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. 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

  9. 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...

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Undergraduate Laboratory for Surface Science

    Science.gov (United States)

    Okumura, Mitchio; Beauchamp, Jesse L.; Dickert, Jeffrey M.; Essy, Blair R.; Claypool, Christopher L.

    1996-02-01

    Surface science has developed into a multidisciplinary field of research with applications ranging from heterogeneous catalysis to semiconductor etching (1). Aspects of surface chemistry are now included in physical chemistry textbooks (2) and undergraduate curricula (3), but the perceived cost and complexity of equipment has deterred the introduction of surface science methods in undergraduate laboratories (4). Efforts to expose chemistry undergraduates to state-of-the-art surface instrumentation have just begun (5). To provide our undergraduates with hands-on experience in using standard techniques for characterizing surface morphology, adsorbates, kinetics, and reaction mechanisms, we have developed a set of surface science experiments for our physical chemistry laboratory sequence. The centerpiece of the laboratory is an ultrahigh vacuum (UHV) chamber for studies of single crystal surfaces. This instrument, shown in the figure, has surface analysis capabilities including low energy electron diffraction (LEED), Auger spectroscopy, and temperature-programmed desorption (TPD). The laboratory exercises involve experiments on the well-studied Pt(111) surface. Students prepare a previously mounted single crystal sample by sputtering it with an argon ion gun and heating it under O2. Electron diffraction patterns from the cleaned surface are then obtained with a reverse view LEED apparatus (Princeton Instruments). Images are captured by a charge-coupled device (CCD) camera interfaced to a personal computer for easy downloading and subsequent analysis. Although the LEED images from a Pt(111) surface can be readily interpreted using simple diffraction arguments, this lab provides an excellent context for introducing Miller indices and reciprocal lattices (6). The surface chemical composition can be investigated by Auger spectroscopy, using the LEED apparatus as a simple energy analyzer. The temperature programmed desorption experiment, which is nearly complete, will be

  20. Topics in theoretical surface science

    Energy Technology Data Exchange (ETDEWEB)

    Todd, R.

    1991-10-25

    The energetics and structures of clean and adsorbate covered surfaces are investigated in this dissertation. First, the formalism, within the Corrected Effective Medium (CEM) method, for calculating the surface energy of a clean surface is derived. The surface energies for many different metals and their low index surfaces are presented. The minimization of the surface energy is then used to predict the multilayer relaxation of the Al(111), (100), Ni(100), (110) and Fe(100) surfaces. Extensions of the surface CEM formalism to calculate the binding energies of ordered adsorbates on metals surfaces are also derived. The minimization of the binding energy allowed determination of the binding heights, sites and the extent of induced multilayer relaxation for H and N atoms on the Fe(110), (100) and W(110) surfaces. The last topic deals with the dynamics of the epitaxial growth of metals on metal surfaces. The CEM method was first modified by making approximations to enable faster evaluations of the potential and its corresponding forces for molecular dynamics simulations. The goal of these simulations was to identify the important steps in the formation of equilibrium epitaxial structures. 180 refs., 31 figs., 18 tabs.

  1. 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...

  2. 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.

  3. 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

  4. How old is surface science?

    Energy Technology Data Exchange (ETDEWEB)

    Paparazzo, E. E-mail: paparazzo@ism.cnr.it

    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.

  5. 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.

  6. International Journal of Molecular Science Best Paper Award 2012

    OpenAIRE

    Kathy Lai

    2012-01-01

    International Journal of Molecular Science is instituting an annual award to recognize the outstanding papers in the area of chemistry, molecular physics and molecular biology published in the International Journal of Molecular Science. [...

  7. 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.

  8. 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...

  9. 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.

  10. Augmentation Award for Surface Science Research Training

    National Research Council Canada - National Science Library

    Sibener, Steven

    1996-01-01

    This AASERT grant provided augmentation funds that helped support US citizen graduate student research in the area of surface science as it pertains to gas-surface reactions, collisional energy transfer...

  11. 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

  12. 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.

  13. The Development of New User Research Capabilities in Environmental Molecular Science: Workshop Report

    Energy Technology Data Exchange (ETDEWEB)

    Felmy, Andrew R.; Baer, Donald R.; Fredrickson, Jim K.; Gephart, Roy E.; Rosso, Kevin M.

    2006-10-31

    On August 1, and 2, 2006, 104 scientists representing 40 institutions including 24 Universities and 5 National Laboratories gathered at the W.R. Wiley Environmental Molecular Sciences Laboratory, a National scientific user facility, to outline important science challenges for the next decade and identify major capabilities needed to pursue advanced research in the environmental molecular sciences. EMSL’s four science themes served as the framework for the workshop. The four science themes are 1) Biological Interactions and Interfaces, 2) Geochemistry/Biogeochemistry and Surface Science, 3) Atmospheric Aerosol Chemistry, and 4) Science of Interfacial Phenomena.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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 [...].

  1. 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

  2. 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

  3. 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.

  4. Molecular Dynamics Simulations for Predicting Surface Wetting

    Directory of Open Access Journals (Sweden)

    Jing Chen

    2014-06-01

    Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.

  5. 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)

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. A model of the ideal molecular surface

    Science.gov (United States)

    Henson, Bryan; Smilowitz, Laura

    2014-03-01

    We utilize two manifestations of the phenomena of the quasiliquid phase on the surface of molecular crystals to formulate a universal thermodynamic theory describing the thickness of the layer as a function of the liquid phase activity. We use direct measurements of the liquid thickness as a function of temperature and measurements of the acceleration of thermal decomposition as a function of temperature approaching the melting point to illustrate the mechanism. We show that given the existence of a liquid phase below the melting point the ideal liquid activity is necessarily a fixed function of the free energies of sublimation and vaporization. We use this activity to create a reduced formula for the liquid thickness generally applicable to the molecular surface. We provide a prediction of the mechanism and kinetics of quasiliquid formation and show that the phase exists as a metastable kinetic steady state. We show that to first order the principle controlling feature of the system is the configurational entropy of the liquid/solid interface, rather than the specifics of the surface potential energy. This is analogous to other bulk colligative phenomena such as ideal gas and solution theories, and is thus an ideal, universal formulation of inherent, thermodynamically driven, surface disorder.

  11. 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

  12. 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

  13. 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

  14. 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...

  15. 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.

  16. Chemical beam epitaxy — a child of surface science

    Science.gov (United States)

    Lüth, Hans

    1994-01-01

    Chemical Beam Epitaxy (CBE) or MOMBE is currently one of the major deposition techniques in semiconductor technology. The growth process is performed in a UHV chamber under low pressure conditions and the source material is supplied by molecular beams, such that only surface kinetics are determining the chemical reactions leading to growth of the epilayer. This paper intends to give a review on the development of this deposition technique. After considering the early period, where this epitaxy method started to develop, partially from ideas being born in surface science, some milestones in the further development and basic understanding are presented. The mutual interaction between CBE/MOMBE as a deposition technique and other fields of surface science is described as well as the impact on the deposition technology of other semiconductors (e.g. for Si-based material systems). Future prospects of CBE are finally discussed, particularly in comparison with the competing techniques MBE and MOCVD (metal-organic chemical vapor deposition).

  17. 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-...

  18. 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.

  19. 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.

  20. 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.

  1. Artificial surface-mounted molecular rotors: Molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Vacek, Jaroslav; Michl, Josef

    2007-01-01

    Roč. 17, č. 5 (2007), s. 730-739 ISSN 1616-301X R&D Projects: GA AV ČR IAA400550616; GA MŠk ME 857 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular dynamics * molecular machines * nanomaterials Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.496, year: 2007

  2. 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

    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......Wetting is essential and ubiquitous in a variety of natural and technological processes. Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... 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...

  3. The surface science of titanium dioxide

    Science.gov (United States)

    Diebold, Ulrike

    2003-01-01

    Titanium dioxide is the most investigated single-crystalline system in the surface science of metal oxides, and the literature on rutile (1 1 0), (1 0 0), (0 0 1), and anatase surfaces is reviewed. This paper starts with a summary of the wide variety of technical fields where TiO 2 is of importance. The bulk structure and bulk defects (as far as relevant to the surface properties) are briefly reviewed. Rules to predict stable oxide surfaces are exemplified on rutile (1 1 0). The surface structure of rutile (1 1 0) is discussed in some detail. Theoretically predicted and experimentally determined relaxations of surface geometries are compared, and defects (step edge orientations, point and line defects, impurities, surface manifestations of crystallographic shear planes—CSPs) are discussed, as well as the image contrast in scanning tunneling microscopy (STM). The controversy about the correct model for the (1×2) reconstruction appears to be settled. Different surface preparation methods, such as reoxidation of reduced crystals, can cause a drastic effect on surface geometries and morphology, and recommendations for preparing different TiO 2(1 1 0) surfaces are given. The structure of the TiO 2(1 0 0)-(1×1) surface is discussed and the proposed models for the (1×3) reconstruction are critically reviewed. Very recent results on anatase (1 0 0) and (1 0 1) surfaces are included. The electronic structure of stoichiometric TiO 2 surfaces is now well understood. Surface defects can be detected with a variety of surface spectroscopies. The vibrational structure is dominated by strong Fuchs-Kliewer phonons, and high-resolution electron energy loss spectra often need to be deconvoluted in order to render useful information about adsorbed molecules. The growth of metals (Li, Na, K, Cs, Ca, Al, Ti, V, Nb, Cr, Mo, Mn, Fe, Co, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) as well as some metal oxides on TiO 2 is reviewed. The tendency to 'wet' the overlayer, the growth morphology, the

  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.

    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...

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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…

  10. Pyridine coordination chemistry for molecular assemblies on surfaces.

    Science.gov (United States)

    de Ruiter, Graham; Lahav, Michal; van der Boom, Milko E

    2014-12-16

    CONSPECTUS: Since the first description of coordination complexes, many types of metal-ligand interactions have creatively been used in the chemical sciences. The rich coordination chemistry of pyridine-type ligands has contributed significantly to the incorporation of diverse metal ions into functional materials. Here we discuss molecular assemblies (MAs) formed with a variety of pyridine-type compounds and a metal containing cross-linker (e.g., PdCl2(PhCN2)). These MAs are formed using Layer-by-Layer (LbL) deposition from solution that allows for precise fitting of the assembly properties through molecular programming. The position of each component can be controlled by altering the assembly sequence, while the degree of intermolecular interactions can be varied by the level of π-conjugation and the availability of metal coordination sites. By setting the structural parameters (e.g., bond angles, number of coordination sites, geometry) of the ligand, control over MA structure was achieved, resulting in surface-confined metal-organic networks and oligomers. Unlike MAs that are constructed with organic ligands, MAs with polypyridyl complexes of ruthenium, osmium, and cobalt are active participants in their own formation and amplify the growth of the incoming molecular layer. Such a self-propagating behavior for molecular systems is rare, and the mechanism of their formation will be discussed. These exponentially growing MAs are capable of storing metal salts that can be used during the buildup of additional molecular layers. Various parameters influencing the film growth mechanism will be presented, including (i) the number of binding sites and geometry of the organic ligands, (ii) the metal and the structure of the polypyridyl complexes, (iii) the influence of the metal cross-linker (e.g., second or third row transition metals), and (iv) the deposition conditions. By systematic variation of these parameters, switching between linear and exponential growth could

  11. Molecular biology of the Chlamydia pneumoniae surface

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Østergaard, Lars; Birkelund, Svend

    1997-01-01

    Chlamydia pneumoniaeis a fastidious microorganism with a characteristic biphasic lifecycle causing a variety of human respiratory tract infections. There is limited knowledge about the molecular biology of C. pneumoniae, and only a few genes have been sequenced. The structure of the chlamydial...

  12. 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.

  13. 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.

  14. 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

  15. Molecular Engineering of Smart Polymer Surfaces

    National Research Council Canada - National Science Library

    Koberstein, Jeffrey

    1999-01-01

    ...; when the surface is placed against poly(methyl methacrylate), release behavior is observed. Bonding to the latter substrate can be enhanced by replacing the silane functionality with a carboxylic acid...

  16. 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.

  17. Light-driven altitudinal molecular motors on surfaces

    NARCIS (Netherlands)

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

    2009-01-01

    A Cu(I)-catalyzed 1,3-dipolar cycloaddition was used to construct a monolayer of an altitudinal molecular motor on quartz and silicon substrates, which represents the fastest light-driven molecular motor, to date, grafted to a solid surface.

  18. Discovering the future of molecular sciences

    CERN Document Server

    Pignataro, Bruno

    2014-01-01

    Bruno Pignataro is Professor of Physical Chemistry at the University of Palermo. He received his degree in chemistry in 1995 from the University of Catania and his PhD in materials science five years later. He has chaired the European Young Chemist Award in 2006, 2008, 2010 and 2012. He has authored more than 100 scientific publications and leads a group working in the fields of nanoscience, nanotechnology, electronics and biotechnology .

  19. 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)

  20. 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

  1. 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

  2. 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.

  3. 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

  4. CF3+ etching silicon surface: A molecular dynamics study

    NARCIS (Netherlands)

    Zhao, C.; Lu, X.; He, P.; Zhang, P.; Sun, W.; Zhang, Jingwei; Chen, F.; Gou, F.

    2012-01-01

    In this study, a molecular dynamics simulation method has been employed to investigate CF3 + ions, bombarding Si surface with the energy of 100, 200, 300 and 400 eV and an incident angle of 45 degrees with respect to the normal. The simulation results show that when CF3+ ions approach the Si surface

  5. 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.

  6. 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

  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

    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. The Chemistry and Physics of Molecular Surfaces

    Science.gov (United States)

    Kaldor, A.; Cox, D. M.; Trevor, D. J.; Zakin, M. R.

    1986-06-01

    This article reviews the results of several recent experiments performed in our laboratory designed to elucidate the fundamental chemical and physical properties of clusters of both transition metals and other refractory elements containing from one to several hundred atoms. The gas-phase reactivity of clusters towards a variety of reagents is explored using a fast-flow reactor system. Strong cluster size-dependent variations in reactivity are observed, especially for the case of hydrogen chemisorption. Measurement of cluster photoionization thresholds (IPs) provides a sensitive probe of the evolution of cluster electronic structure as a function of the number of constituent atoms. Cluster ionization potentials are observed to exhibit fluctuations about the smooth global falloff predicted by the classical drop model, indicating the non-bulk-like behavior of small clusters. Measurement of shifts in IP induced by chemisorption of different reagents provides insight into the nature of adsorbate-cluster bonding. The formation and properties of bare and metal-doped carbon clusters are explored, with particular emphasis on elucidating the photophysics and photochemistry of the postulated ultrastable larger clusters. The results suggest that further work is required to prove soccer ball-like structures for C50, C60, etc. Finally, infrared multiple-photon dissociation (IR-MPD) is demonstrated to be a viable technique for obtaining infrared spectra of absorbate-cluster complexes. This technique is an important new tool for obtaining information about the molecularity of gas-phase reactions beyond that currently available from mass spectrometric analysis. As an illustration of the method, IR-MPD spectra of methanol chemisorbed on small iron clusters are obtained.

  9. 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.

  10. 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

  11. 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.

  12. Vibrational excitation in molecule--surface collisions due to temporary negative molecular ion formation

    International Nuclear Information System (INIS)

    Gadzuk, J.W.

    1983-01-01

    Inelastic electron scattering from gaseous and physisorbed diatomic molecules results in greatly enhanced vibrational overtone excitation if the incident electron has the appropriate energy to form a shape-resonance-induced temporary negative molecular ion. It is proposed here that due to the image potential lowering of the electron affinity level of a diatomic molecule in interaction with a metal surface, somewhere outside the surface an incident molecule would find its affinity level degenerate with or lower than the substrate Fermi level at which point a substrate electron could hop onto the molecule, in analogy with gas phase harpooning processes. A negative molecular ion is thus formed which remains until the molecular ion reflects from the surface and the affinity level rises above the Fermi level, thus permitting reverse electron hopping back into the metal. The lifetime of the molecular ion can be controlled by varying both the kinetic energy of the incident molecule and also the substrate work function. In analogy with the electron scattering events, greatly enhanced vibrational excitation of overtones is expected in the molecules of the scattered beam. Induced fluorescence probing of the vibrational state distribution should then yield fundamental information pertaining to the dynamics of charge transfer reactions and nonadiabatic effects in molecule--surface interactions. A theory of this phenomenon is here presented together with the numerical consequences for a model system designed to simulate N 2 or NO scattering from standard surface science metal surfaces

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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)

  19. 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.

  20. Atomic and molecular layer deposition for surface modification

    International Nuclear Information System (INIS)

    Vähä-Nissi, Mika; Sievänen, Jenni; Salo, Erkki; Heikkilä, Pirjo; Kenttä, Eija; Johansson, Leena-Sisko; Koskinen, Jorma T.; Harlin, Ali

    2014-01-01

    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 2 O 3 due to e.g. complex formation. • Same effect on cellulosic fabrics observed with low temperature deposited TiO 2 . • Different film growth and oxidation potential with different precursors. • Hybrid layer on inorganic layer can be used to improve adhesion of polymer melt

  1. 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.

  2. Molecular clutch drives cell response to surface viscosity.

    Science.gov (United States)

    Bennett, Mark; Cantini, Marco; Reboud, Julien; Cooper, Jonathan M; Roca-Cusachs, Pere; Salmeron-Sanchez, Manuel

    2018-02-06

    Cell response to matrix rigidity has been explained by the mechanical properties of the actin-talin-integrin-fibronectin clutch. Here the molecular clutch model is extended to account for cell interactions with purely viscous surfaces (i.e., without an elastic component). Supported lipid bilayers present an idealized and controllable system through which to study this concept. Using lipids of different diffusion coefficients, the mobility (i.e., surface viscosity) of the presented ligands (in this case RGD) was altered by an order of magnitude. Cell size and cytoskeletal organization were proportional to viscosity. Furthermore, there was a higher number of focal adhesions and a higher phosphorylation of FAK on less-mobile (more-viscous) surfaces. Actin retrograde flow, an indicator of the force exerted on surfaces, was also seen to be faster on more mobile surfaces. This has consequential effects on downstream molecules; the mechanosensitive YAP protein localized to the nucleus more on less-mobile (more-viscous) surfaces and differentiation of myoblast cells was enhanced on higher viscosity. This behavior was explained within the framework of the molecular clutch model, with lower viscosity leading to a low force loading rate, preventing the exposure of mechanosensitive proteins, and with a higher viscosity causing a higher force loading rate exposing these sites, activating downstream pathways. Consequently, the understanding of how viscosity (regardless of matrix stiffness) influences cell response adds a further tool to engineer materials that control cell behavior. Copyright © 2018 the Author(s). Published by PNAS.

  3. Use of molecular beams for kinetic measurements of chemical reactions on solid surfaces

    Science.gov (United States)

    Zaera, Francisco

    2017-05-01

    In this review we survey the contributions that molecular beam experiments have provided to our understanding of the dynamics and kinetics of chemical interactions of gas molecules with solid surfaces. First, we describe the experimental details of the different instrumental setups and approaches available for the study of these systems under the ultrahigh vacuum conditions and with the model planar surfaces often used in modern surface-science experiments. Next, a discussion is provided of the most important fundamental aspects of the dynamics of chemical adsorption that have been elucidated with the help of molecular beam experiments, which include the development of potential energy surfaces, the determination of the different channels for energy exchange between the incoming molecules and the surface, the identification of adsorption precursor states, the understanding of dissociative chemisorption, the determination of the contributions of corrugation, steps, and other structural details of the surface to the adsorption process, the effect to molecular steering, the identification of avenues for assisting adsorption, and the molecular details associated with the kinetics of the uptake of adsorbates as a function of coverage. We follow with a summary of the work directed at the determination of kinetic parameters and mechanistic details of surface reactions associated with catalysis, mostly those promoted by late transition metals. This discussion we initiate with an overview of what has been learned about simple bimolecular reactions such as the oxidation of CO and H2 with O2 and the reaction of CO with NO, and continue with the review of the studies of more complex systems such as the oxidation of alcohols, the conversion of organic acids, the hydrogenation and isomerization of olefins, and the oxidative activation of alkanes under conditions of short contact times. Sections 6 and 7 of this review deal with the advances made in the use of molecular beams with

  4. Probing surface tension additivity on chemically heterogeneous surfaces by a molecular approach.

    Science.gov (United States)

    Wang, Jihang; Bratko, Dusan; Luzar, Alenka

    2011-04-19

    Surface free energy of a chemically heterogeneous surface is often treated as an approximately additive quantity through the Cassie equation [Cassie ABD (1948) Discuss Faraday Soc 3:11-16]. However, deviations from additivity are common, and molecular interpretations are still lacking. We use molecular simulations to measure the microscopic analogue of contact angle, Θ(c), of aqueous nanodrops on heterogeneous synthetic and natural surfaces as a function of surface composition. The synthetic surfaces are layers of graphene functionalized with prototypical nonpolar and polar head group: methyl, amino, and nitrile. We demonstrate positive as well as negative deviations from the linear additivity. We show the deviations reflect the uneven exposure of mixture components to the solvent and the linear relation is recovered if fractions of solvent-accessible surface are used as the measure of composition. As the spatial variations in polarity become of larger amplitude, the linear relation can no longer be obtained. Protein surfaces represent such natural patterned surfaces, also characterized by larger patches and roughness. Our calculations reveal strong deviations from linear additivity on a prototypical surface comprising surface fragments of melittin dimer. The deviations reflect the disproportionately strong influence of isolated polar patches, preferential wetting, and changes in the position of the liquid interface above hydrophobic patches. Because solvent-induced contribution to the free energy of surface association grows as cos Θ(c), deviations of cos Θ(c) from the linear relation directly reflect nonadditive adhesive energies of biosurfaces.

  5. 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.

  6. 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.

  7. 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

    2015-04-28

    The human skin is an organ with a surface area of 1.5-2 m(2) 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.

  8. 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

  9. Learning in Science: A Comparison of Deep and Surface Approaches.

    Science.gov (United States)

    Chin, Christine; Brown, David E.

    2000-01-01

    Explores the differences between deep and surface approaches to learning science. Findings indicate that the deep-surface learning differences fall into five categories: (1) generative thinking; (2) nature of explanations; (3) asking questions; (4) metacognitive activity; and (5) approach to tasks. Suggests that teachers can encourage a deep…

  10. Controlling Molecular Growth between Fractals and Crystals on Surfaces.

    Science.gov (United States)

    Zhang, Xue; Li, Na; Gu, Gao-Chen; Wang, Hao; Nieckarz, Damian; Szabelski, Paweł; He, Yang; Wang, Yu; Xie, Chao; Shen, Zi-Yong; Lü, Jing-Tao; Tang, Hao; Peng, Lian-Mao; Hou, Shi-Min; Wu, Kai; Wang, Yong-Feng

    2015-12-22

    Recent studies demonstrate that simple functional molecules, which usually form two-dimensional (2D) crystal structures when adsorbed on solid substrates, are also able to self-assemble into ordered openwork fractal aggregates. To direct and control the growth of such fractal supramolecules, it is necessary to explore the conditions under which both fractal and crystalline patterns develop and coexist. In this contribution, we study the coexistence of Sierpiński triangle (ST) fractals and 2D molecular crystals that were formed by 4,4″-dihydroxy-1,1':3',1″-terphenyl molecules on Au(111) in ultrahigh vacuum. Growth competition between the STs and 2D crystals was realized by tuning substrate and molecular surface coverage and changing the functional groups of the molecular building block. Density functional theory calculations and Monte Carlo simulations are used to characterize the process. Both experimental and theoretical results demonstrate the possibility of steering the surface self-assembly to generate fractal and nonfractal structures made up of the same molecular building block.

  11. Surface and Bulk Reactivity of Iron Oxyhydroxides : A Molecular Perspective

    OpenAIRE

    Song, Xiaowei

    2013-01-01

    Iron oxyhydroxide (FeOOH) mineral plays an important role in a variety of atmospheric, terrestrial and technological settings. Molecular resolution of reactions involving these minerals is thereby required to develop a fundamental understanding of their contributions in processes taking place in the atmosphere, Earth’s upper crust as well as the hydrosphere. This study resolves interactions involving four different types of synthetic FeOOH particles with distinct and well-defined surfaces, na...

  12. 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

  13. 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.

  14. 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

  15. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

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

    1996-01-01

    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......)7X7 and Si(100)2X1. Strong phonon-assisted sticking was observed for gases at 300 K and surface temperatures between 550 K and 1050 K. The absolute values as well as the temperature variation of the adsorption and desorption rates show surprisingly little isotope effect, and they differ only little...... 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...

  16. 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.)

  17. Molecular characterization of water and surfactant AOT at nanoemulsion surfaces.

    Science.gov (United States)

    Hensel, Jennifer K; Carpenter, Andrew P; Ciszewski, Regina K; Schabes, Brandon K; Kittredge, Clive T; Moore, Fred G; Richmond, Geraldine L

    2017-12-19

    Nanoemulsions and microemulsions are environments where oil and water can be solubilized in one another to provide a unique platform for many different biological and industrial applications. Nanoemulsions, unlike microemulsions, have seen little work done to characterize molecular interactions at their surfaces. This study provides a detailed investigation of the near-surface molecular structure of regular (oil in water) and reverse (water in oil) nanoemulsions stabilized with the surfactant dioctyl sodium sulfosuccinate (AOT). Vibrational sum-frequency scattering spectroscopy (VSFSS) is used to measure the vibrational spectroscopy of these AOT stabilized regular and reverse nanoemulsions. Complementary studies of AOT adsorbed at the planar oil-water interface are conducted with vibrational sum-frequency spectroscopy (VSFS). Jointly, these give comparative insights into the orientation of interfacial water and the molecular characterization of the hydrophobic and hydrophilic regions of AOT at the different oil-water interfaces. Whereas the polar region of AOT and surrounding interfacial water molecules display nearly identical behavior at both the planar and droplet interface, there is a clear difference in hydrophobic chain ordering even when possible surface concentration differences are taken into account. This chain ordering is found to be invariant as the nanodroplets grow by Ostwald ripening and also with substitution of different counterions (Na:AOT, K:AOT, and Mg:AOT) that consequently also result in different sized nanoparticles. The results paint a compelling picture of surfactant assembly at these relatively large nanoemulsion surfaces and allow for an important comparison of AOT at smaller micellar (curved) and planar oil-water interfaces.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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).

  3. Internal Energy Dependence of Molecular Condensation Coefficients Determined from Molecular Beam Surface Scattering Experiments

    Science.gov (United States)

    Sibener, S. J.; Lee, Y. T.

    1978-05-01

    An experiment was performed which confirms the existence of an internal mode dependence of molecular sticking probabilities for collisions of molecules with a cold surface. The scattering of a velocity selected effusive beam of CCl{sub 4} from a 90 K CC1{sub 4} ice surface has been studied at five translational velocities and for two different internal temperatures. At a surface temperature of 90 K (approx. 99% sticking probability) a four fold increase in reflected intensity was observed for the internally excited (560 K) CC1{sub 4} relative to the room temperature (298 K) CC1{sub 4} at a translational velocity of 2.5 X 10{sup 4} cm/sec. For a surface temperature of 90 K all angular distributions were found to peak 15{sup 0} superspecularly independent of incident velocity.

