure, electronic structure, and chemical reactions at the electrode-electrolyte interface is necessary to improve battery performance. However, the interface is located between the electrode and electrolyte materials, hindering the experimental analysis of the interface; thus, the physical properties and chemical processes have remained poorly understood until recently. Investigations of the physical properties and chemical processes at the interface have been performed using advanced surface science techniques. In this review, current knowledge and future research prospects regarding the electrode-electrolyte interface are described for the further development of Li-ion batteries.

  17. Innovations from the “ivory tower”: Wilhelm Barthlott and the paradigm shift in surface science

    Directory of Open Access Journals (Sweden)

    Christoph Neinhuis

    2017-02-01

    Full Text Available This article is mainly about borders that have tremendous influence on our daily life, although many of them exist and act mostly unrecognized. In this article the first objective will be to address more generally the relation between university and society or industry, borders within universities, borders in thinking and the huge amount of misunderstandings and losses resulting from these obvious or hidden borders. In the second part and in more detail, the article will highlight the impact of the research conducted by Wilhelm Barthlott throughout his scientific career during which not only one border was removed, shifted or became more penetrable. Among the various fields of interest not mentioned here (e.g., systematics of Cactaceae, diversity and evolution of epiphytes, the unique natural history of isolated rocky outcrops called inselbergs, or the global distribution of biodiversity, plant surfaces and especially the tremendous diversity of minute structures on leaves, fruits, seeds and other parts of plants represent a common thread through 40 years of scientific career of Wilhelm Barthlott. Based on research that was regarded already old-fashioned in the 1970s and 1980s, systematic botany, results and knowledge were accumulated that, some 20 years later, initiated a fundamental turnover in how surfaces were recognized not only in biology, but even more evident in materials science.

  18. Surface science approach to Pt/carbon model catalysts: XPS, STM and microreactor studies

    Science.gov (United States)

    Motin, Abdul Md.; Haunold, Thomas; Bukhtiyarov, Andrey V.; Bera, Abhijit; Rameshan, Christoph; Rupprechter, Günther

    2018-05-01

    Pt nanoparticles supported on carbon are an important technological catalyst. A corresponding model catalyst was prepared by physical vapor deposition (PVD) of Pt on sputtered HOPG (highly oriented pyrolytic graphite). The carbon substrate before and after sputtering as well as the Pt/HOPG system before and after Pt deposition and annealing were examined by XPS and STM. This yielded information on the surface density of defects, which serve as nucleation centres for Pt, and on the size distribution (mean size/height) of the Pt nanoparticles. Two different model catalysts were prepared with mean sizes of 2.0 and 3.6 nm, both turned out to be stable upon UHV-annealing to 300 °C. After transfer into a UHV-compatible flow microreactor and subsequent cleaning in UHV and under mbar pressure, the catalytic activity of the Pt/HOPG model system for ethylene hydrogenation was examined under atmospheric pressure flow conditions. This enabled to determine temperature-dependent conversion rates, turnover frequencies (TOFs) and activation energies. The catalytic results obtained are in line with the characteristics of technological Pt/C, demonstrating the validity of the current surface science based model catalyst approach.

  19. Quantum molecular dynamics study on energy transfer to the secondary electron in surface collision process of an ion

    International Nuclear Information System (INIS)

    Shibahara, M; Satake, S; Taniguchi, J

    2008-01-01

    In the present study the quantum molecular dynamics method was applied to an energy transfer problem to an electron during ionic surface collision process in order to elucidate how energy of ionic collision transfers to the emitted electrons. Effects of various physical parameters, such as the collision velocity and interaction strength between the observed electron and the classical particles on the energy transfer to the electron were investigated by the quantum molecular dynamics method when the potassium ion was collided with the surface so as to elucidate the energy path to the electron and the predominant factor of energy transfer to the electron. Effects of potential energy between the ion and the electron and that between the surface molecule and the electron on the electronic energy transfer were shown in the present paper. The energy transfer to the observed secondary electron through the potential energy term between the ion and the electron was much dependent on the ion collision energy although the energy increase to the observed secondary electron was not monotonous through the potential energy between the ion and surface molecules with the change of the ion collision energy

  20. Vicinage effects in energy loss and electron emission during grazing scattering of heavy molecular ions from a solid surface

    International Nuclear Information System (INIS)

    Song Yuanhong; Wang Younian; Miskovic, Z.L.

    2005-01-01

    Vicinage effects in the energy loss and the electron emission spectra are studied in the presence of Coulomb explosion of swift, heavy molecular ions, during their grazing scattering from a solid surface. The dynamic response of the surface is treated by means of the dielectric theory within the specular reflection model using the plasmon pole approximation for the bulk dielectric function, whereas the angle-resolved energy spectra of the electrons emitted from the surface are obtained on the basis of the first-order, time-dependent perturbation theory. The evolution of the charge states of the constituent ions in the molecule during scattering is described by a nonequilibrium extension of the Brandt-Kitagawa model. The molecule scattering trajectories and the corresponding Coulomb explosion dynamics are evaluated for the cases of the internuclear axis being either aligned in the beam direction or randomly oriented in the directions parallel to the surface. Our calculations show that the vicinage effect in the energy loss is generally weaker for heavy molecules than for light molecules. In addition, there is clear evidence of the negative vicinage effect in both the energy loss and the energy spectra of the emitted electrons for molecular ions at lower speeds and with the axis aligned in the direction of motion