  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. Low energy atomic and molecular collision with graphite surface

    International Nuclear Information System (INIS)

    Bercu, M.; Grecu, V. V.

    2002-01-01

    The interaction of atomic and molecular species of hydrogen with basal plane of graphite has been investigated by means of atomic cluster models of 10, 24 and 48 carbon atoms using Hartree-Fock - Linear Combination of Atomic Orbitals (HF-LCAO) theory at the ab-initio and semiempirical level of approximation. The last approach was based on an original package developed for carbon clusters. Atomic migration between consecutive basal planes was described by cluster models of two sheets of carbon atoms. Our contribution presents the theoretical results about atomic and molecular interactions with graphite. It was found for H atom bonding energy the value 2.6 eV, using the largest cluster model. The migration of H atoms above the surface and between consecutive basal planes was simulated by extended calculations of potential energy in each point of a mesh containing 450 points describing a local surface of 0.25 nm 2 . A 3D interpolation approach gives the image of a hypersurface potential energy projection at a given distance to the graphite surface. The semi-quantitative results have indicated two significant facts related to atomic species migration. The first is that H atom has the smallest displacement barrier along C-C bonds at a distance of 1.3 A from the basal plane. In the case of absorbed atoms between graphite basal planes an almost free motion channel has been found parallel to the surface. The interaction potential barrier for H atom collision with graphite surface at the center of the carbon ring has been calculated neglecting surface vibration modes and found to be 5.9 eV . The hyperfine interaction between the electron of hydrogen and the proton has been taken as a measure of the interaction between the incident atom and the target local states. The isotropic hyperfine constant obtained at the level of the semiempiric calculations was found to be 402 Gs at the equilibrium position of H atom above a C atom at a distance of 1.3 A. The corresponding value

  6. 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.

  7. 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.

  8. 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

  9. Restriction of molecular twisting on a gold nanoparticle surface.

    Science.gov (United States)

    Debnath, Tushar; Dana, Jayanta; Maity, Partha; Lobo, Hyacintha; Shankarling, Ganapati S; Ghosh, Hirendra N

    2015-04-07

    To understand the photophysical properties of intramolecular charge transfer (ICT) and twisted intramolecular charge transfer (TICT) states on a gold nanoparticle (Au NP) surface, we have designed and synthesized a new coumarin molecule (C3) that exists both as ICT and TICT states in its excited state in a polar environment. On a Au NP surface, an excited C3 molecule only exists as an ICT state owing to restricted molecular rotation of a diethylamino group; as a result, no conversion from the ICT to TICT state was observed. Selection of the preferential state of a molecule with dual emitting states can be helpful for selected biological applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. 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.

  11. Antifreeze Glycoproteins Alter the Molecular Scale Surface Morphology of Ice

    Science.gov (United States)

    Zepeda, Salvador; Orme, Christine A.; Qiu, Roger; Yeh, Yin

    2003-03-01

    Trematomas borchgrevinki live in the harsh super-cooled waters of the Antarctic. Critical to their survival are antifreeze glycoproteins (AFGPs) that further suppress the freezing temperature of their blood serum in addition to the colligative action of salts found in the ocean. These proteins also modify ice crystal growth habits as well as inhibit recrystallization in polycrystalline ice. To date many other types of antifreeze proteins have been identified in cold weather insects, plants, and other fish, but the exact mechanism is not entirely understood. The mechanism is non-colligative since only a few mg/ml are required for ice crystal growth inhibition and a non-equilibrium melting/freezing point hysteresis is observed. Atomic force microscopy (AFM) can yield a wealth of surface information that can reveal molecular scale information of biomineralization processes. We use AFM to directly probe the surface of ice crystals grown from the vapor in the pure phase and in the presence of growth inhibitors/modifiers, AFGPs. Results show that the AFGPs heavily pin the surface of ice.

  12. Controlling molecular deposition and layer structure with supramolecular surface assemblies

    Science.gov (United States)

    Theobald, James A.; Oxtoby, Neil S.; Phillips, Michael A.; Champness, Neil R.; Beton, Peter H.

    2003-08-01

    Selective non-covalent interactions have been widely exploited in solution-based chemistry to direct the assembly of molecules into nanometre-sized functional structures such as capsules, switches and prototype machines. More recently, the concepts of supramolecular organization have also been applied to two-dimensional assemblies on surfaces stabilized by hydrogen bonding, dipolar coupling or metal co-ordination. Structures realized to date include isolated rows, clusters and extended networks, as well as more complex multi-component arrangements. Another approach to controlling surface structures uses adsorbed molecular monolayers to create preferential binding sites that accommodate individual target molecules. Here we combine these approaches, by using hydrogen bonding to guide the assembly of two types of molecules into a two-dimensional open honeycomb network that then controls and templates new surface phases formed by subsequently deposited fullerene molecules. We find that the open network acts as a two-dimensional array of large pores of sufficient capacity to accommodate several large guest molecules, with the network itself also serving as a template for the formation of a fullerene layer.

  13. Associateship | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Specialization: AIMD Simulation, X-ray Science, Ultrafast Science, Surface Science, Molecular Beam Experiments Address: IPC Department, Indian Institute of Science, .... Specialization: Game Theory & Optimisation, Stochastic Control, Information Theory Address: Systems & Control Engineering, Indian Institute of ...

  14. Molecular Tension Probes for Imaging Forces at the Cell Surface.

    Science.gov (United States)

    Liu, Yang; Galior, Kornelia; Ma, Victor Pui-Yan; Salaita, Khalid

    2017-12-19

    Mechanical forces are essential for a variety of biological processes ranging from transcription and translation to cell adhesion, migration, and differentiation. Through the activation of mechanosensitive signaling pathways, cells sense and respond to physical stimuli from the surrounding environment, a process widely known as mechanotransduction. At the cell membrane, many signaling receptors, such as integrins, cadherins and T- or B-cell receptors, bind to their ligands on the surface of adjacent cells or the extracellular matrix (ECM) to mediate mechanotransduction. Upon ligation, these receptor-ligand bonds transmit piconewton (pN) mechanical forces that are generated, in part, by the cytoskeleton. Importantly, these forces expose cryptic sites within mechanosensitive proteins and modulate the binding kinetics (on/off rate) of receptor-ligand complexes to further fine-tune mechanotransduction and the corresponding cell behavior. Over the past three decades, two categories of methods have been developed to measure cell receptor forces. The first class is traction force microscopy (TFM) and micropost array detectors (mPADs). In these methods, cells are cultured on elastic polymers or microstructures that deform under mechanical forces. The second category of techniques is single molecule force spectroscopy (SMFS) including atomic force microscopy (AFM), optical or magnetic tweezers, and biomembrane force probe (BFP). In SMFS, the experimenter applies external forces to probe the mechanics of individual cells or single receptor-ligand complexes, serially, one bond at a time. Although these techniques are powerful, the limited throughput of SMFS and the nN force sensitivity of TFM have hindered further elucidation of the molecular mechanisms of mechanotransduction. In this Account, we introduce the recent advent of molecular tension fluorescence microscopy (MTFM) as an emerging tool for molecular imaging of receptor mechanics in living cells. MTFM probes are

  15. 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

  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. 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

  18. 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...... of air. Hence, nanobubles have been observed and proposed as the origin of long range ``hydrophobic'' forces19-30 even for hydrophilic silica-water interfaces unusual phenomena related to nanobubbles have been observed.31-33 In this work we study the role of air on the wetting of amorphous silica...

  19. 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.

  20. The Accelerator Facility at the Environmental Molecular Sciences Laboratory (EMSL)

    Science.gov (United States)

    Thevuthasan, S.; Peden, C. H. F.; Engelhard, M. H.; Baer, D. R.; Herman, G. S.; Liang, Y.

    1997-03-01

    The EMSL, a new Department of Energy (DOE) user facility located at PNNL, will have several state-of-the-art systems, including an accelerator facility that can be used by scientists from around the world. The accelerator facility at EMSL consists of a model 9SDH-2 Pelletron 3.4 MV electrostatic tandem ion accelerator with three beam lines. These beam lines are dedicated to UHV ion scattering capabilities, implantation capabilities, and HV ion scattering capabilities, respectively. The end station attached to the UHV beam line has several electron spectroscopies such as low energy electron diffraction (LEED) and Auger electron spectroscopy (AES) in addition to the ion scattering capabilities. This end station will be interfaced with the EMSL transfer capability that allows a sample to be synthesized, processed, and characterized in several surface science UHV systems. We will discuss the accelerator facility and the capabilities along with some initial results. (Work supported by the DOE/ER/OHER)

  1. Molecular Analyzer for Complex Refractory Organic-Rich Surfaces (MACROS)

    Science.gov (United States)

    Getty, Stephanie A.; Cook, Jamie E.; Balvin, Manuel; Brinckerhoff, William B.; Li, Xiang; Grubisic, Andrej; Cornish, Timothy; Ferrance, Jerome; Southard, Adrian

    2017-01-01

    The Molecular Analyzer for Complex Refractory Organic-rich Surfaces, MACROS, is a novel instrument package being developed at NASA Goddard Space Flight Center. MACROS enables the in situ characterization of a sample's composition by coupling two powerful techniques into one compact instrument package: (1) laser desorption/ionization time-of-flight mass spectrometry (LDMS) for broad detection of inorganic mineral composition and non-volatile organics, and (2) liquid-phase extraction methods to gently isolate the soluble organic and inorganic fraction of a planetary powder for enrichment and detailed analysis by liquid chromatographic separation coupled to LDMS. The LDMS is capable of positive and negative ion detection, precision mass selection, and fragment analysis. Two modes are included for LDMS: single laser LDMS as the broad survey mode and two step laser mass spectrometry (L2MS). The liquid-phase extraction will be done in a newly designed extraction module (EM) prototype, providing selectivity in the analysis of a complex sample. For the sample collection, a diamond drill front end will be used to collect rock/icy powder. With all these components and capabilities together, MACROS offers a versatile analytical instrument for a mission targeting an icy moon, carbonaceous asteroid, or comet, to fully characterize the surface composition and advance our understanding of the chemical inventory present on that body.

  2. 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 Molecular...cular Formula and Molecular Weight - NBDC NikkajiRDF | LSDB Archive ... ...329 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Mole

  3. 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

  4. 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.

  5. 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.

  6. 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)

  7. 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

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

    Indian Academy of Sciences (India)

    ular immunology; Genetic Recombination and DNA Repair; Biology of RNA – splicing, editing,. 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 ...

  9. Molecular Modeling of Diffusion on a Crystalline PETN Surface

    Energy Technology Data Exchange (ETDEWEB)

    Lin, P; Khare, R; Gee, R H; Weeks, B L

    2007-07-13

    Surface diffusion on a PETN crystal was investigated by treating the surface diffusion as an activated process in the formalism of transition state theory. In particular, surface diffusion on the (110) and (101) facets, as well as diffusion between these facets, were considered. We successfully obtained the potential energy barriers required for PETN surface diffusion. Our results show that the (110) surface is more thermally active than the (101) surface and PETN molecules mainly diffuses from the (110) to (101) facet. These results are in good agreement with experimental observations and previous simulations.

  10. 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

  11. 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).

  12. Designing high-temperature steels via surface science and thermodynamics

    Science.gov (United States)

    Gross, Cameron T.; Jiang, Zilin; Mathai, Allan; Chung, Yip-Wah

    2016-06-01

    Electricity in many countries such as the US and China is produced by burning fossil fuels in steam-turbine-driven power plants. The efficiency of these power plants can be improved by increasing the operating temperature of the steam generator. In this work, we adopted a combined surface science and computational thermodynamics approach to the design of high-temperature, corrosion-resistant steels for this application. The result is a low-carbon ferritic steel with nanosized transition metal monocarbide precipitates that are thermally stable, as verified by atom probe tomography. High-temperature Vickers hardness measurements demonstrated that these steels maintain their strength for extended periods at 700 °C. We hypothesize that the improved strength of these steels is derived from the semi-coherent interfaces of these thermally stable, nanosized precipitates exerting drag forces on impinging dislocations, thus maintaining strength at elevated temperatures.

  13. Surface activity and molecular characteristics of cuttlefish skin gelatin modified by oxidized linoleic acid

    NARCIS (Netherlands)

    Aewsiri, T.; Benjakul, S.; Visessanguan, W.; Wierenga, P.A.; Gruppen, H.

    2011-01-01

    Surface activity and molecular changes of cuttlefish skin gelatin modified with oxidized linoleic acid (OLA) prepared at 60, 70 and 80 °C at different times were investigated. Modification of gelatin with OLA could improve surface activity of resulting gelatin as evidenced by the decreased surface

  14. Engineered cell surfaces: fertile ground for molecular landscaping.

    Science.gov (United States)

    Mahal, L K; Bertozzi, C R

    1997-06-01

    The cell surface contains a wealth of information that determines how cells interact with their environment. Methods for directing the cell surface expression of novel protein-based and oligosaccharide-based epitopes are stimulating new directions in biotechnology and biomedical research.

  15. 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

  16. Science Academies' Refresher Course on Cell and Molecular ...

    Indian Academy of Sciences (India)

    2011-11-25

    Nov 25, 2011 ... This Course is aimed at giving the participants a hands-on training on some cell and molecular biology techniques and the theory behind them. A variety of teaching methods like lectures, discussions and laboratory work will facilitate the learning process. The Course will help the participants to gain and ...

  17. 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

  18. 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.

  19. Molecular dynamics calculation of the surface tension of aluminum nanodrops

    International Nuclear Information System (INIS)

    Gubin, A.S.; Botyachkova, A.I.; Dubrovskij, A.V.

    2012-01-01

    A method has been proposed for calculating the surface tension coefficient of liquid drops. The density and normal and tangential components of the stress tensor have been calculated as functions of the distance to the center of a nanodrop [ru

  20. 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 ...

  1. 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.

  2. 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.

  3. 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)

  4. Atomic and molecular layer activation of dielectric surfaces

    Science.gov (United States)

    Senkevich, John Joseph

    Strong interaction between the material deposit and substrate is critical to stable deposits and interfaces. The work presented here focuses on the surface activation of dielectric surfaces and oxidized metal surfaces to promote the chemisorption of palladium (II) hexafluoroacetylacetonate (PdII (hfac)2). The goal is to develop reliable, robust metallization protocols, which enable strong interactions between the metal and substrate. SiO2, air exposed Ta, Trikon, and SiLK were activated with sulfur or phosphorus. Two types of activations were developed; one based on self-assembled chemistry, and the other a plasma-assisted process. Activation of the surface using self-assembly techniques was carried out using mercaptan-terminated silane and tetrasulfide silane. The resulting films were characterized by variable angle spectroscopic ellipsometry, contact angle goniometry, and X-ray photoelectron spectroscopy. Tetrasulfide silane sources films exhibit self-limiting behavior, even in the presence of water vapor; whereas mercaptan-terminated silane sourced films tend to be thicker. The surface activations using atomic layers of sulfur and phosphorus were carried out in a rf plasma chamber using hydrogen sulfide and phosphine sources, respectively. The activations were studied as functions of rf power, system pressure, and substrate material. Results show that higher rf powers and lower system pressures promote greater surface coverages by sulfur with a reduced oxidation state. The activated dielectrics show evidence of PdII(hfac)2 chemisorption, in contrast to non-activated surfaces. The binding energy shift of the Pd3d 5/2 XPS peak towards elemental Pd provides evidence for the dissociative chemisorption of PdII(hfac)2. The extent of dissociation depends on the substrate temperature and the activation method used. The conclusions of the work presented here have implications for metallization using highly polarizable transition metals. Specifically, it can be applied to

  5. 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.

  6. 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

  7. 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.

  8. Surface Modification and Nanojunction Fabrication with Molecular Wires

    Science.gov (United States)

    2016-11-02

    synthesis, inorganic chemistry , molecular electronics 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT SAR 18. NUMBER OF PAGES   6    19a...contact between molecules and the electrode. For the previous AOARD project (FA2386-12-1-4006), the Taiwan and US PI/co-PIs studied both metal string...measurements for single-molecule studies were developed by the Taiwan team. The highlight of the current project period is the fabrication of high-performance

  9. 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.

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

    Indian Academy of Sciences (India)

    The adsorbed layer formed of PEG and chloride ion (Cl−) in the presence of copper ions has a definite role in controlling the deposition mechanism and the coating characteristics. The adsorption behaviour and suppressor nature of PEG with different MW (200–20000) on the physicochemical and the surface morphological ...

  11. 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.

  12. 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.

  13. 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.)

  14. Formation of Surface Nanobubbles and the Universality of Their Contact Angles: A Molecular Dynamics Approach

    NARCIS (Netherlands)

    Weijs, Joost; Snoeijer, Jacobus Hendrikus; Lohse, Detlef

    2012-01-01

    We study surface nanobubbles using molecular dynamics simulation of ternary (gas, liquid, solid) systems of Lennard-Jones fluids. They form for a sufficiently low gas solubility in the liquid, i.e., for a large relative gas concentration. For a strong enough gas-solid attraction, the surface

  15. Facile assembly of light-driven molecular motors onto a solid surface

    NARCIS (Netherlands)

    Chen, Jiawen; Chen, Kuang-Yen; Carroll, Gregory T; Feringa, Ben L

    2014-01-01

    In order to improve the rotary motion of surface assembled light-driven molecular motors, tetra-acid-functionalized motors were bound to an amine-coated quartz surface without prior activation of the acid groups. In contrast to earlier bipodal motors, the tetravalent motor showed no significant

  16. Molecular dynamics simulation of temperature effects on CF3+ etching of Si surface

    NARCIS (Netherlands)

    Ning, J. P.; Lu, X. D.; Zhao, C. L.; Qin, Y. M.; He, P. N.; Bogaerts, A.; Gou, F. J.

    2010-01-01

    Molecular dynamics method was employed to investigate the effects of the reaction layer formed near the surface region on CF3+ etching of Si at different temperatures. The simulation results show that the coverages of F and C are sensitive to the surface temperature. With increasing temperature, the

  17. External surface adsorption on silicalite-1 zeolite studied by molecular simulation

    NARCIS (Netherlands)

    Garcia-Perez, E.; Schnell, S.K.; Castillo, J.M.; Calero, S.; Kjelstrup, S.; Dubbeldam, D.; Vlugt, T.J.H.

    2011-01-01

    We have studied the adsorption of ethane, propane, and their mixtures on the external surface of silicalite-1 zeolite by molecular simulation using a classical force field. The ideal adsorbed solution theory (IAST) was successfully used to describe mixture adsorption, both on the external surface

  18. Molecular dynamics simulations on surface properties of silicon dioxide melts

    CERN Document Server

    Röder, A

    2000-01-01

    In the present thesis the surface properties of a silicon dioxide melt were studied. As first systems drops (i.e. sytems without periodic boundary conditions) of N=432, 1536, as well as 4608 atoms were considered. The second analyzed geometry corresponds to that of a thin film, i. e. periodic boundary conditions in x- and y-direction were present, while in z-direction one had a free surface. In this case a system of N=1152 atoms was considered. As model potential the two-body potential proposed by Beest, Kramer, and van Santen was applied. For both geometries five temperatures were considered, which lied in the range of 3000 K

  19. 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.

  20. 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.

  1. 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......, 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...

  2. Chemical and Molecular Characterization of Biofilm on Metal Surfaces

    Digital Repository Service at National Institute of Oceanography (India)

    Bhosle, N.B.

    in seawater. Biofouling 17, 129 145. Cowie, G.L., Hedges, J.I., 1984. Carbohydrates sources in a coastal marine environment. Geochimica et Cosmochimica Acta 48, 2075 2087. Cowie, G.L., Hedges, J.I., Prahl, F.G., deLange, G.J., 1995. Elemental... to assess development of conditioning film and biofilm on metal surfaces (Bhosle et al., 1989; Bhosle et al., 1990; Sonak and Bhosle, 1995; Bhosle and Wagh, 1997, D?Souza and Bhosle, 2003). This chapter is a compilation of relevant information...

  3. The dynamics of molecular interactions and chemical reactions at metal surfaces: testing the foundations of theory.

    Science.gov (United States)

    Golibrzuch, Kai; Bartels, Nils; Auerbach, Daniel J; Wodtke, Alec M

    2015-04-01

    We review studies of molecular interactions and chemical reactions at metal surfaces, emphasizing progress toward a predictive theory of surface chemistry and catalysis. For chemistry at metal surfaces, a small number of central approximations are typically made: (a) the Born-Oppenheimer approximation of electronic adiabaticity, (b) the use of density functional theory at the generalized gradient approximation level, (c) the classical approximation for nuclear motion, and (d) various reduced-dimensionality approximations. Together, these approximations constitute a provisional model for surface chemical reactivity. We review work on some carefully studied examples of molecules interacting at metal surfaces that probe the validity of various aspects of the provisional model.

  4. 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)

  5. Silanization of quartz, silicon and mica surfaces with light-driven molecular motors : construction of surface-bound photo-active nanolayers

    NARCIS (Netherlands)

    London, Gabor; Carroll, Gregory T.; Feringa, Ben L.

    2013-01-01

    The attachment of molecular rotary motors containing triethoxysilane functional groups to quartz, silicon and mica surfaces is described. Motors containing silane coupling agents in their structure form stable molecular layers on quartz and silicon surfaces. Motors attached to these surfaces were

  6. 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.

  7. 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 an...

  8. 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

  9. 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

  10. 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...... 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......-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...

  11. 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.

  12. 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)

  13. 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

  14. 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

  15. Acousto-Optic Imaging Spectrometers for Mars Surface Science

    Science.gov (United States)

    Glenar, D. A.; Blaney, D. L.

    2000-01-01

    NASA's long term plan for Mars sample collection and return requires a highly streamlined approach for spectrally characterizing a landing site, documenting the mineralogical make-up of the site and guiding the collections of samples which represent the diversity of the site. Ideally, image data should be acquired at hundreds of VIS and IR wavelengths, in order to separately distinguish numerous anticipated species, using principal component analysis and linear unmixing. Cameras with bore-sighted point spectrometers can acquire spectra of isolated scene elements, but it requires 10(exp 2) to 10(exp 2) successive motions and precise relative pointing knowledge in order to create a single data cube which qualifies as a spectral map. These and other competing science objectives have to be accomplished within very short lander/rover operational lifetime (a few sols). True, 2-D imaging spectroscopy greatly speeds up the data acquisition process, since the spectra of all pixels in the scene are collected at once. This task can be accomplished with cameras that use electronically tunable acousto-optic tunable filters (AOTFs) as the optical tuning element. AOTFs made from TeO2 are now a mature technology, and operate at wavelengths from near-UV to about 5 microns. Because of incremental improvements in the last few years, present generation devices are rugged, radiation-hard and operate at temperatures down to at least 150K so they can be safely integrated into the ambient temperature optics of in-situ instruments such as planetary or small-body landers. They have been used for ground-based astronomy, and were also baselined for the ST-4 Champollion IR comet lander experiment (CIRCLE), prior to cancellation of the ST-4 mission last year. AIMS (for Acousto-optic Imaging spectrometer), is a prototype lander instrument which is being built at GSFC with support by the NASA OSS Advanced Technologies and Mission Studies, Mars Instrument Definition and Development Program (MIDP

  16. Foraging on the potential energy surface: a swarm intelligence-based optimizer for molecular geometry.

    Science.gov (United States)

    Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D; Sebastiani, Daniel

    2012-11-21

    We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

  17. 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.

  18. Analytical performance of molecular beacons on surface immobilized gold nanoparticles of varying size and density.

    Science.gov (United States)

    Uddayasankar, Uvaraj; Krull, Ulrich J

    2013-11-25

    The high quenching efficiency of metal nanoparticles has facilitated its use as quenchers in molecular beacons. To optimize this system, a good understanding of the many factors that influence molecular beacon performance is required. In this study, molecular beacon performance was evaluated as a function of gold nanoparticle size and its immobilization characteristics. Gold nanoparticles of 4 nm, 15 nm and 87 nm diameter, were immobilized onto glass slides. Each size regime offered distinctive optical properties for fluorescence quenching of molecular dyes that were conjugated to oligonucleotides that were immobilized to the gold nanoparticles. Rigid double stranded DNA was used as a model to place fluorophores at different distances from the gold nanoparticles. The effect of particle size and also the immobilization density of nanoparticles was evaluated. The 4 nm and 87 nm gold nanoparticles offered the highest sensitivity in terms of the change in fluorescence intensity as a function of distance (3-fold improvement for Cy5). The optical properties of the molecular fluorophore was of significance, with Cy5 offering higher contrast ratios than Cy3 due to the red-shifted emission spectrum relative to the plasmon peak. A high density of gold nanoparticles reduced contrast ratios, indicating preference for a monolayer of immobilized nanoparticles when considering analytical performance. Molecular beacon probes were then used in place of the double stranded oligonucleotides. There was a strong dependence of molecular beacon performance on the length of a linker used for attachment to the nanoparticle surface. The optimal optical performance was obtained with 4 nm gold nanoparticles that were immobilized as monolayers of low density (5.7×10(11)particles cm(-2)) on glass surfaces. These nanoparticle surfaces offered a 2-fold improvement in analytical performance of the molecular beacons when compared to other nanoparticle sizes investigated. The principles developed

  19. 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)

  20. 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.

  1. 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.

  2. Molecular dynamics study on mechanism of preformed particle gel transporting through nanopores: Surface chemistry and heterogeneity

    Science.gov (United States)

    Cui, Peng; Zhang, Heng; Ma, Ying; Hao, Qingquan; Liu, Gang; Sun, Jichao; Yuan, Shiling

    2017-10-01

    The translocation behavior of preformed particle gel (PPG) in porous media is crucial for its application in enhanced oil recovery. By means of non-equilibrium molecular dynamics simulation, the translocation mechanism of PPG confined in different silica nanopores were investigated. The influence of surface chemistry and chemical heterogeneity of silica nanopore on the translocation process was revealed. As the degree of surface hydroxylation increases and the heterogeneity decreases, the pulling force needed to drive PPG decreases. We infer that the nanopore's surface (i.e. surface chemistry and heterogeneity) affects the translocation of PPG indirectly by forming different hydration layers.

  3. Surface free energy of ultra-high molecular weight polyethylene modified by electron and gamma irradiation

    International Nuclear Information System (INIS)

    Abdul-Kader, A.M.; Turos, A.; Radwan, R.M.; Kelany, A.M.

    2009-01-01

    Surface free energy of biocompatible polymers is important factor which affects the surface properties such as wetting, adhesion and biocompatibility. In the present work, the change in the surface free energy of ultra-high molecular weight polyethylene (UHMWPE) samples, which is produced by electron beam and gamma ray irradiation were, investigated. Mechanism of the changes in surface free energy induced by irradiations of doses ranging from 25 to 500 kGy was studied. FTIR technique was applied for sample analysis. Contact angle measurements showed that wettability and surface free energy of samples have increased with increasing the irradiation dose, where the values of droplet contact angle of the samples decrease gradually with increasing the radiation dose. The increase in the wettability and surface free energy of the irradiated samples are attributed to formation of hydrophilic groups on the polymer surface by the oxidation, which apparently occurs by exposure of irradiated samples to the air.

  4. 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.

  5. Probing the surface profile and friction behavior of heterogeneous polymers: a molecular dynamics study

    Science.gov (United States)

    Dai, L.; Sorkin, V.; Zhang, Y. W.

    2017-04-01

    We perform molecular dynamics simulations to investigate molecular structure alternation and friction behavior of heterogeneous polymer (perfluoropolyether) surfaces using a nanoscale probing tip (tetrahedral amorphous carbon). It is found that depending on the magnitude of the applied normal force, three regimes exist: the shallow depth-sensing (SDS), deep depth-sensing (DDS), and transitional depth-sensing (TDS) regimes; TDS is between SDS and DDS. In SDS, the tip is floating on the polymer surface and there is insignificant permanent alternation in the polymer structure due to largely recoverable atomic deformations, and the surface roughness profile can be accurately measured. In DDS, the tip is plowing through the polymer surface and there is significant permanent alternation in the molecular structure. In this regime, the lateral friction force rises sharply and fluctuates violently when overcoming surface pile-ups. In SDS, the friction can be described by a modified Amonton’s law including the adhesion effect; meanwhile, in DDS, the adhesion effect is negligible but the friction coefficient is significantly higher. The underlying reason for the difference in these regimes rests upon different contributions by the repulsion and attraction forces between the tip and polymer surfaces to the friction force. Our findings here reveal important insights into lateral depth-sensing on heterogeneous polymer surfaces and may help improve the precision of depth-sensing devices.

  6. 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.

  7. 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.

  8. 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

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

    International Nuclear Information System (INIS)

    Ferguson, Ken R.; Bucher, Maximilian; Bozek, John D.; Carron, Sebastian; Castagna, Jean-Charles; Coffee, Ryan; 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; Bostedt, Christoph

    2015-01-01

    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

  10. 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.

  11. 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).

  12. 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.

  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. 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...

  15. Towards Dynamic Control of Wettability by Using Functionalized Altitudinal Molecular Motors on Solid Surfaces

    NARCIS (Netherlands)

    London, Gabor; Chen, Kuang-Yen; Carroll, Gregory T.; Feringa, Ben L.

    2013-01-01

    We report the synthesis of altitudinal molecular motors that contain functional groups in their rotor part. In an approach to achieve dynamic control over the properties of solid surfaces, a hydrophobic perfluorobutyl chain and a relatively hydrophilic cyano group were introduced to the rotor part

  16. Effect of Surface Pollution on Homogeneous Ice Nucleation: A Molecular Dynamics Study

    Czech Academy of Sciences Publication Activity Database

    Pluhařová, Eva; Vrbka, L.; Jungwirth, Pavel

    2010-01-01

    Roč. 114, č. 17 (2010), s. 7831-7838 ISSN 1932-7447 R&D Projects: GA MŠk LC512 Grant - others:NSF(US) CHE0909227 Institutional research plan: CEZ:AV0Z40550506 Keywords : ice nucleation * surface contamination * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.520, year: 2010

  17. Observation of a distinct surface molecular orientation in films of a high mobility conjugated polymer.

    Science.gov (United States)

    Schuettfort, Torben; Thomsen, Lars; McNeill, Christopher R

    2013-01-23

    The molecular orientation and microstructure of films of the high-mobility semiconducting polymer poly(N,N-bis-2-octyldodecylnaphthalene-1,4,5,8-bis-dicarboximide-2,6-diyl-alt-5,5-2,2-bithiophene) (P(NDI2OD-T2)) are probed using a combination of grazing-incidence wide-angle X-ray scattering (GIWAXS) and near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy. In particular a novel approach is used whereby the bulk molecular orientation and surface molecular orientation are simultaneously measured on the same sample using NEXAFS spectroscopy in an angle-resolved transmission experiment. Furthermore, the acquisition of bulk-sensitive NEXAFS data enables a direct comparison of the information provided by GIWAXS and NEXAFS. By comparison of the bulk-sensitive and surface-sensitive NEXAFS data, a distinctly different molecular orientation is observed at the surface of the film compared to the bulk. While a more "face-on" orientation of the conjugated backbone is observed in the bulk of the film, consistent with the lamella orientation observed by GIWAXS, a more "edge-on" orientation is observed at the surface of the film with surface-sensitive NEXAFS spectroscopy. This distinct edge-on surface orientation explains the high in-plane mobility that is achieved in top-gate P(NDI2OD-T2) field-effect transistors (FETs), while the bulk face-on texture explains the high out-of-plane mobilities that are observed in time-of-flight and diode measurements. These results also stress that GIWAXS lacks the surface sensitivity required to probe the microstructure of the accumulation layer that supports charge transport in organic FETs and hence may not necessarily be appropriate for correlating film microstructure and FET charge transport.

  18. Science synergism study for EOS on evolution of desert surfaces

    Science.gov (United States)

    Farr, Tom G.

    1987-01-01

    The effectiveness of EOS data as a basis for the study of desert surfaces' evolution is presently evaluated for both long and short term geomorphic evolution. Attention is given to the usefulness of such sensor systems planned for EOS as MODIS for regional vegetation distribution/variability monitoring, HIRIS for visible-near IR observations, TIMS for lithological identification, HMMR and SSMI for soil characteristics, LASA for atmospheric profiles, SAR for surface roughness, ALT for two-dimensional topography, ACR for the calibration of imaging sensors, and ERBE for climate modeling and regional surface albedo variation determinations.

  19. Surface science studies on titania for solar fuel applications

    Science.gov (United States)

    Hadsell, Courtney Sara Mathews

    Titanium dioxide (titania) is a well-studied material for various applications including but not limited to, paint, sunscreen, pharmaceuticals and solar cell applications (photocatalysis.) It can be found in three main crystal forms; rutile, anatase, and brookite and this work will focus on the anatase form which has been heavily studied for its potential in dye sensitized solar cells (DSSCs.) I propose that aqueous and photo dye stability can be improved by taking special care to the exposed surface of anatase. Additionally, the theoretical maximum open circuit voltage of a DSSC is dependent upon which surface is exposed to the electrolyte. Previous works in this area have not been rigorous with respect to the surface and morphology of titania being used. Standard synthesis techniques of anatase lead to a crystal that generally has 94% of the titania (101) surface exposed, and the other 6% is the higher energy (001) surface. The (101) surface has 5 & 6-fold coordinated titania whereas the (001) surface only has 5-fold (under) coordinated titania. This under-coordination leads to enhanced reactivity of the (001) surface which has been demonstrated by dissassociative adsorption of water, and catalysis applications. Much theoretical work has focused on the minority (001) surface because up until recently synthesizing anatase with enhanced exposure of the (001) surface has been difficult. The initial materials for this study will be multilayer titania nanotubes (TiNTs) and nanosheets (TiNS) which have been previously characterized by my predecessor. The TiNTs and TiNS have 100% exposed (001)-like surface. Both of these materials show enhanced stability of phosphonated dye binding as compared to the current standard of anatase nanoparticles (NPs) however, due to their limited thermal stability the potential of incorporating the TiNTs and TiNSs into devices has been eliminated in this study. To overcome the device limitations I will synthesis a novel titania nanotile

  20. 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}

  1. Surface-mediated molecular events in material-induced blood-plasma coagulation

    Science.gov (United States)

    Chatterjee, Kaushik

    Coagulation and thrombosis persist as major impediments associated with the use of blood-contacting medical devices. We are investigating the molecular mechanism underlying material-induced blood-plasma coagulation focusing on the role of the surface as a step towards prospective development of improved hemocompatible biomaterials. A classic observation in hematology is that blood/blood-plasma in contact with clean glass surface clots faster than when in contact with many plastic surfaces. The traditional biochemical theory explaining the underlying molecular mechanism suggests that hydrophilic surfaces, like that of glass, are specific activators of the coagulation cascade because of the negatively-charged groups on the surface. Hydrophobic surfaces are poor procoagulants or essentially "benign" because they lack anionic groups. Further, these negatively-charged surfaces are believed to not only activate blood factor XII (FXII), the key protein in contact activation, but also play a cofactor role in the amplification and propagation reactions that ultimately lead to clot formation. In sharp contrast to the traditional theory, our investigations indicate a need for a paradigm shift in the proposed sequence of contact activation events to incorporate the role of protein adsorption at the material surfaces. These studies have lead to the central hypothesis for this work proposing that protein adsorption to hydrophobic surfaces attenuates the contact activation reactions so that poorly-adsorbent hydrophilic surfaces appear to be stronger procoagulants relative to hydrophobic surfaces. Our preliminary studies measuring the plasma coagulation response of activated FXII (FXIIa) on different model surfaces suggested that the material did not play a cofactor role in the processing of this enzyme dose through the coagulation pathway. Therefore, we focused our efforts on studying the mechanism of initial production of enzyme at the procoagulant surface. Calculations for the

  2. Path integral molecular dynamics with surface hopping for thermal equilibrium sampling of nonadiabatic systems.

    Science.gov (United States)

    Lu, Jianfeng; Zhou, Zhennan

    2017-04-21

    In this work, a novel ring polymer representation for a multi-level quantum system is proposed for thermal average calculations. The proposed representation keeps the discreteness of the electronic states: besides position and momentum, each bead in the ring polymer is also characterized by a surface index indicating the electronic energy surface. A path integral molecular dynamics with surface hopping (PIMD-SH) dynamics is also developed to sample the equilibrium distribution of the ring polymer configurational space. The PIMD-SH sampling method is validated theoretically and by numerical examples.

  3. 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.

  4. 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.

  5. The effects of zeolite molecular sieve based surface treatments on the properties of wool fabrics

    Energy Technology Data Exchange (ETDEWEB)

    Carran, Richard S.; Ghosh, Arun, E-mail: Arun.Ghosh@agresearch.co.nz; Dyer, Jolon M.

    2013-12-15

    Wool is a natural composite fiber, with keratin and keratin-associated proteins as the key molecular components. The outermost surface of wool fibers comprises a hydrophobic lipid layer that can lead to unsatisfactory processing and properties of fabric products. In this study, molecular sieve 5A, a Na{sup +} and Ca{sup 2+} exchanged type A zeolite with a 1:1 Si:Al ratio was integrated onto the surface of wool using 3-mercaptopropyl trimethoxy silane. The resultant surface morphology, hydrophilicity and mechanical performance of the treated wool fabrics were then evaluated. Notably, the surface hydrophilicity of wool was observed to increase dramatically. When wool was treated with a dispersion of 2 wt% acetic acid, 2.5 wt% zeolite and 0.3 wt% or more silane, the water contact angle was observed to decrease from an average value of 148° to 0° over a period of approximately 30 s. Scanning electron microscopic imaging indicated good coverage of the wool surface with zeolite particles, with infrared spectroscopic evaluation indicating strong bonding of the dealuminated zeolite to wool keratins. This application of zeolite showed no adverse effects on the tensile and other mechanical properties of the fabric. This study indicates that zeolite-based treatment is a potentially efficient approach to increasing the surface hydrophilicity and modifying other key surface properties of wool and wool fabrics.

  6. The effects of zeolite molecular sieve based surface treatments on the properties of wool fabrics

    Science.gov (United States)

    Carran, Richard S.; Ghosh, Arun; Dyer, Jolon M.

    2013-12-01

    Wool is a natural composite fiber, with keratin and keratin-associated proteins as the key molecular components. The outermost surface of wool fibers comprises a hydrophobic lipid layer that can lead to unsatisfactory processing and properties of fabric products. In this study, molecular sieve 5A, a Na+ and Ca2+ exchanged type A zeolite with a 1:1 Si:Al ratio was integrated onto the surface of wool using 3-mercaptopropyl trimethoxy silane. The resultant surface morphology, hydrophilicity and mechanical performance of the treated wool fabrics were then evaluated. Notably, the surface hydrophilicity of wool was observed to increase dramatically. When wool was treated with a dispersion of 2 wt% acetic acid, 2.5 wt% zeolite and 0.3 wt% or more silane, the water contact angle was observed to decrease from an average value of 148° to 0° over a period of approximately 30 s. Scanning electron microscopic imaging indicated good coverage of the wool surface with zeolite particles, with infrared spectroscopic evaluation indicating strong bonding of the dealuminated zeolite to wool keratins. This application of zeolite showed no adverse effects on the tensile and other mechanical properties of the fabric. This study indicates that zeolite-based treatment is a potentially efficient approach to increasing the surface hydrophilicity and modifying other key surface properties of wool and wool fabrics.

  7. 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.)

  8. 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.

  9. Adsorption mechanism of ribosomal protein L2 onto a silica surface: a molecular dynamics simulation study.

    Science.gov (United States)

    Tosaka, Ryo; Yamamoto, Hideaki; Ohdomari, Iwao; Watanabe, Takanobu

    2010-06-15

    A large-scale molecular dynamics simulation was carried out in order to investigate the adsorption mechanism of ribosomal protein L2 (RPL2) onto a silica surface at various pH values. RPL2 is a constituent protein of the 50S large ribosomal subunit, and a recent experimental report showed that it adsorbs strongly to silica surfaces and that it can be used to immobilize proteins on silica surfaces. The simulation results show that RPL2, especially domains 1 (residues 1-60) and 3 (residues 203-273), adsorbed more tightly to the silica surface above pH 7. We found that a major driving force for the adsorption of RPL2 onto the silica surface is the electrostatic interaction and that the structural flexibility of domains 1 and 3 may further contribute to the high affinity.

  10. 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

  11. Molecular Characteristics and Biological Functions of Surface-Active and Surfactant Proteins.

    Science.gov (United States)

    Sunde, Margaret; Pham, Chi L L; Kwan, Ann H

    2017-06-20

    Many critical biological processes take place at hydrophobic:hydrophilic interfaces, and a wide range of organisms produce surface-active proteins and peptides that reduce surface and interfacial tension and mediate growth and development at these boundaries. Microorganisms produce both small lipid-associated peptides and amphipathic proteins that allow growth across water:air boundaries, attachment to surfaces, predation, and improved bioavailability of hydrophobic substrates. Higher-order organisms produce surface-active proteins with a wide variety of functions, including the provision of protective foam environments for vulnerable reproductive stages, evaporative cooling, and gas exchange across airway membranes. In general, the biological functions supported by these diverse polypeptides require them to have an amphipathic nature, and this is achieved by a diverse range of molecular structures, with some proteins undergoing significant conformational change or intermolecular association to generate the structures that are surface active.

  12. 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...... amount of experimental data gathered during the last decades. This article shows how density functional theory can be used to describe the state of the surface during reactions and the rate of catalytic reactions. It will also show how we are beginning to understand the variation in catalytic activity...

  13. Surface science and electrochemical studies of metal-modified carbides for fuel cells and hydrogen production

    Science.gov (United States)

    Kelly, Thomas Glenn

    Carbides of the early transition metals have emerged as low-cost catalysts that are active for a wide range of reactions. The surface chemistry of carbides can be altered by modifying the surface with small amounts of admetals. These metal-modified carbides can be effective replacements for Pt-based bimetallic systems, which suffer from the drawbacks of high cost and low thermal stability. In this dissertation, metal-modified carbides were studied for reactions with applications to renewable energy technologies. It is demonstrated that metal-modified carbides possess high activity for alcohol reforming and electrochemical hydrogen production. First, the surface chemistry of carbides towards alcohol decomposition is studied using density functional theory (DFT) and surface science experiments. The Vienna Ab initio Simulation Package (VASP) was used to calculate the binding energies of alcohols and decomposition intermediates on metal-modified carbides. The calculated binding energies were then correlated to reforming activity determined experimentally using temperature programmed desorption (TPD). In the case of methanol decomposition, it was found that tungsten monocarbide (WC) selectively cleaved the C-O bond to produce methane. Upon modifying the surface with a single layer of metal such as Ni, Pt, or Rh, the selectivity shifted towards scission of the C-H bonds while leaving the C-O bond intact, producing carbon monoxide (CO) and H2. High resolution energy loss spectroscopy (HREELS) was used to examine the bond breaking sequence as a function of temperature. From HREELS, it was shown that the surfaces followed an activity trend of Rh > Ni > Pt. The Au-modified WC surface possessed too low of a methanol binding energy, and molecular desorption of methanol was the most favorable pathway on this surface. Next, the ability of Rh-modified WC to break the C-C bond of C2 and C3 alcohols was demonstrated. HREELS showed that ethanol decomposed through an acetaldehyde

  14. 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.

  15. 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

  16. 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

  17. 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 ...... hardening of titanium alloys, as well as thermo-reactive diffusion for extreme wear resistance...

  18. Surface science studies of model fuel cell electrocatalysts

    Science.gov (United States)

    Marković, N. M.; Ross, P. N.

    2002-04-01

    The purpose of this review is to discuss progress in the understanding of electrocatalytic reactions through the study of model systems with surface spectroscopies. Pure metal single crystals and well-characterized bulk alloys have been used quite successfully as models for real (commercial) electrocatalysts. Given the sheer volume of all work in electrocatalysis that is on fuel cell reactions, we will focus on electrocatalysts for fuel cells. Since Pt is the model fuel cell electrocatalyst, we will focus entirely on studies of pure Pt and Pt bimetallic alloys. The electrode reactions discussed include hydrogen oxidation/evolution, oxygen reduction, and the electrooxidation of carbon monoxide, formic acid, and methanol. Surface spectroscopies emphasized are FTIR, STM/AFM and surface X-ray scattering (SXS). The discussion focuses on the relation between the energetics of adsorption of intermediates and the reaction pathway and kinetics, and how the energetics and kinetics relate to the extrinsic properties of the model system, e.g. surface structure and/or composition. Finally, we conclude by discussing the limitations that are reached by using pure metal single crystals and well-characterized bulk alloys as models for real catalysts, and suggest some directions for developing more realistic systems.

  19. Probing potential energy surfaces with high-resolution spectroscopy : From the Universe's carbon locker to molecular machines

    NARCIS (Netherlands)

    Maltseva, E.O.

    2017-01-01

    Light is a powerful tool that, on the one hand, can alter the molecular state and, on the other hand, can be used to probe molecular properties without changing the state. Fundamentals of these interactions are potential energy surfaces (PESs) of molecular ground and electronically excited states.

  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. Modular "click" chemistry for electrochemically and photoelectrochemically active molecular interfaces to tin oxide surfaces.

    Science.gov (United States)

    Benson, Michelle C; Ruther, Rose E; Gerken, James B; Rigsby, Matthew L; Bishop, Lee M; Tan, Yizheng; Stahl, Shannon S; Hamers, Robert J

    2011-08-01

    We demonstrate the use of "click" chemistry to form electrochemically and photoelectrochemically active molecular interfaces to SnO(2) nanoparticle thin films. By using photochemical grafting to link a short-chain alcohol to the surface followed by conversion to a surface azide group, we enable use of the Cu(I)-catalyzed azide-alkyne [3 + 2] cycloaddition (CuAAC) reaction, a form of "click" chemistry, on metal oxide surfaces. Results are shown with three model compounds to test the surface chemistry and subsequent ability to achieve electrochemical and photoelectrochemical charge transfer. Surface-tethered ferrocene groups exhibit good electron-transfer characteristics with thermal rates estimated at >1000 s(-1). Time-resolved surface photovoltage measurements using a ruthenium terpyridyl coordination compound demonstrate photoelectron charge transfer on time scales of nanoseconds or less, limited by the laser pulse width. The results demonstrate that the CuAAC "click" reaction can be used to form electrochemically and photoelectrochemically active molecular interfaces to SnO(2) and other metal oxide semiconductors.

  2. 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.

  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. Surface-sensitive molecular interferometry: beyond 3He spin echo experiments

    Science.gov (United States)

    Cantin, Joshua T.; Krems, Roman V.; Godsi, Oded; Maniv, Tsofar; Alexandrowicz, Gil

    2017-04-01

    3 He atoms can be used as surface-sensitive atomic interferometers in 3He spin echo experiments to measure surface morphology, molecular and atomic surface diffusion dynamics, and surface vibrations. However, using the hyperfine states of molecules gives experiments the potential to be less expensive, be more sensitive, and include angle-dependent interactions. The manifold of hyperfine states of molecules is large in comparison to the two nuclear spin states used in 3He spin echo experiments and allows for increased precision, while simultaneously complicating experimental interpretation. Here, we present the theoretical formulation required to interpret these experiments. In particular, we show how to determine the effect of magnetic lensing on the molecular hyperfine states and use a modified form of the transfer matrix method to quantum mechanically describe molecular propagation throughout the experiment. We also discuss how to determine the scattering matrix from the experimental observables via machine learning techniques. As an example, we perform numerical calculations using nine hyperfine states of ortho-hydrogen and compare the results to experiment. This work was funded by NSERC of Canada and the European Research Council under the European Union's seventh framework program (FP/2007-2013)/ERC Grant 307267.

  5. Surface Chemistry of CWAs for Decon Enabling Sciences

    Science.gov (United States)

    2014-11-04

    Ultraviolet and Visible Photochemistry of Methanol at 3D Mesoporous Networks: TiO, The Journal of Physical Chemistry C, (07 2013): 15035. doi...A for none) Presentations since most recent interim report for this project: " Photochemistry of Methanol at 3-D Networked Aerogels of TiO2 and...evaporation • Studied the uptake, thermal, and photochemistry of agent simulants on TiO2 surfaces • Initiated experiments on the uptake and

  6. 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.

  7. Probing the molecular structures of plasma-damaged and surface-repaired low-k dielectrics.

    Science.gov (United States)

    Zhang, Xiaoxian; Myers, John N; Lin, Qinghuang; Bielefeld, Jeffery D; Chen, Zhan

    2015-10-21

    Fully understanding the effect and the molecular mechanisms of plasma damage and silylation repair on low dielectric constant (low-k) materials is essential to the design of low-k dielectrics with defined properties and the integration of low-k dielectrics into advanced interconnects of modern electronics. Here, analytical techniques including sum frequency generation vibrational spectroscopy (SFG), Fourier transform infrared spectroscopy (FTIR), contact angle goniometry (CA) and X-ray photoelectron spectroscopy (XPS) have been employed to provide a comprehensive characterization of the surface and bulk structure changes of poly(methyl)silsesquioxane (PMSQ) low-k thin films before and after O2 plasma treatment and silylation repair. O2 plasma treatment altered drastically both the molecular structures and water structures at the surfaces of the PMSQ film while no bulk structural change was detected. For example, ∼34% Si-CH3 groups were removed from the PMSQ surface, and the Si-CH3 groups at the film surface tilted toward the surface after the O2 plasma treatment. The oxidation by the O2 plasma made the PMSQ film surface more hydrophilic and thus enhanced the water adsorption at the film surface. Both strongly and weakly hydrogen bonded water were detected at the plasma-damaged film surface during exposure to water with the former being the dominate component. It is postulated that this enhancement of both chemisorbed and physisorbed water after the O2 plasma treatment leads to the degradation of low-k properties and reliability. The degradation of the PMSQ low-k film can be recovered by repairing the plasma-damaged surface using a silylation reaction. The silylation method, however, cannot fully recover the plasma induced damage at the PMSQ film surface as evidenced by the existence of hydrophilic groups, including C-O/C[double bond, length as m-dash]O and residual Si-OH groups. This work provides a molecular level picture on the surface structural changes of low

  8. 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.

  9. 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

    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 196 kDa), 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...

  10. 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.

  11. 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

    of air in water at different pressures. Using the calibrated force field, we conduct MD simulations to study the interface between a hydrophilic silica substrate and water surrounded by air at different pressures. We find that the static water contact angle is independent of the air pressure imposed......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...... on the system. Our simulations reveal the presence of a nanometer thick layer of gas at the water–silica interface. We believe that this gas layer could promote nucleation and stabilization of surface nanobubbles at amorphous silica surfaces. © 2014 Elsevier B.V. All rights reserved....

  12. Chemical stability and surface stoichiometry of vanadium oxide phases studied by reactive molecular dynamics simulations

    Science.gov (United States)

    Jeon, Byoungseon; Ko, Changhyun; van Duin, Adri C. T.; Ramanathan, Shriram

    2012-02-01

    Compositional stability of various vanadium oxides and oxide growth on vanadium surfaces have been studied using reactive molecular dynamics simulation methods. Vanadium dioxide (VO2), sesquioxide (V2O3), pentoxide (V2O5), and hexavanadium tridecaoxide (V6O13) are studied in bulk crystalline and thin film structures, investigating charge distribution and pair distribution functions of particle interactions. The stability is estimated to be pentoxide, hexavanadium tridecaoxide, sesquioxide, and dioxide respectively in decreasing order in thin film structures. We then analyze oxide growth kinetics on vanadium (100) and (110) surfaces. The oxidation rate, stoichiometry, charge distribution, and the effect of surface orientation on kinetic phenomena are noted. In the early stages of surface oxidation of our simulation configurations, sesquioxide is found to be the dominant component. The modeling and simulation results are compared with experiments where available.

  13. 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

  14. Electron propagator and surface Green's function calculations in transport molecular junctions

    Science.gov (United States)

    Kletsov, Aleksey

    A new theoretical approach to the calculation of electrical current through a molecular wire, based on ab initio electron propagator methodology, is proposed. The analytical expression for electric current is derived for an arbitrary number of terminal transport orbitals, which is given in terms of Dyson poles, Dyson pole strengths, overlap matrix elements, and expansion coefficients of atomic wavefunctions. The proposed approach is applied to calculations of the current-voltage characteristics of the transport molecular junction with a 1,4-benzene dithiol (BDT) molecule as a bridge. The obtained current-voltage characteristics exhibit negative differential resistance, that can be used in practical electronic devices. From the analysis of the output data, the origin of negative differential resistance in BDT molecular wire is explained. The observation of negative differential resistance in transport molecular devices based on a BDT molecule is predicted for certain Fermi energies. To discover the predicted effect, experimentalists should search for the appropriate Fermi energy by varying metal electrodes, coated by a gold monolayer. In addition, a novel computational method for non-recursive calculations of the surface Green's function matrices, using an infinite number of principal layers, is proposed. This method is employed to calculate the spectral function of the gold and aluminum surfaces. It is shown that the surface spectral function of the metal electrode dependence on applied voltage and this dependence can significantly change the electric current through a molecular wire. The new ab initio methods and computational results presented in this work allow for the prediction of novel devices with unusual properties that can be used in nanotechnology applications.

  15. 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.

  16. Molecular Characterization of Cryptosporidium Oocysts in Samples of Raw Surface Water and Wastewater

    OpenAIRE

    Xiao, Lihua; Singh, Ajaib; Limor, Josef; Graczyk, Thaddeus K.; Gradus, Steve; Lal, Altaf

    2001-01-01

    Recent molecular characterizations of Cryptosporidium parasites make it possible to differentiate the human-pathogenic Cryptosporidium parasites from those that do not infect humans and to track the source of Cryptosporidium oocyst contamination in the environment. In this study, we used a small-subunit rRNA-based PCR-restriction fragment length polymorphism (RFLP) technique to detect and characterize Cryptosporidium oocysts in 55 samples of raw surface water collected from several areas in t...

  17. Proceedings of the Edgewood Chemical Biological Center In-House Laboratory Independent Research and Surface Science Initiative Programs FY12

    Science.gov (United States)

    2012-01-01

    APPROVED FOR PUBLIC RELEASE "Designing Strongly Repellant Surfaces via Molecular Dynamics Simulations" (PI: Cabalo ). This study used atomistic simulations...from Metallic Nanoparticles and Nanostructured Surfaces Jason Guicheteau, Ashish Tripathi, Erik Emmons, Jerry Cabalo , Craig Knox, Brandon Scott...Surfaces via Molecular Dynamics Simulations Craig Knox, Jerry Cabalo , Stephanie Ihejirika, Gary Kilper 116 Vll APPROVED FOR PUBLIC RELEASE Vlll

  18. 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.

  19. 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

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

    Science.gov (United States)

    Habuchi, Satoshi

    2014-01-01

    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. PMID:25152893

  1. 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.

  2. 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.

  3. 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)

  4. Activities of working group on atomic, molecular and nuclear data for medical science

    International Nuclear Information System (INIS)

    1985-03-01

    This is a report on the activities of the Working Group on Atomic, Molecular and Nuclear Data for Medical Science, Japanese Nuclear Data Committee in the fisical years of 1982 and 1983. This report consists of (1) brief reviews on stopping powers of charged particles and electrons and related topics, and on problems to use these data for practical radiotheraphy, (2) reports on the investigation of the present status of data activities in other countries, (3) references, and (4) future plans after 1984. (author)

  5. 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

  6. 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.

  7. Liquid flow in surface-nanostructured channels studied by molecular dynamics simulation

    Science.gov (United States)

    Cao, Bing-Yang; Chen, Min; Guo, Zeng-Yuan

    2006-12-01

    Molecular dynamics simulations have been carried out to investigate the fluid wetting and flow in nanochannels whose surfaces are structured by an array of nanoscale triangular modules. We find that the surface nanostructures have a dual effect on the boundary slip and friction of the liquid nanoflow. On the one hand, the nanostructures can enhance the surface hydrophilicity for a hydrophilic liquid-solid interaction, and can increase the hydrophobicity for a hydrophobic interaction due to a nanoscale lotus effect. In particular, the nanostructured surface may show superhydrophobicity and lead to the large velocity slip of the liquid flow. On the other hand, simultaneously, the nanostructures distort the nanoscale streamlines of the liquid flow near the channel surfaces and block the nanoflow directly, which decreases the apparent slip length equivalently. The dual effect of the nanostructures on the surface wettability and the hydrodynamic disturbance results in a nonmonotonic dependence of the slip length on the nanostructure size. The simulations imply that the surface nanostructures can be applied to control the friction of liquid micro- and nanoflows.

  8. In vitro assays of molecular motors--impact of motor-surface interactions.

    Science.gov (United States)

    Mansson, Alf; Balaz, Martina; Albet-Torres, Nuria; Rosengren, K Johan

    2008-05-01

    In many types of biophysical studies of both single molecules and ensembles of molecular motors the motors are adsorbed to artificial surfaces. Some of the most important assay systems of this type (in vitro motility assays and related single molecule techniques) will be briefly described together with an account of breakthroughs in the understanding of actomyosin function that have resulted from their use. A poorly characterized, but potentially important, entity in these studies is the mechanism of motor adsorption to surfaces and the effects of motor surface interactions on experimental results. A better understanding of these phenomena is also important for the development of commercially viable nanotechnological applications powered by molecular motors. Here, we will consider several aspects of motor surface interactions with a particular focus on heavy meromyosin (HMM) from skeletal muscle. These aspects will be related to heavy meromyosin structure and relevant parts of the vast literature on protein-surface interactions for non-motor proteins. An overview of methods for studying motor-surface interactions will also be given. The information is used as a basis for further development of a model for HMM-surface interactions and is discussed in relation to experiments where nanopatterning has been employed for in vitro reconstruction of actomyosin order. The challenges and potentials of this approach in biophysical studies, compared to the use of self-assembly of biological components into supramolecular protein aggregates (e.g. myosin filaments) will be considered. Finally, this review will consider the implications for further developments of motor-powered lab-on-a-chip devices.

  9. 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

  10. 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.

  11. 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.

  12. 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

    one being associated with devastating wear progress. The properties of alkane lubricants confined between two approaching solids are investigated by a model that accounts for the roughness, curvature and elastic properties of the solid surfaces. We consider linear alkanes of different chain lengths, C......The present work investigates the ability of two nm thick lubrication films to stay in a contact and thereby to prevent excessive wear of the surfaces. At this thickness the film is no longer a fluid but it is the very important intermediate between the lubricated and the dry regimes, the latter......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...

  13. 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

  14. Surface-modified silica colloidal crystals: nanoporous films and membranes with controlled ionic and molecular transport.

    Science.gov (United States)

    Zharov, Ilya; Khabibullin, Amir

    2014-02-18

    Nanoporous membranes are important for the study of the transport of small molecules and macromolecules through confined spaces and in applications ranging from separation of biomacromolecules and pharmaceuticals to sensing and controlled release of drugs. For many of these applications, chemists need to gate the ionic and molecular flux through the nanopores, which in turn depends on the ability to control the nanopore geometry and surface chemistry. Most commonly used nanoporous membrane materials are based on polymers. However, the nanostructure of polymeric membranes is not well-defined, and their surface is hard to modify. Inorganic nanoporous materials are attractive alternatives for polymers in the preparation of nanoporous membranes. In this Account, we describe the preparation and surface modification of inorganic nanoporous films and membranes self-assembled from silica colloidal spheres. These spheres form colloidal crystals with close-packed face centered cubic lattices upon vertical deposition from colloidal solutions. Silica colloidal crystals contain ordered arrays of interconnected three dimensional voids, which function as nanopores. We can prepare silica colloidal crystals as supported thin films on various flat solid surfaces or obtain free-standing silica colloidal membranes by sintering the colloidal crystals above 1000 °C. Unmodified silica colloidal membranes are capable of size-selective separation of macromolecules, and we can surface-modify them in a well-defined and controlled manner with small molecules and polymers. For the surface modification with small molecules, we use silanol chemistry. We grow polymer brushes with narrow molecular weight distribution and controlled length on the colloidal nanopore surface using atom transfer radical polymerization or ring-opening polymerization. We can control the flux in the resulting surface-modified nanoporous films and membranes by pH and ionic strength, temperature, light, and small molecule

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Interaction of C2H with molecular hydrogen: Ab initio potential energy surface and scattering calculations

    Science.gov (United States)

    Dagdigian, Paul J.

    2018-01-01

    The potential energy surface (PES) describing the interaction of the ethynyl (C2H) radical in its ground X˜ 2Σ+ electronic state with molecular hydrogen has been computed through restricted coupled cluster calculations including single, double, and (perturbative) triple excitations [RCCSD(T)], with the assumption of fixed molecular geometries. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants. A representative set of energy dependent state-to-state cross sections is presented and discussed. The PES and cross sections for collisions of H2(j = 0) are compared with a previous study [F. Najar et al., Chem. Phys. Lett. 614, 251 (2014)] of collisions of C2H with H2 treated as a spherical collision partner. Good agreement is found between the two sets of calculations when the H2 molecule in the present calculation is spherically averaged.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Surface-Bound Molecular Film Structure Effects on Electronic and Magnetic Properties

    Science.gov (United States)

    Pronschinske, Alex M.

    This thesis dissertation will discuss the importance of understanding the driving forces of molecular assembly on surfaces and the need to characterize the electronic and magnetic properties of the resulting organic films. Furthermore, experimental results on model organic molecular assemblies, benzoate on Cu(110) and Fe[(H2BPz2)2bpy] ("Fe-bpy") on Au(111), and their novel film properties will be presented. The primary experimental techniques used in this work are scanning tunneling microscopy and spectroscopy (STM, STS), and so a theoretical characterization of constant current distance-voltage STS (z(V)-STS) will also be developed. Deposition of benzoic acid (C6H5COOH) on to Cu(110) will be used to create a diverse molecular environment of benzoate molecules (C6H5COO+). In this film we will utilize structural phases consisting of co-existing orientation (alpha-phase) and uniform molecular orientation (c(8x2) phase) to probe electric potential variation across the surface of the film. Using z( V)-STS find that the electron affinity level of a molecule's near-neighbor will exert a substrate-mediated influence on the energy of the molecule's image potential state; which we describe using a 1-D dielectric continuum model. Motivated by the unique utility of z(V)-STS for gentle probing of molecular electronic structure and electric potential we perform a thorough theoretical characterize of z( V)-STS. We derive a differential equation for simulating z(V)-STS spectra under the standard approximation of a square tunneling barrier. Moreover, we derive an equation for sample density of states (DOS) that is applicable for all modes of STS. The central result of this work for interpretation of z(V)-STS results is a characterization of systematic error between state energy and z(V)-STS peak location, as well we show that empirical normalization procedure for removing background distortion from constant height current-voltage STS, (V/I)dI/dV, is also applicable to z(V)-STS is

  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. 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.

  9. 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)

  10. 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.

  11. 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

    This study explores atomic and molecular adsorption on a number of early transition-metal carbides (TMCs) in NaCl structure by means of density-functional theory calculations. The investigated substrates are the TM-terminated TMC(111) surfaces, of interest because of the presence of different types......, surface relaxations, Bader charges, and surface-localized densities of states (DOSs). Detailed comparisons between surface and bulk DOSs reveal the existence of transition-metal localized SRs (TMSRs) in the pseudogap and of several C-localized SRs (CSRs) in the upper valence band on all considered TMC(111......) 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...

  12. 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

  13. 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

  14. The Center for Environmental Kinetics Analysis: an NSF- and DOE-funded Environmental Molecular Science Institute (EMSI) at Penn State

    Energy Technology Data Exchange (ETDEWEB)

    S. L. Brantley; William D. Burgos; Brian A. Dempsey; Peter J. Heaney; James D. Kubicki; Peter C. Lichtner; Bruce E. Logan; Carmen E. Martinez; Karl T. Mueller; Kwadwo A. Osseo-Asare; Ming Tien; Carl I. Steefel, Glenn A. Waychunas; and John M. Zachara

    2007-04-19

    Physicochemical and microbiological processes taking place at environmental interfaces influence natural processes as well as the transport and fate of environmental contaminants, the remediation of toxic chemicals, and the sequestration of anthropogenic CO2. A team of scientists and engineers has been assembled to develop and apply new experimental and computational techniques to expand our knowledge of environmental kinetics. We are also training a cohort of talented and diverse students to work on these complex problems at multiple length scales and to compile and synthesize the kinetic data. Development of the human resources capable of translating molecular-scale information into parameters that are applicable in real world, field-scale problems of environmental kinetics is a major and relatively unique objective of the Institute's efforts. The EMSI team is a partnership among 10 faculty at The Pennsylvania State University (funded by the National Science Foundation Divisions of Chemistry and Earth Sciences), one faculty member at Juniata College, one faculty member at the University of Florida, and four researchers drawn from Los Alamos National Laboratory, Pacific Northwest National Laboratory, and Lawrence Berkeley National Laboratory (funded by the Department of Energy Division of Environmental Remediation Sciences). Interactions among the applied and academic scientists drives research approaches aimed toward solving important problems of national interest. The Institute is organized into three interest groups (IGs) focusing on the processes of dissolution (DIG), precipitation (PIG), and microbial reactions at surfaces (BIG). Some of the research activity from each IG is highlighted to the right. The IGs interact with each other as each interest group studies reactions across the molecular, microscopic, mesoscopic and, in most cases, field scales. For example, abiotic dissolution and precipitation reactions of Fe oxides as studied in the Dissolution

  15. 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.

  16. Molecular surface structural changes of plasticized PVC materials after plasma treatment.

    Science.gov (United States)

    Zhang, Xiaoxian; Zhang, Chi; Hankett, Jeanne M; Chen, Zhan

    2013-03-26

    In this research, a variety of analytical techniques including sum frequency generation vibrational spectroscopy (SFG), coherent anti-Stokes Raman spectroscopy (CARS), and X-ray photoelectron spectroscopy (XPS) have been employed to investigate the surface and bulk structures of phthalate plasticized poly(vinyl chloride) (PVC) at the molecular level. Two types of phthalate molecules with different chain lengths, diethyl phthalate (DEP) and dibutyl phthalate (DBP), mixed with PVC in various weight ratios were examined to verify their different surface and bulk behaviors. The effects of oxygen and argon plasma treatment on PVC/DBP and PVC/DEP hybrid films were investigated on both the surface and bulk of films using SFG and CARS to evaluate the different plasticizer migration processes. Without plasma treatment, SFG results indicated that more plasticizers segregate to the surface at higher plasticizer bulk concentrations. SFG studies also demonstrated the presence of phthalates on the surface even at very low bulk concentration (5 wt %). Additionally, the results gathered from SFG, CARS, and XPS experiments suggested that the PVC/DEP system was unstable, and DEP molecules could leach out from the PVC under low vacuum after several minutes. In contrast, the PVC/DBP system was more stable; the migration process of DBP out of PVC could be effectively suppressed after oxygen plasma treatment. XPS results indicated the increase of C═O/C-O groups and decrease of C-Cl functionalities on the polymer surface after oxygen plasma treatment. The XPS results also suggested that exposure to argon plasma induced chemical bond breaking and formation of cross-linking or unsaturated groups with chain scission on the surface. Finally, our results indicate the potential risk of using DEP molecules in PVC since DEP can easily leach out from the polymeric bulk.

  17. 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...... are obtained from the literature. The silica surface is modeled by a large 32 ⨯ 32 ⨯ 2 nm amorphous SiO2 structure consisting of 180000 atoms. The water consists of 18000 water molecules surrounded by N2 and O2 air molecules corresponding to air pressures of 0 bar (vacuum), 50 bar, 100 bar and 200 bar. We...... the effect of air and find a consistent increase in the water contact angle reaching 53º at 200 bar air pressure. These results are important for the creation and stability of nanobubbles at hydrophilic interfaces....

  18. The quantum magnetism of individual manganese-12-acetate molecular magnets anchored at surfaces.

    Science.gov (United States)

    Kahle, Steffen; Deng, Zhitao; Malinowski, Nikola; Tonnoir, Charlène; Forment-Aliaga, Alicia; Thontasen, Nicha; Rinke, Gordon; Le, Duy; Turkowski, Volodymyr; Rahman, Talat S; Rauschenbach, Stephan; Ternes, Markus; Kern, Klaus

    2012-01-11

    The high intrinsic spin and long spin relaxation time of manganese-12-acetate (Mn(12)) makes it an archetypical single molecular magnet. While these characteristics have been measured on bulk samples, questions remain whether the magnetic properties replicate themselves in surface supported isolated molecules, a prerequisite for any application. Here we demonstrate that electrospray ion beam deposition facilitates grafting of intact Mn(12) molecules on metal as well as ultrathin insulating surfaces enabling submolecular resolution imaging by scanning tunneling microscopy. Using scanning tunneling spectroscopy we detect spin excitations from the magnetic ground state of the molecule at an ultrathin boron nitride decoupling layer. Our results are supported by density functional theory based calculations and establish that individual Mn(12) molecules retain their intrinsic spin on a well chosen solid support. © 2011 American Chemical Society

  19. SHARC: ab Initio Molecular Dynamics with Surface Hopping in the Adiabatic Representation Including Arbitrary Couplings.

    Science.gov (United States)

    Richter, Martin; Marquetand, Philipp; González-Vázquez, Jesús; Sola, Ignacio; González, Leticia

    2011-05-10

    We present a semiclassical surface-hopping method which is able to treat arbitrary couplings in molecular systems including all degrees of freedom. A reformulation of the standard surface-hopping scheme in terms of a unitary transformation matrix allows for the description of interactions like spin-orbit coupling or transitions induced by laser fields. The accuracy of our method is demonstrated in two systems. The first one, consisting of two model electronic states, validates the semiclassical approach in the presence of an electric field. In the second one, the dynamics in the IBr molecule in the presence of spin-orbit coupling after laser excitation is investigated. Due to an avoided crossing that originates from spin-orbit coupling, IBr dissociates into two channels: I + Br((2)P3/2) and I + Br*((2)P1/2). In both systems, the obtained results are in very good agreement with those calculated from exact quantum dynamical simulations.

  20. Fiber optic apparatus for detecting molecular species by surface enhanced Raman spectroscopy

    Science.gov (United States)

    Angel, S.M.; Sharma, S.K.

    1987-11-30

    Optrode apparatus for detecting constituents of a fluid medium includes an optical fiber having a metal coating on at least a portion of a light transmissive core. The metal is one, such as silver, gold or copper, which enhances emission of Raman signal frequencies by molecules adsorbed on the surface of the coating when monochromatic probe light of a different frequency is scattered by such molecules and the metal coating is sufficiently thin to transmit light between the adsorbed molecules and the core of the fiber. Probe light is directed into one end of the fiber and a detector analyzes light emitted from the fiber for Raman frequencies that identify one or more particular molecular species. In one form, the optrode may function as a working electrode of an electrochemical cell while also serving to detect the products of oxidation or reduction reactions which occur at the electrode surface. 6 figs.

  1. 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

  2. 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

  3. Near-Surface Geophysics: Advancing Earth Science Through Advances in Imaging

    Science.gov (United States)

    Knight, R.

    2006-05-01

    The near-surface of Earth (the top ~100 m) is the region that supports human infrastructure, provides water and mineral resources, and is the interface between solid Earth and atmosphere for many of the biogeochemical cycles that sustain life. Developing an understanding of the processes and properties that occur here is essential for advancing our understanding of many parts of the Earth system. Yet our ability to study, sample, or probe this zone is remarkably primitive. Many investigations rely on drilling, trenching, and direct sampling. But given the pervasive spatial heterogeneity of the region, such methods yield information that is inadequate in terms of the spatial extent and density of sampling. As a result, the Earth science community is turning to geophysical imaging. The area of research that is focused on developing and applying geophysical methods to study this region of Earth is referred to as near-surface geophysics. Near-surface geophysics, as an area of research, includes many types of research, and many types of researchers. Some researchers are drawn to near-surface geophysics due to an interest in specific properties, processes, or applications, which can range from applied to basic science. As examples, near-surface geophysical methods are used for resource exploration and extraction, for the characterization of contaminated sites, for the assessment and design of built infrastructure; and to address scientific questions in neotectonics, volcanology, glaciology, hydrology, sedimentology, archaeology, geochemistry and biogeochemistry. Other researchers are drawn to near-surface geophysics due to an interest in the science of imaging as the driving scientific question. Advances in imaging require investigating the ways in which physical sensors can (or cannot) capture the complexity of a natural system, determining how best to quantify and enhance the spatial and temporal resolution of a measurement, developing new methods for the inversion of

  4. 4th-International Symposium on Ultrafast Surface Science - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Hrvoje Petek

    2005-01-26

    The 4-th International Symposium on Ultrafast Surface Dynamics (UDS4) was held at the Telluride Summer Research Center on June 22-27, 2003. The International Organizing Committee consisting of Hrvoje Petek (USA), Xiaoyang Zhu (USA), Pedro Echenique (Spain) and Maki Kawai (Japan) brought together a total of 51 participants 16 of whom were from Europe, 10 from Japan, and 25 from the USA. The focus of the conference was on ultrafast electron or light induced processes at well-defined surfaces. Ultrafast surface dynamics concerns the transfer of charge and energy at solid surfaces on the femtosecond time scale. These processes govern rates of fundamental steps in surface reactions, interfacial electron transfer in molecular electronics, and relaxation in spin transport. Recent developments in femtosecond laser technology make it possible to measure by a variety of nonlinear optical techniques directly in the time domain the microscopic rates underlying these interfacial processes. Parallel progress in scanning probe microscopy makes it possible at a single molecular level to perform the vibrational and electronic spectroscopy measurements, to induce reactions with tunneling electrons, and to observe their outcome. There is no doubt that successful development in the field of ultrafast surface dynamics will contribute to many important disciplines.

  5. 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.

  6. Nanostructured organic semiconductor films for molecular detection with surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Yilmaz, Mehmet; Babur, Esra; Ozdemir, Mehmet; Gieseking, Rebecca L.; Dede, Yavuz; Tamer, Ugur; Schatz, George C.; Facchetti, Antonio; Usta, Hakan; Demirel, Gokhan

    2017-09-01

    π-Conjugated organic semiconductors have been explored in several optoelectronic devices, yet their use in molecular detection as surface-enhanced Raman spectroscopy (SERS)-active platforms is unknown. Herein, we demonstrate that SERS-active, superhydrophobic and ivy-like nanostructured films of a molecular semiconductor, α,ω-diperfluorohexylquaterthiophene (DFH-4T), can be easily fabricated by vapour deposition. DFH-4T films without any additional plasmonic layer exhibit unprecedented Raman signal enhancements up to 3.4 × 103 for the probe molecule methylene blue. The combination of quantum mechanical computations, comparative experiments with a fluorocarbon-free α,ω-dihexylquaterthiophene (DH-4T), and thin-film microstructural analysis demonstrates the fundamental roles of the π-conjugated core fluorocarbon substitution and the unique DFH-4T film morphology governing the SERS response. Furthermore, Raman signal enhancements up to ~1010 and sub-zeptomole (films with a thin gold layer. Our results offer important guidance for the molecular design of SERS-active organic semiconductors and easily fabricable SERS platforms for ultrasensitive trace analysis.

  7. 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.

  8. 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.

  9. 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.

  10. Synthesis of surface nano-molecularly imprinted polymers for sensitive baicalin detection from biological samples.

    Science.gov (United States)

    Gu, Xiaoli; He, Hongliang; Wang, Chong-Zhi; Gao, Yankun; Zhang, Hongjuan; Hong, Junli; Du, Shuhu; Chen, Lina; Yuan, Chun-Su

    2015-01-01

    Surface molecularly imprinted polymers (MIP@SBA-15) imprinted on the surface of hybrid nanostructured organic/inorganic materials (SBA-15) were prepared for the selective extraction and detection of baicalin (BA) from biological samples. The surface morphologies and characteristics of the imprinted and non-imprinted polymers were characterized by Fourier transform infrared (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermo-gravimetric analysis (TGA) and nitrogen adsorption-desorption isotherms. The results indicated that the polymers were successfully grafted on the surface of SBA-15 and possessed a highly ordered mesoporous structure. In binding tests, MIP@SBA-15 reached saturated adsorption within 80 min and exhibited significant specific recognition toward BA with large adsorption capacity. Meanwhile, the prepared MIP@SBA-15 was used as a selective sorbent for solid-phase extraction of BA from biological samples. Recoveries of BA from the liver and spleen ranged from 90.6% to 90.9% with RSD < 3.7%. All these results reveal that this method is simple, rapid and sensitive for effectively extracting and detecting trace BA in biological samples.

  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. Molecular Imprinting of Silica Nanoparticle Surfaces via Reversible Addition-Fragmentation Polymerization for Optical Biosensing Applications

    Science.gov (United States)

    Oluz, Zehra; Nayab, Sana; Kursun, Talya Tugana; Caykara, Tuncer; Yameen, Basit; Duran, Hatice

    Azo initiator modified surface of silica nanoparticles were coated via reversible addition-fragmentation polymerization (RAFT) of methacrylic acid and ethylene glycol dimethacrylate using 2-phenylprop 2-yl dithobenzoate as chain transfer agent. Using L-phenylalanine anilide as template during polymerization led molecularly imprinted nanoparticles. RAFT polymerization offers an efficient control of grafting process, while molecularly imprinted polymers shows enhanced capacity as sensor. L-phenylalanine anilide imprinted silica particles were characterized by X-Ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM). Performances of the particles were followed by surface plasmon resonance spectroscopy (SPR) after coating the final product on gold deposited glass substrate against four different analogous of analyte molecules: D-henylalanine anilide, L-tyrosine, L-tryptophan and L-phenylalanine. Characterizations indicated that silica particles coated with polymer layer do contain binding sites for L-phenylalanine anilide, and are highly selective for the molecule of interest. This project was supported by TUBITAK (Project No:112M804).

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Update in Molecular Biology and Biotechnology: providing alternative for Sciences and Biology Teachers

    Directory of Open Access Journals (Sweden)

    M. F. Silva

    2008-05-01

    Full Text Available One of the goals of the Coordination of Education and Dissemination of CBME is to contribute for the dissemination and the learning in Molecular Biology and Biotechnology in  all the educational levels. Thus, composing one of our actions in 2007, a course of update in Molecular Biology and Biotechnology directed to 21 teachers of Sciences and Biology of São Carlos (SP, Brazil was carried through, totalizing 24 hours. In one of the meetings, we presented the techniques involving restriction enzymes, gel electrophoresis and its applications, followed of an experimental activity. Also we constructed and  considered the use, for the teachers, of a macroscopic model of a gel box that would represent the displacement of DNA fragments. After that a written questionnaire was used to evaluate the importance attributed for the teachers to the subject, the possibilities of didactic transposition, as well as their interests for other activities that would deal this thematic at great length. From this,  we registered that the 93% of the teachers showed interest in the subject, considering it important and also, 79% of them affirmed to have possibility of didactic transposition of this subject after they have experienced the course. On the other hand, 86% of the teachers did not work the subject in their classes , amongst which 50% for the lack of time or not enough preparation. Therefore, the data suggest that the course had an impact on the vision of the teachers concerning the alternatives to include the subject Molecular Biology and Biotechnology in their curricular planning.

  1. Fabrication and evaluation of temperature responsive molecularly imprinted sorbents based on surface of yeast via surface-initiated AGET ATRP

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Jianming, E-mail: pjm@ujs.edu.cn; Hang, Hui; Li, Xiuxiu; Zhu, Wenjing; Meng, Minjia; Dai, Xiaohui; Dai, Jiangdong; Yan, Yongsheng

    2013-12-15

    Temperature responsive molecularly imprinted polymers (T-MIPs) were prepared based on the surface of yeast by electron transfer atom transfer radical polymerization (AGET ATRP). The as-prepared T-MIPs were charcterized by FT-IR, SEM, TGA and elemental analysis, which indicated that T-MIPs exhibited thermal stability and composed of temperature responsive imprinted layer. Then T-MIPs were evaluated as sorbents to selectively recognise and release cefalexin (CFX) molecules. The results suggested binding properties of T-MIPs were related to the testing temperature. The maximum adsorption capacity of T-MIPs at 303 K was 59.4 mg g{sup −1}, and the maximum release proportion for T-MIPs at 293 K in water for 24 h was 71.08%. The selective recognition experiments demonstrated high affinity and selectivity of T-MIPs towards CFX over competitive compounds, and the specific recognition of binding sites may be based on the distinct size, structure and functional group to the template molecules.

  2. Hybridization Efficiency of Molecular Beacons Bound to Gold Nanowires: Effect of Surface Coverage and Target Length

    Science.gov (United States)

    2010-01-01

    Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3′ dye moiety and a 5′ thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1−2) × 1012 probes/cm2 and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3−4) × 1011 probes/cm2), but not at higher probe coverages (1 × 1012/cm2). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3′ or 5′ end of the complementary target sequence. Additional nucleotides on the 3′ end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5′ end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution. PMID:21038880

  3. Adsorption mechanism of an antimicrobial peptide on carbonaceous surfaces: A molecular dynamics study

    Science.gov (United States)

    Roccatano, Danilo; Sarukhanyan, Edita; Zangi, Ronen

    2017-02-01

    Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptaken by living cells, and their high surface-to-volume ratio facilitates the adsorption of molecules of different natures. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutical agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A-Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surfaces through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalizable Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to the loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus into the interior of the CNT, was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion.

  4. 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...

  5. 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.

  6. Molecular organization of the nanoscale surface structures of the dragonfly Hemianax papuensis wing epicuticle.

    Directory of Open Access Journals (Sweden)

    Elena P Ivanova

    Full Text Available The molecular organization of the epicuticle (the outermost layer of insect wings is vital in the formation of the nanoscale surface patterns that are responsible for bestowing remarkable functional properties. Using a combination of spectroscopic and chromatographic techniques, including Synchrotron-sourced Fourier-transform infrared microspectroscopy (FTIR, x-ray photoelectron spectroscopy (XPS depth profiling and gas chromatography-mass spectrometry (GCMS, we have identified the chemical components that constitute the nanoscale structures on the surface of the wings of the dragonfly, Hemianax papuensis. The major components were identified to be fatty acids, predominantly hexadecanoic acid and octadecanoic acid, and n-alkanes with even numbered carbon chains ranging from C14 to C30. The data obtained from XPS depth profiling, in conjunction with that obtained from GCMS analyses, enabled the location of particular classes of compounds to different regions within the epicuticle. Hexadecanoic acid was found to be a major component of the outer region of the epicuticle, which forms the surface nanostructures, and was also detected in deeper layers along with octadecanoic acid. Aliphatic compounds were detected throughout the epicuticle, and these appeared to form a third discrete layer that was separate from both the inner and outer epicuticles, which has never previously been reported.

  7. Characterisation of engineered surfaces and molecular sensing by neutron and X-ray reflectometry

    International Nuclear Information System (INIS)

    James, Michael

    2010-01-01

    This presentation will give a theoretical and experimental background to the techniques of X-ray and neutron reflectometry for the study of nanoscale thin-films and processes occurring at surfaces. It will discuss the design of optimum samples; as well as the limits of X-ray and neutron reflectometry for such studies. Investigations of thin-films and surfaces in Australia has entered a 'golden age', with the combination of the Platypus time-of-flight neutron reflectometer and a modern laboratory-based X-ray reflectometer at the OPAL research reactor in Sydney. The presentation will then concentrate on studies of engineered thin-film nanostructures. These studies represent a cross-section of results from the first 18 months of operation of the Platypus neutron reflectometer in 2009 and 2010. Molecular systems that will be reported include self-assembled monolayers, diblock copolymer thin-films, bioimetic membranes and light-emitting surfaces created by polymers or fluorescent dendrimers. (author)

  8. 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

  9. Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Kazuya; Liang, Yunfeng, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp; Matsuoka, Toshifumi, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp [Environment and Resource System Engineering, Kyoto University, Kyoto 615-8540 (Japan); Sakka, Tetsuo [Department of Energy and Hydrocarbon Chemistry, Kyoto University, Kyoto 615-8510 (Japan)

    2014-04-14

    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.

  10. Understanding the influence of buckwheat bran on wheat dough baking performance: Mechanistic insights from molecular and material science approaches

    NARCIS (Netherlands)

    Zanoletti, M.; Marti, A.; Marengo, M.; Iametti, S.; Pagani, M.A.; Renzetti, S.

    2017-01-01

    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)

  11. 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

  12. 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

  13. 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

  14. 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:

  15. 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...

  16. 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.

  17. Magnetotransport properties of lateral-surface superlattices by molecular-dynamics Monte Carlo simulation

    Science.gov (United States)

    Yamada, Toshishige; Ferry, D. K.

    1993-01-01

    The magnetotransport properties of a lateral-surface superlattice, a two-dimensional (2D) electron system in a 2D periodic potential, are studied with use of a Monte Carlo technique, where the effect of the magnetic field is included through a Lorentz force and the interparticle Coulomb interaction is included with a molecular-dynamics method. Excellent numerical energy conservation is achieved by adopting a predictor-corrector algorithm to integrate the equations of motion. The simulation shows that the diffusion constant, as a function of the magnetic field, is not a simple monotone function but has a structure with multiple minima. This structure is attributed to the correlated circular electron motion, and this is reminiscent of classical pinning orbits in a 2D antidot array, even in the presence of the Coulomb interaction. The radial-distribution function shows no significant dependence upon the magnetic field up to ten flux quanta per unit cell.

  18. 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)

  19. 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...

  20. 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.

  1. Potentiometric Sensors Based on Surface Molecular Imprinting: Detection of Cancer Biomarkers and Viruses

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.; Zhang, Z; Jain, V; Yi, J; Mueller, S; Sokolov, J; Liu, Z; Levon, K; Rigas, B; Rafailovich, M

    2010-01-01

    The continuing discovery of cancer biomarkers necessitates improved methods for their detection. Molecular imprinting using artificial materials provides an alternative to the detection of a wide range of substances. We applied surface molecular imprinting using self-assembled monolayers to design sensing elements for the detection of cancer biomarkers and other proteins. These elements consist of a gold-coated silicon chip onto which hydroxyl-terminated alkanethiol molecules and template biomolecule are co-adsorbed, where the thiol molecules are chemically bound to the metal substrate and self-assembled into highly ordered monolayers, the biomolecules can be removed, creating the foot-print cavities in the monolayer matrix for this kind of template molecules. Re-adsorption of the biomolecules to the sensing chip changes its potential, which can be measured potentiometrically. We applied this method to the detection of carcinoembryonic antigen (CEA) in both solutions of purified CEA and in the culture medium of a CEA-producing human colon cancer cell line. The CEA assay, validated also against a standard immunoassay, was both sensitive (detection range 2.5-250 ng/mL) and specific (no cross-reactivity with hemoglobin; no response by a non-imprinted sensor). Similar results were obtained for human amylase. In addition, we detected virions of poliovirus in a specific manner (no cross-reactivity to adenovirus, no response by a non-imprinted sensor). Our findings demonstrate the application of the principles of molecular imprinting to the development of a new method for the detection of protein cancer biomarkers and to protein-based macromolecular structures such as the capsid of a virion. This approach has the potential of generating a general assay methodology that could be highly sensitive, specific, simple and likely inexpensive.

  2. Bacillus Cellulase Molecular Cloning, Expression, and Surface Display on the Outer Membrane of Escherichia coli

    Directory of Open Access Journals (Sweden)

    Daehwan Kim

    2018-02-01

    Full Text Available One of the main challenges of using recombinant enzymes is that they are derived from genetically-modified microorganisms commonly located in the intracellular region. The use of these recombinant enzymes for commercial purposes requires the additional processes of cell disruption and purification, which may result in enzyme loss, denaturation, and increased total production cost. In this study, the cellulase gene of Bacillus licheniformis ATCC 14580 was cloned, over-expressed, and surface displayed in recombinant Escherichia coli using an ice-nucleation protein (INP. INP, an outer membrane-bound protein from Pseudomonas syringae, was utilized as an anchor linker, which was cloned with a foreign cellulase gene into the pET21a vector to develop a surface display system on the outer membrane of E. coli. The resulting strain successfully revealed cellulase on the host cell surface. The over-expressed INP-cellulase fusion protein was confirmed via staining assay for determining the extracellular cellulase and Western blotting method for the molecular weight (MW of cellulase, which was estimated to be around 61.7 kDa. Cell fractionation and localization tests demonstrated that the INP-cellulase fusion protein was mostly present in the supernatant (47.5% and outer membrane (19.4%, while the wild-type strain intracellularly retained enzymes within cytosol (>61%, indicating that the INP gene directed the cellulase expression on the bacteria cell surface. Further studies of the optimal enzyme activity were observed at 60 °C and pH 7.0, and at least 75% of maximal enzyme activity was preserved at 70 °C.

  3. 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.

  4. Nontypable Haemophilus influenzae Displays a Prevalent Surface Structure Molecular Pattern in Clinical Isolates

    Science.gov (United States)

    Mauro, Silvia; Hood, Derek W.; Viadas, Cristina; Calatayud, Laura; Morey, Pau; Servin, Alain; Liñares, Josefina; Oliver, Antonio; Bengoechea, José Antonio; Garmendia, Junkal

    2011-01-01

    Non-typable Haemophilus influenzae (NTHi) is a Gram negative pathogen that causes acute respiratory infections and is associated with the progression of chronic respiratory diseases. Previous studies have established the existence of a remarkable genetic variability among NTHi strains. In this study we show that, in spite of a high level of genetic heterogeneity, NTHi clinical isolates display a prevalent molecular feature, which could confer fitness during infectious processes. A total of 111 non-isogenic NTHi strains from an identical number of patients, isolated in two distinct geographical locations in the same period of time, were used to analyse nine genes encoding bacterial surface molecules, and revealed the existence of one highly prevalent molecular pattern (lgtF+, lic2A+, lic1D+, lic3A+, lic3B+, siaA−, lic2C+, ompP5+, oapA+) displayed by 94.6% of isolates. Such a genetic profile was associated with a higher bacterial resistance to serum mediated killing and enhanced adherence to human respiratory epithelial cells. PMID:21698169

  5. Nontypable Haemophilus influenzae displays a prevalent surface structure molecular pattern in clinical isolates.

    Directory of Open Access Journals (Sweden)

    Pau Martí-Lliteras

    Full Text Available Non-typable Haemophilus influenzae (NTHi is a gram negative pathogen that causes acute respiratory infections and is associated with the progression of chronic respiratory diseases. Previous studies have established the existence of a remarkable genetic variability among NTHi strains. In this study we show that, in spite of a high level of genetic heterogeneity, NTHi clinical isolates display a prevalent molecular feature, which could confer fitness during infectious processes. A total of 111 non-isogenic NTHi strains from an identical number of patients, isolated in two distinct geographical locations in the same period of time, were used to analyse nine genes encoding bacterial surface molecules, and revealed the existence of one highly prevalent molecular pattern (lgtF+, lic2A+, lic1D+, lic3A+, lic3B+, siaA-, lic2C+, ompP5+, oapA+ displayed by 94.6% of isolates. Such a genetic profile was associated with a higher bacterial resistance to serum mediated killing and enhanced adherence to human respiratory epithelial cells.

  6. Evaporation Flux Distribution of Drops on a Hydrophilic or Hydrophobic Flat Surface by Molecular Simulations.

    Science.gov (United States)

    Xie, Chiyu; Liu, Guangzhi; Wang, Moran

    2016-08-16

    The evaporation flux distribution of sessile drops is investigated by molecular dynamic simulations. Three evaporating modes are classified, including the diffusion dominant mode, the substrate heating mode, and the environment heating mode. Both hydrophilic and hydrophobic drop-substrate interactions are considered. To count the evaporation flux distribution, which is position dependent, we proposed an azimuthal-angle-based division method under the assumption of spherical crown shape of drops. The modeling results show that the edge evaporation, i.e., near the contact line, is enhanced for hydrophilic drops in all the three modes. The surface diffusion of liquid molecular absorbed on solid substrate for hydrophilic cases plays an important role as well as the space diffusion on the enhanced evaporation rate at the edge. For hydrophobic drops, the edge evaporation flux is higher for the substrate heating mode, but lower than elsewhere of the drop for the diffusion dominant mode; however, a nearly uniform distribution is found for the environment heating mode. The evidence shows that the temperature distribution inside drops plays a key role in the position-dependent evaporation flux.

  7. 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)...

  8. A Simple Nanocellulose Coating for Self-Cleaning upon Water Action: Molecular Design of Stable Surface Hydrophilicity.

    Science.gov (United States)

    Huang, Shu; Wang, Dayang

    2017-07-24

    Coating solid surfaces with cellulose nanofibril (CNF) monolayers via physical deposition was found to keep the surfaces free of a variety of oils, ranging from viscous engine oil to polar n-butanol, upon water action. The self-cleaning function was well correlated with the unique molecular structure of the CNF, in which abundant surface carboxyl and hydroxy groups are uniformly, densely, and symmetrically arranged to form a polar corona on a crystalline nanocellulose strand. This isotropic core-corona configuration offers new and easily adoptable guidance to design self-cleaning surfaces at the molecular level. Thanks to its excellent self-cleaning behavior, the CNF coating converted conventional meshes into highly effective membranes for oil-water separation with no prior surface treatment required. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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

  10. Early science with the Large Millimetre Telescope: fragmentation of molecular clumps in the Galaxy

    Science.gov (United States)

    Heyer, M.; Wilson, G. W.; Gutermuth, R.; Lizano, S.; Gomez-Ruiz, A.; Kurtz, S.; Luna, A.; Serrano Bernal, E. O.; Schloerb, F. P.

    2018-01-01

    Sensitive, imaging observations of the λ1.1 mm dust continuum emission from a 1 deg2 area collected with the AzTEC bolometer camera on the Large Millimeter Telescope are presented. A catalogue of 1545 compact sources is constructed based on a Wiener-optimization filter. These sources are linked to larger clump structures identified in the Bolocam Galactic Plane Survey. Hydrogen column densities are calculated for all sources and mass and mean volume densities are derived for the subset of sources for which kinematic distances can be assigned. The AzTEC sources are localized, high-density peaks within the massive clumps of molecular clouds and comprise 5-15 per cent of the clump mass. We examine the role of the gravitational instability in generating these fragments by comparing the mass of embedded AzTEC sources to the Jeans mass of the parent BGPS object. For sources with distances less than 6 kpc the fragment masses are comparable to the clump Jeans mass, despite having isothermal Mach numbers between 1.6 and 7.2. AzTEC sources linked to ultra compact H II regions have mass surface densities greater than the critical value implied by the mass-size relationship of infrared dark clouds with high-mass star formation, while AzTEC sources associated with Class II methanol masers have mass surface densities greater than 0.7 g cm-2 that approaches the proposed threshold required to form massive stars.

  11. 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.

  12. 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.

  13. 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.

  14. Successful grafting of isolated molecular Cr7Ni rings on Au(111) surface

    Science.gov (United States)

    Corradini, V.; Moro, F.; Biagi, R.; de Renzi, V.; Del Pennino, U.; Bellini, V.; Carretta, S.; Santini, P.; Milway, V. A.; Timco, G.; Winpenny, R. E. P.; Affronte, M.

    2009-04-01

    We deeply investigated the properties of submonolayer distributions of isolated molecular Cr7Ni rings deposited on Au(111) by liquid phase. X-ray absorption spectra measured at the Cr and NiL2,3 edges show that the grafting of the Cr7Ni rings onto the gold surface does not affect the oxidation state and the local symmetry of the Cr and Ni sites. The circular dichroism shows a change in sign of the Ni magnetic moment. This is due to a reduction in the exchange coupling constants that, however, preserves the structure of the low-energy levels of the grafted rings, as corroborated by spin-Hamiltonian simulations and comparison with measurements on bulk sample. Density-functional theory calculations show that the Ni-Cr bond gets weaker with slight ring distortion suggesting possible explanation for the observed magnetic behavior. These results show that complex magnetic molecules can be grafted onto surfaces, and that changes in their magnetic behavior must be examined in individual cases.

  15. 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.

  16. Molecular modeling of interactions between heavy crude oil and the soil organic matter coated quartz surface.

    Science.gov (United States)

    Wu, Guozhong; Zhu, Xinzhe; Ji, Haoqing; Chen, Daoyi

    2015-01-01

    Molecular dynamic (MD) simulation was applied to evaluate the mobility, diffusivity and partitioning of SARA (saturates, aromatics, resins, asphaltenes) fractions of heavy crude oil on soil organic matter (SOM) coated quartz surface. Four types of SOM were investigated including Leonardite humic acid, Temple-Northeastern-Birmingham humic acid, Chelsea soil humic acid and Suwannee river fulvic acid. The SOM aggregation at oil-quartz interface decreased the adsorption of SARA on the quartz surface by 13-83%. Although the SOM tended to promote asphaltenes aggregation, the overall mobility of SARA was significantly greater on SOM-quartz complex than on pure quartz. Particularly, the diffusion coefficient of asphaltenes and resins increased by up to one-order of magnitude after SOM addition. The SOM increased the overall oil adsorption capacity but also mobilized SARA by driving them from the viscous oil phase and rigid quartz to the elastic SOM. This highlighted the potential of SOM addition for increasing the bioavailability of heavy crude oil without necessarily increasing the environmental risks. The MD simulation was demonstrated to be helpful for interpreting the role of SOM and the host oil phase for the adsorption and partitioning of SARA molecules, which is the key for developing more realistic remediation appraisal for heavy crude oil in soils. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Fourier transform photoelectron diffraction and its application to molecular orbitals and surface structure

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Xin [Pennsylvania State Univ., University Park, PA (United States)

    1998-11-30

    Photoemission intensities from the molecular orbitals of c(2x2)CO/Pt(111) over a wide photon energy range were measured and analyzed by the same methods developed for structural studies using core levels. The 4{sigma} orbital center of gravity is found to be concentrated between the C and O atoms, while that of the 5{sigma} orbital lies between the C atom and the Pt surface. The C 1s photoelectron diffraction was used to determine the adsorption geometry. The earlier ambiguity that multiple scattering is needed to correctly model a {chi} curve while single scattering is sufficient for understanding major peaks in the ARPEFS-FTS is clarified by studying the clean Ni(111) surface. In the normal emission case, several different combinations of scattering events have similar path length differences (PLDs), and can either cancel each other or enhance the corresponding FT peak. In the off-normal case the degeneracy is greatly reduced due to the lower degree of symmetry. In normal emission AR PEFS, up to third order multiple scattering is needed to describe fully both the {chi} curve and its FT spectrum. To improve the spectral resolution in the ARPEFS-FT analysis, several new spectral analysis methods are introduced. With both autocorrelation autoregression (ACAR) and autocorrelation eigenvector (ACE), we can produce a reliable power spectrum by following the order-closing procedure. The best spectra are usually obtained when the autocorrelation sequence is computed with lags up to half the data range. A simple way of determining surface adsorption sites is proposed as follows: First use a single scattering cluster for possible adsorption sites to construct the geometrical PLDs from the strong backscattering events; then compare these PLDs with those obtained from the ARPEFS-FT analysis of the experimental data. After the preferred adsorption site is determined, fine tune the interlayer distances according to the positional R-factor.

  18. 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.

  19. 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.

  20. 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…

  1. Molecular Self-Assembly of Short Aromatic Peptides: From Biology to Nanotechnology and Material Science

    Science.gov (United States)

    Gazit, Ehud

    2013-03-01

    The formation of ordered amyloid fibrils is the hallmark of several diseases of unrelated origin. In spite of grave clinical consequence, the mechanism of amyloid formation is not fully understood. We have suggested, based on experimental and bioinformatic analysis, that aromatic interactions may provide energetic contribution as well as order and directionality in the molecular-recognition and self-association processes that lead to the formation of these assemblies. This is in line with the well-known central role of aromatic-stacking interactions in self-assembly processes. Our works on the mechanism of aromatic peptide self-assembly, lead to the discovery that the diphenylalanine recognition motif self-assembles into peptide nanotubes with a remarkable persistence length. Other aromatic homodipeptides could self-assemble in nano-spheres, nano-plates, nano-fibrils and hydrogels with nano-scale order. We demonstrated that the peptide nanostructures have unique chemical, physical and mechanical properties including ultra-rigidity as aramides, semi-conductive, piezoelectric and non-linear optic properties. We also demonstrated the ability to use these peptide nanostructures as casting mold for the fabrication of metallic nano-wires and coaxial nano-cables. The application of the nanostructures was demonstrated in various fields including electrochemical biosensors, tissue engineering, and molecular imaging. Finally, we had developed ways for depositing of the peptide nanostructures and their organization. We had use inkjet technology as well as vapour deposition methods to coat surface and from the peptide ``nano-forests''. We recently demonstrated that even a single phenylalanine amino-acid can form well-ordered fibrilar assemblies.

  2. Writing droplets of molecularly imprinted polymers by nano fountain pen and detecting their molecular interactions by surface-enhanced Raman scattering.

    Science.gov (United States)

    Kantarovich, Keren; Tsarfati, Inbal; Gheber, Levi A; Haupt, Karsten; Bar, Ilana

    2009-07-15

    Molecularly imprinted polymer (MIP) droplets were printed using a pipet or a nano fountain pen on surface-enhanced Raman scattering (SERS)-active surfaces, to directly monitor the uptake and release of a template molecule, the beta-blocking drug propranolol, by SERS. The monitored SERS bands can be related to the template, allowing for its detection but also identification in the MIP. This is an advantage if the technique is to be used during the development phase of MIPs as microstructures, but equally for the readout of MIP-based biochips.

  3. The ISIS Mission Concept: An Impactor for Surface and Interior Science

    Science.gov (United States)

    Chesley, Steven R.; Elliot, John O.; Abell, Paul A.; Asphaug, Erik; Bhaskaran, Shyam; Lam, Try; Lauretta, Dante S.

    2013-01-01

    The Impactor for Surface and Interior Science (ISIS) mission concept is a kinetic asteroid impactor mission to the target of NASA's OSIRIS-REx (Origins-Spectral Interpretation-Resource Identification-Security-Regolith Explorer) asteroid sample return mission. The ISIS mission concept calls for the ISIS spacecraft, an independent and autonomous smart impactor, to guide itself to a hyper-velocity impact with 1999 RQ36 while the OSIRIS-REx spacecraft observes the collision. Later the OSIRIS-REx spacecraft descends to reconnoiter the impact site and measure the momentum imparted to the asteroid through the impact before departing on its journey back to Earth. In this paper we discuss the planetary science, human exploration and impact mitigation drivers for mission, and we describe the current mission concept and flight system design.

  4. 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

  5. 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

  6. 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.

  7. Manipulating the surface active and anticoagulant properties of heparin through amphiphilic molecular constructs

    Science.gov (United States)

    Mintz, Rosita Candida

    Cardiovascular devices implanted within the vasculature are subjected to non-specific adsorption of plasma proteins. This initiates the blood coagulation cascade and platelet adhesion and activation, leading to thrombus formation. In this thesis Heparin Alkyl Diblock (HAD) surfactants were developed to improve the blood compatibility of cardiovascular biomaterials. The material designs involved using heparin, a natural anticoagulant, to inhibit coagulation pathway enzymes and mimic the cell glycocalyx to provide a repulsive force field to inhibit non-specific protein adsorption. Type AB linear (HAD Cn, n = 6,10,12,18) and branched (HAD nx 18, n = 2,3,4) heparin surfactants were synthesized by end point coupling primary and secondary alkyl amines to heparin via reductive amination. Surfactant yields (83--4%) and anticoagulant activity (149.8 +/- 3.7--39.6 +/- 0.6 IU/mg) decreased with increased branching and hydrocarbon number. Surfactant adsorption, self assembly and molecular packing of HAD surfactants at the air/liquid and liquid/solid interface were a function of the number of hydrocarbons in the surfactant alkyl segment and the presence or absence of an ionic liquid phase. Increased molecular packing was observed at the air/PBS and PBS/graphite interface, relative to aqueous interfaces, resulting from buffer cations shielding heparin's negatively charged sulfate and carboxyl groups. At the PBS/graphite interface, the surfactant's apparent heparin head group cross section decreased in diameter (1.84 to 1.05 nm) and increased in tilt angle (75.7 to 81.9°) with increasing alkyl carbon number (n = 6 to 18). The heparin head group reached a minimum diameter, equivalent to the surfactant's diameter at the air/PBS interface (0.57 nm) just prior to 36 hydrocarbons in the surfactant. For surfactants with 36 to 78 hydrocarbons, the surfactant's heparin head group oriented normal to the graphite surface and alkyl overlap or interdigitation increased (0.02 to 0.59 nm

  8. 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.

  9. 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.

  10. Computational investigation of surface freezing in a molecular model of water.

    Science.gov (United States)

    Haji-Akbari, Amir; Debenedetti, Pablo G

    2017-03-28

    Water freezes in a wide variety of low-temperature environments, from meteors and atmospheric clouds to soil and biological cells. In nature, ice usually nucleates at or near interfaces, because homogenous nucleation in the bulk can only be observed at deep supercoolings. Although the effect of proximal surfaces on freezing has been extensively studied, major gaps in understanding remain regarding freezing near vapor-liquid interfaces, with earlier experimental studies being mostly inconclusive. The question of how a vapor-liquid interface affects freezing in its vicinity is therefore still a major open question in ice physics. Here, we address this question computationally by using the forward-flux sampling algorithm to compute the nucleation rate in a freestanding nanofilm of supercooled water. We use the TIP4P/ice force field, one of the best existing molecular models of water, and observe that the nucleation rate in the film increases by seven orders of magnitude with respect to bulk at the same temperature. By analyzing the nucleation pathway, we conclude that freezing in the film initiates not at the surface, but within an interior region where the formation of double-diamond cages (DDCs) is favored in comparison with the bulk. This, in turn, facilitates freezing by favoring the formation of nuclei rich in cubic ice, which, as demonstrated by us earlier, are more likely to grow and overcome the nucleation barrier. The films considered here are ultrathin because their interior regions are not truly bulk-like, due to their subtle structural differences with the bulk.

  11. PREFACE: 6th Vacuum and Surface Sciences Conference of Asia and Australia (VASSCAA-6)

    Science.gov (United States)

    Ahsan Bhatti, Javaid; Hussain, Talib; Khan, Wakil

    2013-06-01

    The Vacuum and Surface Sciences Conference of Asia and Australia (VASSCAA) conference series has been organized to create a new forum in Asia and Australia to discuss vacuum, surface and related sciences, techniques and applications. The conference series is officially endorsed by the International Union for Vacuum Science, Technique and Application (IUVSTA). The International Steering Committee of VASSCAA is comprised of Vacuum Societies in seven countries: Australia, China, India, Iran, Japan, South Korea and Pakistan. VASSCAA-1 was organized by the Vacuum Society of Japan in 1999 in Tokyo, Japan. VASSCAA-2 was held in 2002 in Hong Kong, VASSCAA-3 in Singapore in 2005. VASSCAA-4 was held in Matsue, Japan in 2008 and VASSCAA-5 in 2010 in Beijing, China. The 6th Vacuum and Surface Sciences Conference of Asia and Australia (VASSCAA-6) was held from 9-13 October 2012 in the beautiful city of Islamabad, Pakistan. The venue of the conference was the Pak-China Friendship Centre, Islamabad. More than six hundred local delgates and around seventy delegates from different countries participated in this mega event. These delegates included scientists, researchers, engineers, professors, plant operators, designers, vendors, industrialists, businessmen and students from various research organizations, technical institutions, universities, industries and companies from Pakistan and abroad. The focal point of the event was to enhance cooperation between Pakistan and the international community in the fields of vacuum, surface science and other applied technologies. At VASSCAA-6 85 oral presentations were delivered by local and foreign speakers. These were divided into different sessions according to their fields. A poster session was organized at which over 70 researchers and students displayed their posters. The best three posters won prizes. In parallel to the main conference sessions four technical short courses were held. The participants showed keen interest in all these

  12. 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

  13. 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...

  14. Ambient pressure photoelectron spectroscopy: a new tool for surface science and nanotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Salmeron, Miquel; Salmeron, Miquel; Schlogl, Robert

    2008-03-12

    Progress in science often follows or parallels the development of new techniques. The optical microscope helped convert medicine and biology from a speculative activity in old times to today's sophisticated scientific disciplines. The telescope changed the study and interpretation of heavens from mythology to science. X-ray diffraction enabled the flourishing of solid state physics and materials science. The technique object of this review, Ambient Pressure Photoelectron Spectroscopy or APPES for short, has also the potential of producing dramatic changes in the study of liquid and solid surfaces, particularly in areas such as atmospheric, environment and catalysis sciences. APPES adds an important missing element to the host of techniques that give fundamental information, i.e., spectroscopy and microscopy, about surfaces in the presence of gases and vapors, as encountered in industrial catalysis and atmospheric environments. APPES brings electron spectroscopy into the realm of techniques that can be used in practical environments. Decades of surface science in ultra high vacuum (UHV) has shown the power of electron spectroscopy in its various manifestations. Their unique property is the extremely short elastic mean free path of electrons as they travel through condensed matter, of the order of a few atomic distances in the energy range from a few eV to a few thousand eV. As a consequence of this the information obtained by analyzing electrons emitted or scattered from a surface refers to the top first few atomic layers, which is what surface science is all about. Low energy electron diffraction (LEED), Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), Ultraviolet photoelectron spectroscopy (UPS), and other such techniques have been used for decades and provided some of the most fundamental knowledge about surface crystallography, composition and electronic structure available today. Unfortunately the high interaction cross section of

  15. Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces.

    Science.gov (United States)

    Qin, Wu; Li, Xin; Bian, Wen-Wen; Fan, Xiu-Juan; Qi, Jing-Yao

    2010-02-01

    There is increasing attention in the unique biological and medical properties of graphene, and it is expected that biomaterials incorporating graphene will be developed for the graphene-based drug delivery systems and biomedical devices. Despite the importance of biomolecules-graphene interactions, a detailed understanding of the adsorption mechanism and features of biomolecules onto the surfaces of graphene is lacking. To address this, we have performed density functional theory (DFT) and molecular dynamics (MD) methods exploring the adsorption geometries, adsorption energies, electronic band structures, adsorption isotherms, and adsorption dynamics of l-leucine (model biomolecule)/graphene composite system. DFT calculations confirmed the energetic stability of adsorption model and revealed that electronic structure of graphene can be controlled by the adsorption direction of l-leucine. MD simulations further investigate the potential energy and van der Waals energy for the interaction processes of l-leucine/graphene system at different temperatures and pressures. We find that the van der Waals interaction between the l-leucine and the graphene play a dominant role in the adsorption process under a certain range of temperature and pressure, and the l-leucine molecule could be adsorbed onto graphene spontaneously in aqueous solution.

  16. 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.

  17. 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.

  18. Transport Properties of Lateral Surface Superlattices Studied by Molecular Dynamics Monte Carlo Simulation.

    Science.gov (United States)

    Yamada, Toshishige

    The transport properties of a lateral surface superlattice, a two-dimensional (2D) electron system with a superposed 2D periodic potential, are studied with a molecular dynamics Monte Carlo technique. Excellent numerical energy conservation is achieved by adopting a predictor -corrector algorithm to integrate the equations of motion. With increasing 2D potential amplitude, electrons show a transition from a mobile phase to an immobile phase where the radial distribution function has characteristic peaks, indicating the beginning of the long-range ordering of the electrons in the potential minima. The velocity autocorrelation function shows a 2D plasma oscillation in the mobile phase, while in the immobile phase the classical oscillation at the bottom of the potential well is observed. Raising the temperature improves the transport since electrons are released from the constraint of the 2D potential and Coulomb potential. The conductance as a function of the magnetic field is not a simple decreasing function but has a structure with several local conductance minima. This structure is attributed to the correlated circular electron motion, and the reminiscence of the classical pinning orbits in the pinball machine model for a 2D antidot array.

  19. Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

    International Nuclear Information System (INIS)

    Valentini, Paolo; Schwartzentruber, Thomas E.; Bender, Jason D.; Nompelis, Ioannis; Candler, Graham V.

    2015-01-01

    The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N 2 –N 2 collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications

  20. Molecular recognition by a polymorphic cell surface receptor governs cooperative behaviors in bacteria.

    Directory of Open Access Journals (Sweden)

    Darshankumar T Pathak

    2013-11-01

    Full Text Available Cell-cell recognition is a fundamental process that allows cells to coordinate multicellular behaviors. Some microbes, such as myxobacteria, build multicellular fruiting bodies from free-living cells. However, how bacterial cells recognize each other by contact is poorly understood. Here we show that myxobacteria engage in recognition through interactions between TraA cell surface receptors, which leads to the fusion and exchange of outer membrane (OM components. OM exchange is shown to be selective among 17 environmental isolates, as exchange partners parsed into five major recognition groups. TraA is the determinant of molecular specificity because: (i exchange partners correlated with sequence conservation within its polymorphic PA14-like domain and (ii traA allele replacements predictably changed partner specificity. Swapping traA alleles also reprogrammed social interactions among strains, including the regulation of motility and conferred immunity from inter-strain killing. We suggest that TraA helps guide the transition of single cells into a coherent bacterial community, by a proposed mechanism that is analogous to mitochondrial fusion and fission cycling that mixes contents to establish a homogenous population. In evolutionary terms, traA functions as a rare greenbeard gene that recognizes others that bear the same allele to confer beneficial treatment.

  1. 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

  2. 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

  3. 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)

  4. 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.

  5. Adsorption of DNA onto gold nanoparticles and graphene oxide: surface science and applications.

    Science.gov (United States)

    Liu, Juewen

    2012-08-14

    The interaction between DNA and inorganic surfaces has attracted intense research interest, as a detailed understanding of adsorption and desorption is required for DNA microarray optimization, biosensor development, and nanoparticle functionalization. One of the most commonly studied surfaces is gold due to its unique optical and electric properties. Through various surface science tools, it was found that thiolated DNA can interact with gold not only via the thiol group but also through the DNA bases. Most of the previous work has been performed with planar gold surfaces. However, knowledge gained from planar gold may not be directly applicable to gold nanoparticles (AuNPs) for several reasons. First, DNA adsorption affinity is a function of AuNP size. Second, DNA may interact with AuNPs differently due to the high curvature. Finally, the colloidal stability of AuNPs confines salt concentration, whereas there is no such limit for planar gold. In addition to gold, graphene oxide (GO) has emerged as a new material for interfacing with DNA. GO and AuNPs share many similar properties for DNA adsorption; both have negatively charged surfaces but can still strongly adsorb DNA, and both are excellent fluorescence quenchers. Similar analytical and biomedical applications have been demonstrated with these two surfaces. The nature of the attractive force however, is different for each of these. DNA adsorption on AuNPs occurs via specific chemical interactions but adsorption on GO occurs via aromatic stacking and hydrophobic interactions. Herein, we summarize the recent developments in studying non-thiolated DNA adsorption and desorption as a function of salt, pH, temperature and DNA secondary structures. Potential future directions and applications are also discussed.

  6. Ultra high vacuum fabrication of metallic contacts for molecular devices on an insulating surface

    Science.gov (United States)

    Fostner, Shawn

    The preparation and characterization of metallic wires on insulating substrates by a variety of mechanisms has been explored. A multi-scale approach utilizing microfabricated silicon stencil masks, feedback controlled electromigration, and field induced metal cluster deposition in a novel geometry has been explored on potassium bromide (KBr), indium phosphide (InP), and silicon oxide substrates in an ultra-high vacuum environment (UHV). The initial deposition of gold, and tantalum wires between one hundred nanometers and micrometers in size was performed using reinforced silicon nanostencils. The stencil fabrication was discussed, and an examination of the deformation of the integrated structures under the deposition of highly stressed tantalum films was shown to be significantly smaller than typical structures. Metallic wires deposited using these stencils as well as electron beam lithography were electrically stressed and the breaking characteristics analyzed. Typical nanometer scale gaps were observed, as well as larger features more commonly found in the breaking of bamboo-like structures in gold wires 100 nm in size or less, particularly with a significant series resistance. These larger gaps are expected to be more applicable for the deposition of subsequent metallic clusters and preparation of molecular devices. As a step towards connecting the initially deposited wires as well as localized molecules in an a fashion allowing atomic scale imaging by AFM, modelling and experiments of field induced deposition of gold clusters on KBr and InP substrates was carried out. Deposition on InP substrates with a backside 2D electron gas as a counter-electrode demonstrated the feability of this deposition technique in UHV. Subsequent depositions on or adjacent to metallic pads on the bulk insulating KBr provided a proof of principle of the technique, though some experimental limitations such as large current pulses with the tip in close proximity to the surface are

  7. 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

  8. 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

    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......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...

  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. Poly(glycidyl ether)-Based Monolayers on Gold Surfaces: Control of Grafting Density and Chain Conformation by Grafting Procedure, Surface Anchor, and Molecular Weight.

    Science.gov (United States)

    Heinen, Silke; Weinhart, Marie

    2017-03-07

    For a meaningful correlation of surface coatings with their respective biological response reproducible coating procedures, well-defined surface coatings, and thorough surface characterization with respect to layer thickness and grafting density are indispensable. The same applies to polymeric monolayer coatings which are intended to be used for, e.g., fundamental studies on the volume phase transition of surface end-tethered thermoresponsive polymer chains. Planar gold surfaces are frequently used as model substrates, since they allow a variety of straightforward surface characterization methods. Herein we present reproducible grafting-to procedures performed with thermoresponsive poly(glycidyl ether) copolymers composed of glycidyl methyl ether (GME) and ethyl glycidyl ether (EGE). The copolymers feature different molecular weights (2 kDa, 9 kDa, 24 kDa) and are equipped with varying sulfur-containing anchor groups in order to achieve adjustable grafting densities on gold surfaces and hence control the tethered polymers' chain conformation. We determined "wet" and "dry" thicknesses of these coatings by QCM-D and ellipsometry measurements and deduced anchor distances and degrees of chain overlap of the polymer chains assembled on gold. Grafting under cloud point conditions allowed for higher degrees of chain overlap compared to grafting from a good solvent like ethanol, independent of the used sulfur-containing anchor group for polymers with low (2 kDa) and medium (9 kDa) molecular weights. By contrast, the achieved grafting densities and thus chain overlaps of surface-tethered polymers with high (24 kDa) molecular weights were identical for both grafting methods. Monolayers prepared from an ethanolic solution of poly(glycidyl ether)s equipped with sterically demanding disulfide-containing anchors revealed the lowest degrees of chain overlap. The ratio of the radius of gyration to the anchor distance (2 R g /l) of the latter coating was found to be lower than 1

  11. Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection from a PbSe quantum dot into the TiO2 surface.

    Science.gov (United States)

    Long, Run; Prezhdo, Oleg V

    2011-11-30

    Following recent experiments [Science 2010, 328, 1543; PNAS 2011, 108, 965], we report an ab initio nonadiabatic molecular dynamics (NAMD) simulation of the ultrafast photoinduced electron transfer (ET) from a PbSe quantum dot (QD) into the rutile TiO(2) (110) surface. The system forms the basis for QD-sensitized semiconductor solar cells and demonstrates that ultrafast interfacial ET is instrumental for achieving high efficiencies in solar-to-electrical energy conversion. The simulation supports the observation that the ET successfully competes with energy losses due to electron-phonon relaxation. The ET proceeds by the adiabatic mechanism because of strong donor-acceptor coupling. High frequency polar vibrations of both QD and TiO(2) promote the ET, since these modes can rapidly influence the donor-acceptor state energies and coupling. Low frequency vibrations generate a distribution of initial conditions for ET, which shows a broad variety of scenarios at the single-molecule level. Compared to the molecule-TiO(2) interfaces, the QD-TiO(2) system exhibits pronounced differences that arise due to the larger size and higher rigidity of QDs relative to molecules. Both donor and acceptor states are more delocalized in the QD system, and the ET is promoted by optical phonons, which have relatively low frequencies in the QD materials composed of heavy elements. In contrast, in molecular systems, optical phonons are not thermally accessible under ambient conditions. Meanwhile, TiO(2) acceptor states resemble surface impurities due to the local influence of molecular chromophores. At the same time, the photoinduced ET at both QD-TiO(2) and molecule-TiO(2) interfaces is ultrafast and occurs by the adiabatic mechanism, as a result of strong donor-acceptor coupling. The reported state-of-the-art simulation generates a detailed time-domain atomistic description of the interfacial ET process that is fundamental to a wide variety of applications.

  12. 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

  13. 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

  14. JPRS Report Science & Technology USSR: Life Sciences

    National Research Council Canada - National Science Library

    1988-01-01

    ...: Life sciences, aerospace medicine, agriculture science, biochemistry, biophysics, genetics, immunology, industrial medicine, laser bioeffects, medicine, molecular biology, nonionizing radiation...

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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...

  20. Vibrational Analysis of Brucite Surfaces and the Development of an Improved Force Field for Molecular Simulation of Interfaces.

    Science.gov (United States)

    Zeitler, Todd R; Greathouse, Jeffery A; Gale, Julian D; Cygan, Randall T

    2014-04-17

    We introduce a nonbonded three-body harmonic potential energy term for Mg-O-H interactions for improved edge surface stability in molecular simulations. The new potential term is compatible with the Clayff force field and is applied here to brucite, a layered magnesium hydroxide mineral. Comparisons of normal mode frequencies from classical and density functional theory calculations are used to verify a suitable spring constant ( k parameter) for the Mg-O-H bending motion. Vibrational analysis of hydroxyl librations at two brucite surfaces indicates that surface Mg-O-H modes are shifted to frequencies lower than the corresponding bulk modes. A comparison of DFT and classical normal modes validates this new potential term. The methodology for parameter development can be applied to other clay mineral components (e.g., Al, Si) to improve the modeling of edge surface stability, resulting in expanded applicability to clay mineral applications.

  1. 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

  2. Quantifying the Molecular-Scale Aqueous Response to the Mica Surface

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, Arushi [Department; Pfaendtner, Jim [Department; Senior; Chun, Jaehun [Physical; Mundy, Christopher J. [Physical; Affiliate

    2017-08-09

    Modeling assembly at surfaces requires a multi-scale understanding of the interactions between solutes, solvents, and surfaces. We investigated the solvent response (water structure and orientation) to a dielectric surface (mica) using density functional theory. A different water structure is engendered by replacing naturally-occurring surface ions (K+) with H3O+ and validates classical models for the mica surface (CLAYFF). The detailed microscopic response of water to mica can be used as input into continuum models for the total interactions between two mica surfaces supporting a strong correlation between physicochemical phenomena at different scales.

  3. Determining the fate of fluorescent quantum dots on surface of engineered budding S. cerevisiae cell molecular landscape.

    Science.gov (United States)

    Chouhan, Raghuraj S; Qureshi, Anjum; Niazi, Javed H

    2015-07-15

    In this study, we surface engineered living S. cerevisiae cells by decorating quantum dots (QDs) and traced the fate of QDs on molecular landscape of single mother cell through several generation times (progeny cells). The fate of QDs on cell-surface was tracked through the cellular division events using confocal microscopy and fluorescence emission profiles. The extent of cell-surface QDs distribution among the offspring was determined as the mother cell divides into daughter cells. Fluorescence emission from QDs on progeny cells was persistent through the second-generation time (~240min) until all of the progeny cells lost their cell-bound QDs during the third generation time (~360min). The surface engineered yeast cells were unaffected by the QDs present on their molecular landscapes and retained their normal cellular growth, architecture and metabolic activities as confirmed by their viability, scanning electron microscopy (SEM) examinations and cytotoxicity tests, respectively. Our results demonstrated that QDs on mother cell landscape tend to distribute among its progeny cells that accompanied with concomitant reduction in QDs' fluorescence, which can be quantified. We suggest that surface engineered cells with QDs will enable investigating the cellular behavior and monitoring cell growth patterns as nanobiosensors for screening of drugs/chemicals at single cell level with fewer side effects. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. 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.

  5. A simple and sensitive surface molecularly imprinted polymers based fluorescence sensor for detection of λ-Cyhalothrin.

    Science.gov (United States)

    Liu, Chunbo; Song, Zhilong; Pan, Jianming; Yan, Yongsheng; Cao, Zhijing; Wei, Xiao; Gao, Lin; Wang, Juan; Dai, Jiangdong; Meng, Minjia; Yu, Ping

    2014-07-01

    In this study, surface molecularly imprinted YVO4:Eu(3+) nanoparticles with molecular recognitive optosensing activity were successfully prepared by precipitation polymerization using λ-Cyhalothrin (LC) as template molecules, methacrylic acid and ethylene glycol dimethacrylate as the polymerization precursors which could complex with template molecules, and the material has been characterized by SEM, TEM, FT-IR, XRD, TGA and so on. Meanwhile, the as-prepared core-shell structured nanocomposite (YVO4:Eu(3+)@MIPs), which was composed of lanthanide doped YVO4:Eu(3+) as fluorescent signal and surface molecular imprinted polymers as molecular selective recognition sites, could selectively and sensitively optosense the template molecules. After the experimental conditions were optimized, two linear relationship were obtained covering the concentration range of 2.0-10.0 μM and 10.0-90.0 μM, and the limit of detection (LOD) for LC was found to be 1.76 μM. Furthermore, a possible mechanism was put forward to explain the fluorescence quenching of YVO4:Eu(3+)@MIPs. More importantly, the obtained sensor was proven to be suitable for the detection of residues of LC in real examples. And the excellent performance of this sensor will facilitate future development of rapid and high-efficiency detection of LC. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Raman Under Water - Nonlinear and Nearfield Approaches for Electrochemical Surface Science.

    Science.gov (United States)

    Martín Sabanés, Natalia; Domke, Katrin F

    2017-08-01

    Electrochemistry is re-gaining attention among scientists because the complex interplay between electronic and chemical interfacial processes lies at the bottom of a broad range of important research disciplines like alternative energy conversion or green catalysis and synthesis. While rapid progress has been made in recent years regarding novel technological applications, the community increasingly recognizes that the understanding of the molecular processes that govern macroscopic device properties is still rather limited - which hinders a systematic and more complete exploration of novel material and functionality space. Here, we discuss advanced Raman spectroscopies as valuable analysis tools for electrochemists. The chemical nature of a material and its interaction with the environment is contained in the label-free vibrational fingerprint over a broad energy range so that organic species, solid-state materials, and hybrids thereof can be investigated alike. For surface studies, the inherently small Raman scattering cross sections can be overcome with advanced nonlinear or nearfield-based approaches that provide signal enhancements between three and seven orders of magnitude, sufficient to detect few scatterers in nano-confined spaces or adsorbate (sub)monolayers. Our article highlights how advanced Raman techniques with extreme chemical, spatial and temporal resolution constitute valuable alternative surface analysis tools and provide otherwise inaccessible information about complex interfacial (electro)chemical processes.

  7. MOLECULAR DYNAMICS MODELING OF SORPTION OF PESTICIDES ONTO THE SURFACES OF KAOLINITE

    Science.gov (United States)

    To accurately predict the fate of contaminants in the environment and to make sound decisions about environmental remediation, we must accurately understand sorption mechanisms and surface reactivity of environmental particles. Sorption of selected pesticides on kaolinite surface...

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. Surface-enhanced Raman scattering from a single molecularly bridged silver nanoparticle aggregate

    Czech Academy of Sciences Publication Activity Database

    Sládková, M.; Vlčková, B.; Pavel, I.; Šišková, Karolína; Šlouf, Miroslav

    924-26, SI (2009), s. 567-570 ISSN 0022-2860. [European Congress on Molecular Spectroscopy /29./. Opatija, 31.08.2008-05.09.2008] R&D Projects: GA ČR GA203/07/0717; GA AV ČR KAN100500652 Institutional research plan: CEZ:AV0Z40500505 Keywords : single molecule SERS * 4,4"-diaminoterphenyl * molecularly bridget Ag nanoparticle aggregates Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.551, year: 2009

  16. 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), ...

  17. Building a 'Repository of Science': The importance of integrating biobanks within molecular pathology programmes.

    Science.gov (United States)

    Lewis, Claire; McQuaid, Stephen; Hamilton, Peter W; Salto-Tellez, Manuel; McArt, Darragh; James, Jacqueline A

    2016-11-01

    Repositories containing high quality human biospecimens linked with robust and relevant clinical and pathological information are required for the discovery and validation of biomarkers for disease diagnosis, progression and response to treatment. Current molecular based discovery projects using either low or high throughput technologies rely heavily on ready access to such sample collections. It is imperative that modern biobanks align with molecular diagnostic pathology practices not only to provide the type of samples needed for discovery projects but also to ensure requirements for ongoing sample collections and the future needs of researchers are adequately addressed. Biobanks within comprehensive molecular pathology programmes are perfectly positioned to offer more than just tumour derived biospecimens; for example, they have the ability to facilitate researchers gaining access to sample metadata such as digitised scans of tissue samples annotated prior to macrodissection for molecular diagnostics or pseudoanonymised clinical outcome data or research results retrieved from other users utilising the same or overlapping cohorts of samples. Furthermore, biobanks can work with molecular diagnostic laboratories to develop standardised methodologies for the acquisition and storage of samples required for new approaches to research such as 'liquid biopsies' which will ultimately feed into the test validations required in large prospective clinical studies in order to implement liquid biopsy approaches for routine clinical practice. We draw on our experience in Northern Ireland to discuss how this harmonised approach of biobanks working synergistically with molecular pathology programmes is a key for the future success of precision medicine. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Efficient Capture of Cancer Cells by Their Replicated Surfaces Reveals Multiscale Topographic Interactions Coupled with Molecular Recognition.

    Science.gov (United States)

    Wang, Wenshuo; Cui, Haijun; Zhang, Pengchao; Meng, Jingxin; Zhang, Feilong; Wang, Shutao

    2017-03-29

    Cell-surface topographic interactions can direct the design of biointerfaces, which have been widely used in isolation of circulating tumor cells or fundamental cell biological research. By using three kinds of cancer cell-replicated surfaces with differentiated structures, we uncover that multiscale-cooperative topographic interactions (at both nanoscale and microscale) coupled with molecular recognition enable efficient and specific isolation of cancer cells. The cell replicas precisely inherit the structural features from the original cancer cells, providing not only preferable structures for matching with cancer cells but also a unique platform to interrogate whether certain cancer cells can optimally match with their own replicated surfaces. The results reveal that cancer cells do not show preferential recognitions to their respective replicas, while the capture agent-modified surfaces with hierarchical structures exhibit improved cancer cell capture efficiencies. Two levels of topographic interactions between cancer cells and cell replica surfaces exist. Nanoscale filopodia on cancer cells can topographically interact with different nanostructures on replica surfaces. In addition, microscale concave/convex on surfaces provide suitable sites for trapping cancer cells. This study may promote smart design of multiscale biofunctional materials that can specifically recognize cancer cells.

  19. 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

  20. 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.

  1. 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

  2. Molecular explanation for why talc surfaces can be both hydrophilic and hydrophobic.

    Science.gov (United States)

    Rotenberg, Benjamin; Patel, Amish J; Chandler, David

    2011-12-21

    While individual water molecules adsorb strongly on a talc surface (hydrophilic behavior), a droplet of water beads up on the same surface (hydrophobic behavior). To rationalize this dichotomy, we investigated the influence of the microscopic structure of the surface and the strength of adhesive (surface-water) interactions on surface hydrophobicity. We have shown that at low relative humidity, the competition between adhesion and the favorable entropy of being in the vapor phase determines the surface coverage. However, at saturation, it is the competition between adhesion and cohesion (water-water interactions) that determines the surface hydrophobicity. The adhesive interactions in talc are strong enough to overcome the unfavorable entropy, and water adsorbs strongly on talc surfaces. However, they are too weak to overcome the cohesive interactions, and water thus beads up on talc surfaces. Surprisingly, even talc-like surfaces that are highly adhesive do not fully wet at saturation. Instead, a water droplet forms on top of a strongly adsorbed monolayer of water. Our results imply that the interior of hydrophobic zeolites suspended in water may contain adsorbed water molecules at pressures much lower than the intrusion pressure. © 2011 American Chemical Society

  3. Combinatorial near-edge x-ray absorption fine structure: Simultaneous determination of molecular orientation and bond concentration on chemically heterogeneous surfaces

    International Nuclear Information System (INIS)

    Genzer, Jan; Fischer, Daniel A.; Efimenko, Kirill

    2003-01-01

    We show that simultaneous molecular orientation and bond chemistry of planar chemically heterogeneous surfaces can be obtained by combining near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and rastering the incident x-ray beam on the specimen. This rastering produces serially two-dimensional NEXAFS images in space and energy, revealing information about the chemistry (including bond concentration) and orientation of the surface-bound molecules with submillimeter planar spatial resolution and submonolayer molecular sensitivity. We illustrate the power of the combinatorial NEXAFS method by simultaneously probing the concentration and molecular orientation of semifluorinated (SF) molecules in double-SF molecular gradients on flat silica substrates

  4. The impact of computer science in molecular medicine: enabling high-throughput research.

    Science.gov (United States)

    de la Iglesia, Diana; García-Remesal, Miguel; de la Calle, Guillermo; Kulikowski, Casimir; Sanz, Ferran; Maojo, Víctor

    2013-01-01

    The Human Genome Project and the explosion of high-throughput data have transformed the areas of molecular and personalized medicine, which are producing a wide range of studies and experimental results and providing new insights for developing medical applications. Research in many interdisciplinary fields is resulting in data repositories and computational tools that support a wide diversity of tasks: genome sequencing, genome-wide association studies, analysis of genotype-phenotype interactions, drug toxicity and side effects assessment, prediction of protein interactions and diseases, development of computational models, biomarker discovery, and many others. The authors of the present paper have developed several inventories covering tools, initiatives and studies in different computational fields related to molecular medicine: medical informatics, bioinformatics, clinical informatics and nanoinformatics. With these inventories, created by mining the scientific literature, we have carried out several reviews of these fields, providing researchers with a useful framework to locate, discover, search and integrate resources. In this paper we present an analysis of the state-of-the-art as it relates to computational resources for molecular medicine, based on results compiled in our inventories, as well as results extracted from a systematic review of the literature and other scientific media. The present review is based on the impact of their related publications and the available data and software resources for molecular medicine. It aims to provide information that can be useful to support ongoing research and work to improve diagnostics and therapeutics based on molecular-level insights.

  5. 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...... of cylindrical SWNTs oil the aluminum surface can be improved through the surface modification method. The stability of SWNTs call be enhanced by increasing the modification coverage. When the modification coverage exceeds 3.3% and 3.8% coverage, respectively, both amidogen- and carboxyl-modified SWNTs can...... basically maintain the cylindrical structure in our described systems. The results also show that, to avoid SWNTs collapse by chemical modification, the longer and larger SWNTs are, the more modification coverage SWNTs require. and vice versa. Our method allows potentially used modified SWNTs...

  6. Curcumin induced nanoscale CD44 molecular redistribution and antigen-antibody interaction on HepG2 cell surface

    Energy Technology Data Exchange (ETDEWEB)

    Wang Mu [Department of Chemistry, Jinan University, 601 Huangpu Road West, Tianhe District, Guangzhou 510632 (China); Ruan Yuxia [Department of Ophthalmology, The First Affiliated Hospital, Jinan University, 601 Huangpu Road West, Tianhe District, Guangzhou 510632 (China); Xing Xiaobo; Chen Qian; Peng, Yuan [Department of Chemistry, Jinan University, 601 Huangpu Road West, Tianhe District, Guangzhou 510632 (China); Cai Jiye, E-mail: tjycai@jnu.edu.cn [Department of Chemistry, Jinan University, 601 Huangpu Road West, Tianhe District, Guangzhou 510632 (China)

    2011-07-04

    Graphical abstract: Highlights: > In this study, we investigate the changes of CD44 expression and distribution on HepG2 cells after curcumin treatment. > We find curcumin is able to change the morphology and ultrastructure of HepG2 cells. > Curcumin can reduce the expression of CD44 molecules and induce the nanoscale molecular redistribution on cell surface. > The binding force between CD44-modified AFM tip and the HepG2 cell surface decreases after curcumin-treatment. - Abstract: The cell surface glycoprotein CD44 was implicated in the progression, metastasis and apoptosis of certain human tumors. In this study, we used atomic force microscope (AFM) to monitor the effect of curcumin on human hepatocellular carcinoma (HepG2) cell surface nanoscale structure. High-resolution imaging revealed that cell morphology and ultrastructure changed a lot after being treated with curcumin. The membrane average roughness increased (10.88 {+-} 4.62 nm to 129.70 {+-} 43.72 nm) and the expression of CD44 decreased (99.79 {+-} 0.16% to 75.14 {+-} 8.37%). Laser scanning confocal microscope (LSCM) imaging showed that CD44 molecules were located on the cell membrane. The florescence intensity in control group was weaker than that in curcumin treated cells. Most of the binding forces between CD44 antibodies and untreated HepG2 cell membrane were around 120-220 pN. After being incubated with curcumin, the major forces focused on 70-150 pN (10 {mu}M curcumin-treated) and 50-120 pN (20 {mu}M curcumin-treated). These results suggested that, as result of nanoscale molecular redistribution, changes of the cell surface were in response to external treatment of curcumin. The combination of AFM and LSCM could be a powerful method to detect the distribution of cell surface molecules and interactions between molecules and their ligands.

  7. Spatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal Swedish lake

    Science.gov (United States)

    Tolu, Julie; Rydberg, Johan; Meyer-Jacob, Carsten; Gerber, Lorenz; Bindler, Richard

    2017-04-01

    The composition of sediment organic matter (OM) exerts a strong control on biogeochemical processes in lakes, such as those involved in the fate of carbon, nutrients and trace metals. While between-lake spatial variability of OM quality is increasingly investigated, we explored in this study how the molecular composition of sediment OM varies spatially within a single lake and related this variability to physical parameters and elemental geochemistry. Surface sediment samples (0-10 cm) from 42 locations in Härsvatten - a small boreal forest lake with a complex basin morphometry - were analyzed for OM molecular composition using pyrolysis gas chromatography mass spectrometry for the contents of 23 major and trace elements and biogenic silica. We identified 162 organic compounds belonging to different biochemical classes of OM (e.g., carbohydrates, lignin and lipids). Close relationships were found between the spatial patterns of sediment OM molecular composition and elemental geochemistry. Differences in the source types of OM (i.e., terrestrial, aquatic plant and algal) were linked to the individual basin morphometries and chemical status of the lake. The variability in OM molecular composition was further driven by the degradation status of these different source pools, which appeared to be related to sedimentary physicochemical parameters (e.g., redox conditions) and to the molecular structure of the organic compounds. Given the high spatial variation in OM molecular composition within Härsvatten and its close relationship with elemental geochemistry, the potential for large spatial variability across lakes should be considered when studying biogeochemical processes involved in the cycling of carbon, nutrients and trace elements or when assessing lake budgets.

  8. Effect of molecular weight and density of ambient gas on shock wave in laser-induced surface nanostructuring

    International Nuclear Information System (INIS)

    Guo Liying; Wang Xinwei

    2009-01-01

    This paper presents the results of molecular dynamics studies about the shock wave during laser-induced surface nanostructuring. A quasi-three dimensional model is constructed to study systems consisting of over 2 million atoms. Detailed studies are carried out about the shock wave front and Mach number, evolution of plume and ambient gas interaction zone, and energy exchange between the ambient gas and plume. Under an ambience of lower pressure or lighter molecular mass, the plume affects a larger area while the strength of the shock wave front is weaker. With the same ambient pressure, the ablated material features the same kinetic energy at the late stage regardless of the molecular weight of the ambient gas. The same conclusion holds for the energy increase of the ambient gas as well. When the ambient pressure is reduced, more kinetic energy is carried out by the ablated material while less energy is transferred to the ambient gas. It is observed that heavier ambient gas could bounce back the ablated material to the target surface.

  9. Serological versus molecular typing of surface-associated immune evading polysaccharide antigens-based phenotypes of Staphylococcus aureus.

    Science.gov (United States)

    Waryah, Charlene B; Gogoi-Tiwari, Jully; Wells, Kelsi; Costantino, Paul; Al-Salami, Hani; Sunagar, Raju; Isloor, Shrikrishna; Hegde, Nagendra; Richmond, Peter; Mukkur, Trilochan

    2014-11-01

    The aim of this study was to compare the performance of serological versus molecular typing methods to detect capsular polysaccharide (CP) and surface-associated polysaccharide antigen 336 phenotypes of Staphylococcus aureus isolates. Molecular typing of CP types 1, 5 and 8 was carried out using PCR, whereas serological typing of CP1, 2, 5, 8 and antigen 336 was carried out by slide agglutination using specific antisera. By genotyping, 14/31 strains were CP8 positive, 12/31 strains were CP5 and the remaining 6/31 isolates were non-typable (NT). One isolate was positive for both CP5 and CP8 by PCR, but was confirmed as CP8 type serologically. Detection of CP2 and type 336 by PCR was not possible because specific primers were either not available or non-specific. Using serotyping, 14/31 strains were CP8 positive, 11/31 CP5 positive and 2/31 positive for antigen 336. The remaining four S. aureus isolates were serologically NT. However, three of four NT and two 336-positive S. aureus isolates were encapsulated as determined by light microscopy after capsular staining. This discovery was surprising and warrants further investigations on the identification and characterization of additional capsular phenotypes prevalent among S. aureus clinical isolates. It was concluded that serological typing was a better method than molecular typing for use in epidemiological investigations based upon the distribution of surface-associated polysaccharide antigens-based phenotypes. © 2014 The Authors.

  10. Sorption and distribution of asphaltene, resin, aromatic and saturate fractions of heavy crude oil on quartz surface: molecular dynamic simulation.

    Science.gov (United States)

    Wu, Guozhong; He, Lin; Chen, Daoyi

    2013-09-01

    The molecular scale sorption, diffusion and distribution of asphaltene, resin, aromatic and saturate fractions of heavy crude oil on quartz surface were studied using molecular dynamic simulation. Sorption of saturates on quartz decreased by 31% when temperature increased from 298 to 398K while opposite trend was observed for resins, but insignificant changes were found in asphaltenes and aromatics. Despite of this variety, the main contribution of interactions was van der Waals energy (>90%) irrespective of molecular components and temperatures. The diffusion coefficient of saturates was predicted as 10.8×10(-10)m(2)s(-1) while that of the remaining fractions was about 4×10(-10)m(2)s(-1) at 298K. The most likely oil distribution on quartz surface was that aromatics and saturates transported randomly into and out of the complex consisting of asphaltenes surrounded by resins, which was influenced by temperature. Overall, the knowledge on quartz-oil and oil-oil interactions gained in this study is essential for future risk assessment and remediation activities as previous studies on soil remediation either limited to light oil fractions with <40 carbons or treated the heavy crude oil as a single pseudo entity ignoring the interactions between oil fractions. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Ab initio molecular dynamics calculations on reactions of molecules with metal surfaces

    NARCIS (Netherlands)

    Nattino, Francesco

    2015-01-01

    Reactions on metal surfaces are of scientific interest due to the tremendous relevance of heterogeneous catalysis. Single crystal surfaces under controlled physical conditions are generally employed as a model for the real catalysts, with the aim of improving the fundamental understanding of the

  12. Film growth by polyatomic C2H5+ bombarding a diamond (100) surfaces: Molecular dynamics study

    NARCIS (Netherlands)

    Lu, X. D.; Qin, Y.; Ning, J.; Zhou, T.; Deng, C. Y.; Meng, C.; Qian, Q.; Gou, F.; Chuanwu, Z.; Ying, Y.; Ming, J.

    2009-01-01

    The deposition of polyatomic C2H5+ ions is studied using classical molecular dynamics simulations with a new improved Brenner potentials developed by Brenner. The simulation results show that when the incident energy is less than 65 eV, the deposition coefficient of H is larger than that of C atoms.

  13. Investigate the complex process in particle-fluid based surface generation technology using reactive molecular dynamics method

    Science.gov (United States)

    Han, Xuesong; Li, Haiyan; Zhao, Fu

    2017-07-01

    Particle-fluid based surface generation process has already become one of the most important materials processing technology for many advanced materials such as optical crystal, ceramics and so on. Most of the particle-fluid based surface generation technology involves two key process: chemical reaction which is responsible for surface softening; physical behavior which is responsible for materials removal/deformation. Presently, researchers cannot give a reasonable explanation about the complex process in the particle-fluid based surface generation technology because of the small temporal-spatial scale and the concurrent influence of physical-chemical process. Molecular dynamics (MD) method has already been proved to be a promising approach for constructing effective model of atomic scale phenomenon and can serve as a predicting simulation tool in analyzing the complex surface generation mechanism and is employed in this research to study the essence of surface generation. The deformation and piles of water molecule is induced with the feeding of abrasive particle which justifies the property mutation of water at nanometer scale. There are little silica molecule aggregation or materials removal because the water-layer greatly reduce the strength of mechanical interaction between particle and materials surface and minimize the stress concentration. Furthermore, chemical effect is also observed at the interface: stable chemical bond is generated between water and silica which lead to the formation of silconl and the reaction rate changes with the amount of water molecules in the local environment. Novel ring structure is observed in the silica surface and it is justified to be favored of chemical reaction with water molecule. The siloxane bond formation process quickly strengthened across the interface with the feeding of abrasive particle because of the compressive stress resulted by the impacting behavior.

  14. Investigate the complex process in particle-fluid based surface generation technology using reactive molecular dynamics method

    Directory of Open Access Journals (Sweden)

    Xuesong Han

    2017-07-01

    Full Text Available Particle-fluid based surface generation process has already become one of the most important materials processing technology for many advanced materials such as optical crystal, ceramics and so on. Most of the particle-fluid based surface generation technology involves two key process: chemical reaction which is responsible for surface softening; physical behavior which is responsible for materials removal/deformation. Presently, researchers cannot give a reasonable explanation about the complex process in the particle-fluid based surface generation technology because of the small temporal-spatial scale and the concurrent influence of physical-chemical process. Molecular dynamics (MD method has already been proved to be a promising approach for constructing effective model of atomic scale phenomenon and can serve as a predicting simulation tool in analyzing the complex surface generation mechanism and is employed in this research to study the essence of surface generation. The deformation and piles of water molecule is induced with the feeding of abrasive particle which justifies the property mutation of water at nanometer scale. There are little silica molecule aggregation or materials removal because the water-layer greatly reduce the strength of mechanical interaction between particle and materials surface and minimize the stress concentration. Furthermore, chemical effect is also observed at the interface: stable chemical bond is generated between water and silica which lead to the formation of silconl and the reaction rate changes with the amount of water molecules in the local environment. Novel ring structure is observed in the silica surface and it is justified to be favored of chemical reaction with water molecule. The siloxane bond formation process quickly strengthened across the interface with the feeding of abrasive particle because of the compressive stress resulted by the impacting behavior.

  15. Evaporation of water droplets on Pt-surface in presence of external electric field—A molecular dynamics study

    Science.gov (United States)

    Hens, Abhiram; Biswas, Gautam; De, Sudipta

    2015-09-01

    Evaporation of a sessile droplet on a hot solid substrate is an important problem in fluid mechanics. It is relevant to theoretical issues in heat transfer as well as several practical applications. This study investigates the spreading and evaporation of a nanoscale water droplet on a solid platinum surface. The major objective was to analyze the effect of an external electric field on these phenomena. Varying the intensity and direction of the external electric field, a series of molecular dynamics simulations were carried out to understand these phenomena at a molecular level. The results reveal that a horizontal electric field assists in droplet spreading, whereas a vertical electric field enhances the rate of evaporation for a certain range of field intensities. It also shows that the substrate temperature plays an important role in such processes. It is seen that the effect of an external electric field on droplet evaporation becomes significant at an intermediate range of surface temperatures and this effect is not clearly visible for either very high or very low range of surface temperatures.

  16. Evaporation of water droplets on Pt-surface in presence of external electric field--A molecular dynamics study.

    Science.gov (United States)

    Hens, Abhiram; Biswas, Gautam; De, Sudipta

    2015-09-07

    Evaporation of a sessile droplet on a hot solid substrate is an important problem in fluid mechanics. It is relevant to theoretical issues in heat transfer as well as several practical applications. This study investigates the spreading and evaporation of a nanoscale water droplet on a solid platinum surface. The major objective was to analyze the effect of an external electric field on these phenomena. Varying the intensity and direction of the external electric field, a series of molecular dynamics simulations were carried out to understand these phenomena at a molecular level. The results reveal that a horizontal electric field assists in droplet spreading, whereas a vertical electric field enhances the rate of evaporation for a certain range of field intensities. It also shows that the substrate temperature plays an important role in such processes. It is seen that the effect of an external electric field on droplet evaporation becomes significant at an intermediate range of surface temperatures and this effect is not clearly visible for either very high or very low range of surface temperatures.

  17. On the molecular mechanism of surface charge amplification and related phenomena at aqueous polyelectrolyte-graphene interfaces

    Directory of Open Access Journals (Sweden)

    J.M. Simonson

    2011-09-01

    Full Text Available In this communication we illustrate the occurrence of a recently reported new phenomenon of surface-charge amplification, SCA, (originally dubbed overcharging, OC, [Jimenez-Angeles F. and Lozada-Cassou M., J. Phys. Chem. B, 2004, 108, 7286] by means of molecular dynamics simulation of aqueous electrolytes solutions involving multivalent cations in contact with charged graphene walls and the presence of short-chain lithium polystyrene sulfonates where the solvent water is described explicitly with a realistic molecular model. We show that the occurrence of SCA in these systems, in contrast to that observed in primitive models, involves neither contact co-adsorption of the negatively charged macroions nor divalent cations with a large size and charge asymmetry as required in the case of implicit solvents. In fact the SCA phenomenon hinges around the preferential adsorption of water (over the hydrated ions with an average dipolar orientation such that the charges of the water's hydrogen and oxygen sites induce magnification rather than screening of the positive-charged graphene surface, within a limited range of surface-charge density.

  18. Research briefing on selected opportunities in atomic, molecular, and optical sciences

    International Nuclear Information System (INIS)

    1991-01-01

    This report discusses research on the following topics: The Laser-Atom Revolution; Controlling Dynamical Pathways; Nonclassical States of Light; Transient States of Atomic Systems; New Light Generation and Handling; Clusters; Atomic Physics at User Facilities; and Impacts of AMO Sciences on Modern Technologies

  19. Ab initio potential energy and dipole moment surfaces for CS2: determination of molecular vibrational energies.

    Science.gov (United States)

    Pradhan, Ekadashi; Carreón-Macedo, José-Luis; Cuervo, Javier E; Schröder, Markus; Brown, Alex

    2013-08-15

    The ground state potential energy and dipole moment surfaces for CS2 have been determined at the CASPT2/C:cc-pVTZ,S:aug-cc-pV(T+d)Z level of theory. The potential energy surface has been fit to a sum-of-products form using the neural network method with exponential neurons. A generic interface between neural network potential energy surface fitting and the Heidelberg MCTDH software package is demonstrated. The potential energy surface has also been fit using the potfit procedure in MCTDH. For fits to the low-energy regions of the potential, the neural network method requires fewer parameters than potfit to achieve high accuracy; global fits are comparable between the two methods. Using these potential energy surfaces, the vibrational energies have been computed for the four most abundant CS2 isotopomers. These results are compared to experimental and previous theoretical data. The current potential energy surfaces are shown to accurately reproduce the low-lying vibrational energies within a few wavenumbers. Hence, the potential energy and dipole moments surfaces will be useful for future study on the control of quantum dynamics in CS2.

  20. Molecular beam study of the mechanism of catalyzed hydrogen--deuterium exchange on platinum single crystal surfaces

    International Nuclear Information System (INIS)

    Bernasek, S.L.; Somorjai, G.A.

    1975-01-01

    The hydrogen--deuterium exchange reaction was studied by molecular beam scattering on low and high Miller index crystal faces of platinum in the surface temperature range of 300--1300degreeK. Under the condition of the experiments which put strict limitation on the residence time of the detected molecules, the reaction product, HD, was readily detectable from the high Miller index, stepped surfaces (integrated reaction probability, defined as total desorbed HD flux divided by D 2 flux, is approx.10/sup -1/) while HD formation was below the limit of detectability on the Pt(111) low Miller index surface (reaction probability 2 beam pressure and half-order in H 2 background pressure. The absence of beam kinetic energy dependence of the rate indicates that the molecular adsorption does not require activation energy. The surface is able to store a sufficiently large concentration of atoms which react with the molecules by a two-branch mechanism. The rate constants for this two-branch mechanism were determined under conditions of constant H atom coverage, reducing the bimolecular reaction to a pseudo-first-order reaction. At lower temperatures ( 1 = (2plus-or-minus1) times10 5 exp(-4.5plus-or-minus0.5 kcal/RT) sec/sup -1/. The rate determining step appears to be the diffusion of the D 2 molecule on the surface to a step site where HD is formed via a three-center (atom--molecule) reaction, or via a two-center (atom--atom) reaction subsequent to D 2 dissociation at the step. At higher temperatures (>600degreeK) the reaction between an adsorbed H atom and an incident D 2 gas molecule competes with the low temperature branch. The rate constant for this branch is k 2 = (1plus-or-minus2) times10 2 exp(-0.6plus-or-minus0.3 kcal/RT) sec/sup -1/

  1. Bioadhesion of mussels and geckos: Molecular mechanics, surface chemistry, and nanoadhesives

    Science.gov (United States)

    Lee, Haeshin

    The adhesive strategies of living creatures are diverse, ranging from temporary to permanent adhesions with various functions such as locomotion, self-defense, communication, colony formation, and so on. The classic example of temporary adhesion is the gecko, which is known for its ability to walk along vertical and even inverted surfaces; this remarkable adhesion arises from the interfacial weak interactions of van der Waals and capillary forces. In contrast, a celerbrated example of permanent adhesion is found in marine mussels which secrete protein adhesives that function in aqueous environments without mechanical failure against turbulent conditions on the seashore. In addition, mussel adhesives stick to virtually all inorganic and organic surfaces. However, most commonly used man-made adhesives lack such unique adhesion properties compared to their natural counterparts. For example, many commercial adhesives quickly lose their adhesive strength when exposed to solvents, particularly water. The first part of this thesis focused on adhesion mechanics of mussels at a single-molecule level, in which the adhesive molecule showed surprisingly strong yet reversible adhesion on inorganic surfaces but exhibited irreversible covalent bond formation on organic surfaces. Strong and reversible adhesion on mucin surfaces was found, indicating potential application for drug delivery via mucus layers. Next, inspired by the mussel's versatile adhesion on a wide variety of material surfaces, a material-independent surface modification chemistry called 'polydopamine coating' is described. This concept was subsequently adapted to develop a surface-independent polymeric primer for layer-by-layer assembly of multifunctional coatings. Finally, a new bio-hybrid adhesive 'geckel' was developed by the functional combination of adhesion strategies of geckos and mussels. The new bio-inspired adhesive and material-independent surface chemistry can revolutionize the research areas such as

  2. Fractal Surfaces of Molecular Crystals Mimicking Lotus Leaf with Phototunable Double Roughness Structures.

    Science.gov (United States)

    Nishimura, Ryo; Hyodo, Kengo; Sawaguchi, Haruna; Yamamoto, Yoshiaki; Nonomura, Yoshimune; Mayama, Hiroyuki; Yokojima, Satoshi; Nakamura, Shinichiro; Uchida, Kingo

    2016-08-17

    Double roughness structure, the origin of the lotus effect of natural lotus leaf, was successfully reproduced on a diarylethene microcrystalline surface. Static superwater-repellency and dynamic water-drop-bouncing were observed on the surface, in the manner of natural lotus leaves. Double roughness structure was essential for water-drop-bouncing. This ability was not observed on a single roughness microcrystalline surface showing the lotus effect of the same diarylethene derivative. The double roughness structure was reversibly controlled by alternating irradiation with UV and visible light.

  3. Improved molecular fingerprint analysis employing multi-branched gold nanoparticles in conjunction with surface-enhanced Raman scattering

    Directory of Open Access Journals (Sweden)

    Johnston J

    2015-12-01

    Full Text Available Jencilin Johnston,1 Erik N Taylor,1,2 Richard J Gilbert,2 Thomas J Webster1,3 1Department of Chemical Engineering, 2Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA; 3Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, Saudi Arabia Abstract: Vibrational spectroscopy is a powerful analytical tool that assesses molecular properties based on spectroscopic signatures. In this study, the effect of gold nanoparticle morphology (spherical vs multi-branched was assessed for the characterization of a Raman signal (ie, molecular fingerprint that may be helpful for numerous medical applications. Multi-branched gold nanoparticles (MBAuNPs were fabricated using a green chemistry method which employed the reduction of gold ion solute by 2-[4-(2-hydroxyethyl-1-piperazyl] ethane sulfonic acid. Two types of reporter dyes, indocyanine (IR820 and IR792 and carbocyanine (DTTC [3,3'-diethylthiatricarbocyanine iodide] and DTDC [3,3'-diethylthiadicarbocyanine iodide], were functionalized to the surface of the MBAuNPs and stabilized with denatured bovine serum albumin, thus forming the surface-enhanced Raman spectroscopy tag. Fluorescein isothiocyanate-conjugated anti-epidermal growth factor receptor to the surface-enhanced Raman spectroscopy tags and the properties of the resulting conjugates were assessed through determination of the Raman signal. Using the MBAuNP Raman probes synthesized in this manner, we demonstrated that MBAuNP provided significantly more surface-enhanced Raman scattering signal when compared with the associated spherical gold nanoparticle of similar size and concentration. MBAuNP enhancements were retained in the surface-enhanced Raman spectroscopy tags complexed to anti-epidermal growth factor receptor, providing evidence that this could be a useful biological probe for enhanced Raman molecular fingerprinting. Furthermore, while utilizing IR820 as a novel reporter dye

  4. Molecular Energy and Environmental Science: A Workshop Sponsored by The National Science Foundation and The Department of Energy May 26-27, 1999 in Rosemont, Illinois

    Energy Technology Data Exchange (ETDEWEB)

    Stair, Peter C [Northwestern Univ., Evanston, IL (United States); DeSimone, Joseph M. [University of North Carolina Chapel Hill; Frost, John W. [Michigan State Univ., East Lansing, MI (United States)

    1999-05-26

    Energy and the environment pose major scientific and technological challenges for the 21st century. New technologies for increasing the efficiency of harvesting and utilizing energy resources are essential to the nation’s economic competitiveness. At the same time, the quality of life in the United States depends inherently on the environmental impact of energy production and utilization. This interdependence makes it imperative to develop a better understanding of the environment and new strategies for minimizing the impact of energy-related activities. Recent advances in techniques for the synthesis and characterization of chemicals and materials and for the molecular control of biological organisms make it possible, for the first time, to address this imperative. Chemistry, with its focus on the molecular level, plays a central role in addressing the needs for fundamental understanding and technology development in both the energy and environmental fields. Understanding environmental processes and consequences requires studying natural systems, rather than focussing exclusively on laboratory models. Natural systems and their complexity pose an enormous, perhaps the ultimate, challenge to chemists, and will provide them with varied and exciting new problems for years to come. In addition, the complexity of the underlying systems and processes often requires multi-disciplinary programs that bridge the interfaces between chemistry and other disciplines. (See Figure 1) This has ramifications in the approach to funding research and suggests needs for broadening the educational training of future scientists and engineers in these programs. Figure 1. NSF and DOE should consider sponsoring research centers and focused research groups organized to optimize their impact on Technological Challenges of national interest. The research will have significant impact if it addresses issues of fundamental molecular science in one or more Enabling Research Areas. Approximately 7

  5. Production of High Molecular Weight Organic Compounds on the Surfaces of Amorphous Iron Silicate Catalysts: Implications for Organic Synthesis in the Solar Nebula

    Science.gov (United States)

    Gilmour, I.; Hill, H. G. M.; Pearson, V. K.; Sephton, M. A.; Nuth, J. A., III

    2002-01-01

    The high molecular weight organic products of Fischer-Tropsch/Haber-Bosch syntheses on the surfaces of Fe-silicate catalysts have been studied by GCMS. Additional information is contained in the original extended abstract.

  6. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    Science.gov (United States)

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-08

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.

  7. Acetylene on Cu(111): imaging a molecular surface arrangement with a constantly rearranging tip.

    Science.gov (United States)

    Zhu, Yeming; Wyrick, Jonathan; Cohen, Kamelia D; Magnone, Katie Marie; Holzke, Connor; Salib, Daniel; Ma, Quan; Sun, Dezheng; Bartels, Ludwig

    2012-09-05

    Acetylene on Cu(111) is investigated by scanning tunnelling microscopy (STM); a surface pattern previously derived from diffraction measurements can be validated, if the variation of the STM image transfer function through absorption of an acetylene molecule onto the tip apex is taken into account. Density functional theory simulations point to a balance between short-range repulsive interactions of acetylene/Cu(111) associated with surface stress and longer range attractive interactions as the origin of the ordering.

  8. Direct Observation of Molecular Preorganization for Chirality Transfer on a Catalyst Surface

    DEFF Research Database (Denmark)

    Demers-Carpentier, Vincent; Goubert,, Guillaume; Masini, Federico

    2011-01-01

    functional theory calculations reveals the stereodirecting forces governing preorganization into precise chiral modifier-substrate bimolecular surface complexes. The study shows that the chiral modifier induces prochiral switching on the surface and that different prochiral ratios prevail at different...... that continued progress in the area is uncertain. We show that the investigation of heterogeneous asymmetric induction with single-site resolution sufficient to distinguish stereochemical conformations at the submolecular level is finally accessible. A combination of scanning tunneling microscopy and density...

  9. NEXAFS characterization of DNA components and molecular-orientation of surface-bound DNA oligomers

    International Nuclear Information System (INIS)

    Samuel, Newton T.; Lee, C.-Y.; Gamble, Lara J.; Fischer, Daniel A.; Castner, David G.

    2006-01-01

    Single stranded DNA oligomers (ssDNA) immobilized onto solid surfaces forms the basis for several biotechnological applications such as DNA microarrays, affinity separations, and biosensors. Surface structure of Surface-bound oligomers is expected to significantly influence their biological activity and interactions with the environment. In this study near-edge X-ray absorption fine structure spectroscopy (NEXAFS) is used to characterize the components of DNA (nucleobases, nucleotides and nucleosides) and the orientation information of surface-bound ssDNA. The K-edges of carbon, nitrogen and oxygen have spectra with features that are characteristic of the different chemical species present in the nucleobases of DNA. The effect of addition of the DNA sugar and phosphate components on the NEXAFS K-edge spectra was also investigated. The polarization-dependent nitrogen K-edge NEXAFS data show significant changes for different orientations of surface bound ssDNA. These results establish NEXAFS as a powerful technique for chemical and structural characterization of surface-bound DNA oligomers

  10. EPR Studies of Spin Labels Bound to Ceramic Surfaces, and Simulation of Magnetic Resonance Spectra by Molecular Trajectory.

    Science.gov (United States)

    Auteri, Francesco Paul

    Electron paramagnetic resonance (EPR) spectroscopy is sensitive to molecular rotational correlation times in the range of 10^{-6} to 10^{-11} seconds. EPR spin labels are often attached or incorporated into molecular structures as probes of local viscosities and dynamics. In part I of this work, methods of covalently attaching a variety of spin labels to silica and alumina ceramic surfaces are developed in an attempt to study local viscosities at varying distances from about 5 A^circ to 25 A^circ from the ceramic/liquid interface. Three solvents, diethyl ether, benzene, and cyclohexane, are chosen for detailed study in combination with the spin labels, TEMPOL, 5-DOXYL, and 12-DOXYL. EPR spectra of each system are taken over the range of temperatures from -140 ^circC to 50^circ C (or just below the solvent boiling point). Spectra show good sensitivity to solvent, temperature, and probe. The effect of adding 3% (w/o) poly-(octadecyl-methacrylate) (PODM) to benzene and cyclohexane on spin label mobility is also studied in this work. Rotational correlation times from lineshapes are analyzed assuming isotropic rotation using spectral splitting, line width, and simulation methods. These approaches are often inadequate for the more complex spectral line shapes observed for tethered spin labels, especially in the intermediate motional regime where sensitivity to anisotropic dynamics is greatest. In part II of this work, a novel approach to the prediction of spectral line shapes is developed. It is shown that EPR spectra may be computed directly from molecular trajectories using classical approximations to describe the time evolution of the magnetization vector under fluctuating effective interaction tensor values. Line shape simulations using molecular trajectories generated by Brownian dynamics theory are less time intensive than existing methods. Simulation of magnetic resonance line shapes by molecular trajectories as generated by programs such as CHARMM promises to be

  11. Science review: Mechanisms of impaired adrenal function in sepsis and molecular actions of glucocorticoids

    OpenAIRE

    Prigent, Hélène; Maxime, Virginie; Annane, Djillali

    2004-01-01

    This review describes current knowledge on the mechanisms that underlie glucocorticoid insufficiency in sepsis and the molecular action of glucocorticoids. In patients with severe sepsis, numerous factors predispose to glucocorticoid insufficiency, including drugs, coagulation disorders and inflammatory mediators. These factors may compromise the hypothalamic–pituitary axis (i.e. secondary adrenal insufficiency) or the adrenal glands (i.e. primary adrenal failure), or may impair glucocorticoi...

  12. Imaging and Tuning Molecular Levels at the Surface of a Gated Graphene Device

    Science.gov (United States)

    2014-01-01

    Gate-controlled tuning of the charge carrier density in graphene devices provides new opportunities to control the behavior of molecular adsorbates. We have used scanning tunneling microscopy (STM) and spectroscopy (STS) to show how the vibronic electronic levels of 1,3,5-tris(2,2-dicyanovinyl)benzene molecules adsorbed onto a graphene/BN/SiO2 device can be tuned via application of a backgate voltage. The molecules are observed to electronically decouple from the graphene layer, giving rise to well-resolved vibronic states in dI/dV spectroscopy at the single-molecule level. Density functional theory (DFT) and many-body spectral function calculations show that these states arise from molecular orbitals coupled strongly to carbon–hydrogen rocking modes. Application of a back-gate voltage allows switching between different electronic states of the molecules for fixed sample bias. PMID:24746016

  13. Mercury-Mediated Attachment of Metal-Sandwich-Based Altitudinal Molecular Rotors to Gold Surfaces

    Czech Academy of Sciences Publication Activity Database

    Mulcahy, M. E.; Bastl, Zdeněk; Stensrud, Kenneth F.; Magnera, T. F.; Michl, Josef

    2010-01-01

    Roč. 114, č. 33 (2010), s. 14050-14060 ISSN 1932-7447 R&D Projects: GA AV ČR KAN100400702; GA ČR GA203/07/1619 Grant - others:ERC Advanced Grant(XE) 227756 Program:FP7 Institutional research plan: CEZ:AV0Z40400503; CEZ:AV0Z40550506 Keywords : XPS * STM * molecular rotors Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.520, year: 2010

  14. (Al)MCM-41 Molecular Sieves. Aluminium Distribution, Uniformity and Structure of Inner Surface

    Czech Academy of Sciences Publication Activity Database

    Dědeček, Jiří; Žilková, Naděžda; Kotrla, Josef; Čejka, Jiří

    2003-01-01

    Roč. 68, č. 10 (2003), s. 1998-2018 ISSN 0010-0765 R&D Projects: GA ČR GA104/02/0571; GA AV ČR IAA4040001; GA AV ČR IBS4040017 Grant - others: Volkswagen Stiftung(DE) I/75886 Institutional research plan: CEZ:AV0Z4040901 Keywords : molecular sieves * mesoporous materials * Vis spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.041, year: 2003

  15. Surface-attached molecular beacons light the way for DNA sequencing

    Czech Academy of Sciences Publication Activity Database

    Paleček, Emil

    2004-01-01

    Roč. 22, č. 2 (2004), s. 55-58 ISSN 0167-7799 R&D Projects: GA AV ČR IBS5004355; GA ČR GA204/03/0566 Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular beacon * DNA stem-loop structure * DNA sensors Subject RIV: BO - Biophysics Impact factor: 8.606, year: 2004

  16. Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics

    OpenAIRE

    Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele

    2003-01-01

    The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metady- namics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.

  17. Copper(II) adsorption on the kaolinite(001) surface: Insights from first-principles calculations and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Xiang-Ping, E-mail: kxp2004@163.com; Wang, Juan, E-mail: juaner80@163.com

    2016-12-15

    Highlights: • Several issues about Cu(II) adsorption on the kaolinite (0 0 1) surface were solved. • Complexation of water molecules with Cu(II) was considered for adsorption complex. • Charge transfer and bonding mechanism of Cu–O{sub s} (surface oxygen) were explored. - Abstract: The adsorption behavior of Cu(II) on the basal hydroxylated kaolinite(001) surface in aqueous environment was investigated by first-principles calculations and molecular dynamics simulations. Structures of possible monodentate and bidentate inner-sphere adsorption complexes of Cu(II) were examined, and the charge transfer and bonding mechanism were analyzed. Combining the binding energy of complex, the radial distribution function of Cu(II) with oxygen and the extended X-ray absorption fine structure data, monodentate complex on site of surface oxygen with “upright” hydrogen and bidentate complex on site of two oxygens (one with “upright” hydrogen and one with “lying” hydrogen) of single Al center have been found to be the major adsorption species of Cu(II). Both adsorption species are four-coordinated with a square planar geometry. The distribution of surface hydroxyls with “lying” hydrogen around Cu(II) plays a key role in the structure and stability of adsorption complex. Upon the Mulliken population analysis and partial density of states, charge transfer occurs with Cu(II) accepting some electrons from both surface oxygens and aqua oxygens, and the bonding Cu 3d-O 2p state filling is primarily responsible for the strong covalent interaction of Cu(II) with surface oxygen.

  18. Molecular dynamics study of the interactions of incident N or Ti atoms with the TiN(001) surface

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhenhai [National Key Laboratory for Precision Hot Processing of Metals & School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China); Centre for Precision Manufacturing, Department of Design, Manufacture and Engineering Management, The University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Zeng, Quanren [Centre for Precision Manufacturing, Department of Design, Manufacture and Engineering Management, The University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Yuan, Lin [National Key Laboratory for Precision Hot Processing of Metals & School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Qin, Yi [Centre for Precision Manufacturing, Department of Design, Manufacture and Engineering Management, The University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Chen, Mingjun [School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China); Shan, Debin, E-mail: d.b.shan@gmail.com [National Key Laboratory for Precision Hot Processing of Metals & School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China)

    2016-01-01

    Graphical abstract: - Highlights: • Interactions of incident N or Ti atoms with TiN(001) surface are studied by CMD. • The impact position of incident N on the surface determines the interaction modes. • Adsorption could occur due to the atomic exchange process. • Resputtering and reflection may simultaneously occur. • The initial sticking coefficient of N on TiN(001) is much smaller than that of Ti. - Abstract: The interaction processes between incident N or Ti atoms and the TiN(001) surface are simulated by classical molecular dynamics based on the second nearest-neighbor modified embedded-atom method potentials. The simulations are carried out for substrate temperatures between 300 and 700 K and kinetic energies of the incident atoms within the range of 0.5–10 eV. When N atoms impact against the surface, adsorption, resputtering and reflection of particles are observed; several unique atomic mechanisms are identified to account for these interactions, in which the adsorption could occur due to the atomic exchange process while the resputtering and reflection may simultaneously occur. The impact position of incident N atoms on the surface plays an important role in determining the interaction modes. Their occurrence probabilities are dependent on the kinetic energy of incident N atoms but independent on the substrate temperature. When Ti atoms are the incident particles, adsorption is the predominant interaction mode between particles and the surface. This results in the much smaller initial sticking coefficient of N atoms on the TiN(001) surface compared with that of Ti atoms. Stoichiometric TiN is promoted by N/Ti flux ratios larger than one.

  19. A surface science compatible epifluorescence microscope for inspection of samples under ultra high vacuum and cryogenic conditions.

    Science.gov (United States)

    Marquardt, Christian; Paulheim, Alexander; Rohbohm, Nils; Merkel, Rudolf; Sokolowski, Moritz

    2017-08-01

    We modified an epi-illumination light microscope and mounted it on an ultra high vacuum chamber for investigating samples used in a surface science experiment. For easy access and bake out, all optical components are placed outside the vacuum and the sample is imaged through a glass window. The microscope can be operated in reflection brightfield or epifluorescence mode to image the sample surface or fluorescent dye molecules adsorbed on it. The homemade sample mounting was made compatible for the use under the microscope; sample temperatures as low as 6 K can be achieved. The performance of the microscope is demonstrated on two model samples: Brightfield-images of a well-prepared Ag(100) surface show a macroscopic corrugation of the surface, although low energy electron diffraction data indicate a highly ordered crystalline surface. The surface shows macroscopic protrusions with flat regions, about 20-200 μm in diameter, in between. Fluorescence images of diluted 3,4,9,10-perylene tetracarboxylicacid dianhydride (PTCDA) molecules adsorbed on an ultrathin epitaxial KCl film on the Ag(100) surface show a shading effect at surface protrusions due to an inclined angle of incidence of the PTCDA beam during deposition. For some preparations, the distribution of the fluorescence intensity is inhomogeneous and shows a dense network of bright patches about 5 μm in diameter related to the macroscopic corrugation of the surface. We propose that such a light microscope can aid many surface science experiments, especially those dealing with epitaxial growth or fluorescent materials.

  20. A surface science compatible epifluorescence microscope for inspection of samples under ultra high vacuum and cryogenic conditions

    Science.gov (United States)

    Marquardt, Christian; Paulheim, Alexander; Rohbohm, Nils; Merkel, Rudolf; Sokolowski, Moritz

    2017-08-01

    We modified an epi-illumination light microscope and mounted it on an ultra high vacuum chamber for investigating samples used in a surface science experiment. For easy access and bake out, all optical components are placed outside the vacuum and the sample is imaged through a glass window. The microscope can be operated in reflection brightfield or epifluorescence mode to image the sample surface or fluorescent dye molecules adsorbed on it. The homemade sample mounting was made compatible for the use under the microscope; sample temperatures as low as 6 K can be achieved. The performance of the microscope is demonstrated on two model samples: Brightfield-images of a well-prepared Ag(100) surface show a macroscopic corrugation of the surface, although low energy electron diffraction data indicate a highly ordered crystalline surface. The surface shows macroscopic protrusions with flat regions, about 20-200 μm in diameter, in between. Fluorescence images of diluted 3,4,9,10-perylene tetracarboxylicacid dianhydride (PTCDA) molecules adsorbed on an ultrathin epitaxial KCl film on the Ag(100) surface show a shading effect at surface protrusions due to an inclined angle of incidence of the PTCDA beam during deposition. For some preparations, the distribution of the fluorescence intensity is inhomogeneous and shows a dense network of bright patches about 5 μm in diameter related to the macroscopic corrugation of the surface. We propose that such a light microscope can aid many surface science experiments, especially those dealing with epitaxial growth or fluorescent materials.

  1. Structure–Property Relationships of Inorganically Surface-Modified Zeolite Molecular Sieves for Nanocomposite Membrane Fabrication

    KAUST Repository

    Lydon, Megan E.

    2012-05-03

    A multiscale experimental study of the structural, compositional, and morphological characteristics of aluminosilicate (LTA) and pure-silica (MFI) zeolite materials surface-modified with MgO xH y nanostructures is presented. These characteristics are correlated with the suitability of such materials in the fabrication of LTA/Matrimid mixed-matrix membranes (MMMs) for CO 2/CH 4 separations. The four functionalization methods studied in this work produce surface nanostructures that may appear superficially similar under SEM observation but in fact differ considerably in shape, size, surface coverage, surface area/roughness, degree of attachment to the zeolite surface, and degree of zeolite pore blocking. The evaluation of these characteristics by a combination of TEM, HRTEM, N 2 physisorption, multiscale compositional analysis (XPS, EDX, and ICP-AES elemental analysis), and diffraction (ED and XRD) allows improved understanding of the origin of disparate gas permeation properties observed in MMMs made with four types of surface-modified zeolite LTA materials, as well as a rational selection of the method expected to result in the best enhancement of the desired properties (in the present case, CO 2/CH 4 selectivity increase without sacrificing permeability). A method based on ion exchange of the LTA with Mg 2+, followed by base-induced precipitation and growth of MgO xH y nanostructures, deemed "ion exchange functionalization" here, offers modified particles with the best overall characteristics resulting in the most effective MMMs. LTA/Matrimid MMMs containing ion exchange functionalized particles had a considerably higher CO 2/CH 4 selectivity (∼40) than could be obtained with the other functionalization techniques (∼30), while maintaining a CO 2 permeability of ∼10 barrers. A parallel study on pure silica MFI surface nanostructures is also presented to compare and contrast with the zeolite LTA case. © 2012 American Chemical Society.

  2. Squeezing molecular thin alkane lubrication films between curved solid surfaces with long-range elasticity: Layering transitions and wear

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, V. N.; Persson, B. N. J.

    2003-01-01

    The properties of alkane lubricants confined between two approaching solids are investigated by a model that accounts for the curvature and the elastic properties of the solid surfaces. We consider linear alkane molecules of different chain lengths, C3H8, C4H10, C8H18, C9H20, C10H22, C12H26 and C14......H30 confined between smooth gold surfaces. In most cases we observe well defined molecular layers develop in the lubricant film when the width of the film is of the order of a few atomic diameters. An external squeezing-pressure induces discontinuous, thermally activated changes in the number n...... of lubricant layers. We find that with increasing alkane chain length, the transition from n to n-1 layers occurs at higher pressure, as expected based on the increasing wettability ~or spreading pressure with increasing chain length. Thus, the longer alkanes are better boundary lubricants than the shorter...

  3. On the lipid head group hydration of floating surface monolayers bound to self-assembled molecular protein layers

    DEFF Research Database (Denmark)

    Lösche, M.; Erdelen, C.; Rump, E.

    1994-01-01

    The structure of monomolecular layers of the protein streptavidin, specifically bound to biotin-functionalized lipid monolayers at aqueous surfaces, has been characterized. Neutron and X-ray reflectivity measurements allowed an assessment of the organization of these self-assembled systems...... with molecular resolution. Emphasis here is placed on the hydration of the lipid head groups in the bound state. For three functionalized lipids with spacers of different lengths between the biotin and their chains it was observed that the head groups were dehydrated in monolayers of the pure lipids, which were...... kept at low surface pressure before protein adsorption. The introduction of dipole moments at the interface by the admixture of phospholipids or the application of lateral pressure on the lipid monolayer before protein adsorption were found to impose an extension of the spacer moieties. The biotin...

  4. Absence of molecular slip on ultraclean and SAM-coated surfaces

    Science.gov (United States)

    Pye, Justin; Wood, Clay; Burton, Justin

    2016-11-01

    The liquid/solid boundary condition is a complex problem that is becoming increasingly important for the development of nanoscale fluidic devices. Many groups have now measured slip near an interface at nanoscale dimensions using a variety of experimental techniques. In simple systems, large slip lengths are generally measured for non-wetting liquid/solid combinations, but many conflicting measurements and interpretations remain. We have developed a novel pseudo-differential technique using a quartz crystal microbalance (QCM) to measure slip lengths on various surfaces. A drop of one liquid is grown on the QCM in the presence of a second, ambient liquid. We have isolated any anomalous boundary effects such as interfacial slip by choosing two liquids which have identical bulk effects on the QCM frequency and dissipation in the presence of no-slip. Slip lengths are -less than 2 nm- for water (relative to undecane) on all surfaces measured, including plasma cleaned gold, SiO2, and two different self assembled monolayers (SAMs), regardless of contact angle. We also find that surface cleanliness is crucial to accurately measure slip lengths. Additionally, clean glass substrates appear to have a significant adsorbed water layer and SAM surfaces show excess dissipation, possibly associated with contact line motion. In addition to investigating other liquid pairs, future work will include extending this technique to surfaces with independently controllable chemistry and roughness, both of which are known to strongly affect interfacial hydrodynamics.

  5. Season Spotter: Using Citizen Science to Validate and Scale Plant Phenology from Near-Surface Remote Sensing

    Directory of Open Access Journals (Sweden)

    Margaret Kosmala

    2016-09-01

    Full Text Available The impact of a rapidly changing climate on the biosphere is an urgent area of research for mitigation policy and management. Plant phenology is a sensitive indicator of climate change and regulates the seasonality of carbon, water, and energy fluxes between the land surface and the climate system, making it an important tool for studying biosphere–atmosphere interactions. To monitor plant phenology at regional and continental scales, automated near-surface cameras are being increasingly used to supplement phenology data derived from satellite imagery and data from ground-based human observers. We used imagery from a network of phenology cameras in a citizen science project called Season Spotter to investigate whether information could be derived from these images beyond standard, color-based vegetation indices. We found that engaging citizen science volunteers resulted in useful science knowledge in three ways: first, volunteers were able to detect some, but not all, reproductive phenology events, connecting landscape-level measures with field-based measures. Second, volunteers successfully demarcated individual trees in landscape imagery, facilitating scaling of vegetation indices from organism to ecosystem. And third, volunteers’ data were used to validate phenology transition dates calculated from vegetation indices and to identify potential improvements to existing algorithms to enable better biological interpretation. As a result, the use of citizen science in combination with near-surface remote sensing of phenology can be used to link ground-based phenology observations to satellite sensor data for scaling and validation. Well-designed citizen science projects targeting improved data processing and validation of remote sensing imagery hold promise for providing the data needed to address grand challenges in environmental science and Earth observation.

  6. 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......BACKGROUND: The association of Chlamydia pneumoniae with the development of atherosclerosis is based on serology and on detection of C pneumoniae-specific DNA by polymerase chain reaction in the atheromas. METHODS AND RESULTS: Because the humoral immune response frequently recognizes epitopes...... these antibodies in immunofluorescence microscopy of experimentally infected mice. In lung sections, a massive infiltration with polymorph nuclear neutrophil cells was observed. In the bronchial epithelial cells, C pneumoniae inclusions were seen. Evidence was found of differential expression of the GGAI proteins...

  7. Transport properties of water molecules confined between hydroxyapaptite surfaces: A Molecular dynamics simulation approach

    Science.gov (United States)

    Prakash, Muthuramalingam; Lemaire, Thibault; Di Tommaso, Devis; de Leeuw, Nora; Lewerenz, Marius; Caruel, Matthieu; Naili, Salah

    2017-10-01

    Water diffusion in the vicinity of hydroxyapatite (HAP) crystals is a key issue to describe biomineralization process. In this study, a configuration of parallel HAP platelets mimicking bone nanopores is proposed to characterize the nanoscopic transport properties of water molecules at HAP-water surface and interfaces using various potential models such as combination of the Core-Shell (CS) model, Lennard-Jones (LJ) potentials with SPC or SPC/E water models. When comparing all these potentials models, it appears that the core-shell potential for HAP together with the SPC/E water model more accurately predicts the diffusion properties of water near HAP surface. Moreover, we have been able to put into relief the possibility of observing hydroxyl (OH-) ion dissociation that modifies the water structure near the HAP surface.

  8. Atomic and molecular sciences. Progress report No. 8, April 1, 1981-March 31, 1982

    International Nuclear Information System (INIS)

    Walters, G.K.; Lane, N.F.

    1981-01-01

    The atomic and molecular physics program at Rice University addresses fundamental problems in structure, radiation-induced gas- and condensed-phase reaction kinetics and dynamics, and the mutual interactions of radiation, atoms, molecules, electrons and ions, particularly in highly unusual or exotic environments. The program emphasizes fundamental studies relating to new sources of energy, with close interaction between experimental and theoretical aspects of the research. Progress in the experimental program is reported in two principal areas, A) time resolved spectroscopy, and B) reactions in a flowing helium afterglow

  9. Comparison of wear of ultra-high molecular weight polyethylene acetabular cups against surface-engineered femoral heads.

    Science.gov (United States)

    Galvin, A; Brockett, C; Williams, S; Hatto, P; Burton, A; Isaac, G; Stone, M; Ingham, E; Fisher, J

    2008-10-01

    Alumina ceramic heads have been previously shown to reduce polyethylene wear in comparison to cobalt chrome (CoCr) heads in artificial hip joints. However, there are concerns about the brittle nature of ceramics. It is therefore of interest to investigate ceramic-like coatings on metallic heads. The aim of this study was to compare the friction and wear of ultra-high molecular weight polyethylene (UHMWPE) against alumina ceramic, CoCr, and surface-engineered ceramic-like coatings in a friction simulator and a hip joint simulator. All femoral heads tested were 28 mm diameter and included: Biolox Forte alumina, CoCr, arc evaporative physical vapour deposition (AEPVD) chromium nitride (CrN) coated CoCr, plasma-assisted chemical vapour deposition (PACVD) amorphous diamond-like carbon (aDLC) coated CoCr, sputter CrN coated CoCr, reactive gas controlled arc (RGCA) AEPVD titanium nitride (TiN) coated CoCr, and Graphit-iC coated CoCr. These were articulated against UHMWPE acetabular cups in a friction simulator and a hip joint simulator. Alumina and CoCr gave the lowest wear volumes whereas the sputter coated CrN gave the highest. Alumina also had the lowest friction factor. There was an association between surface parameters and wear. This study indicates that surface topography of surface-engineered femoral heads is more important than friction and wettability in controlling UHMWPE wear.

  10. Molecular-scale model for the mass density of electrolyte solutions bound by clay surfaces: application to bentonites.

    Science.gov (United States)

    Gonçalvès, J; Rousseau-Gueutin, P

    2008-04-15

    A model to simulate the density of solutions adsorbed onto clay mineral surfaces is proposed. In this model, the alteration of the ionic distribution caused by the electric field associated with the surface charge of clay platelets is accounted for using an electrical triple-layer model with an overlapping diffuse layer. The combined effects of ion hydration and the electric field on the structure of water are introduced through their influence on the partial molar volume of water. This model, applied to Na-montmorillonite, simulates the distribution of the interplatelet solution density as a function of the distance to the mineral surface. High densities in the direct vicinity of the surface and slightly lower density (a few percent) than the normal density in the diffuse layer are obtained. These results show good consistency with the available data on bentonite and with the densities that can be inferred from molecular dynamics simulations. This model shows that the interplatelet distance plays an important role in the distribution of the mass density of the solution in the pore space of clay rocks.

  11. The laboratory technology of discrete molecular separation: the historical development of gel electrophoresis and the material epistemology of biomolecular science, 1945-1970.

    Science.gov (United States)

    Chiang, Howard Hsueh-hao

    2009-01-01

    Preparative and analytical methods developed by separation scientists have played an important role in the history of molecular biology. One such early method is gel electrophoresis, a technique that uses various types of gel as its supporting medium to separate charged molecules based on size and other properties. Historians of science, however, have only recently begun to pay closer attention to this material epistemological dimension of biomolecular science. This paper substantiates the historiographical thread that explores the relationship between modern laboratory practice and the production of scientific knowledge. It traces the historical development of gel electrophoresis from the mid-1940s to the mid-1960s, with careful attention to the interplay between technical developments and disciplinary shifts, especially the rise of molecular biology in this time-frame. Claiming that the early 1950s marked a decisive shift in the evolution of electrophoretic methods from moving boundary to zone electrophoresis, I reconstruct various trajectories in which scientists such as Oliver Smithies sought out the most desirable solid supporting medium for electrophoretic instrumentation. Biomolecular knowledge, I argue, emerged in part from this process of seeking the most appropriate supporting medium that allowed for discrete molecular separation and visualization. The early 1950s, therefore, marked not only an important turning point in the history of separation science, but also a transformative moment in the history of the life sciences as the growth of molecular biology depended in part on the epistemological access to the molecular realm available through these evolving technologies.

  12. Surface tectonics of nanoporous networks of melamine-capped molecular building blocks formed through interface Schiff-base reactions.

    Science.gov (United States)

    Liu, Xuan-He; Wang, Dong; Wan, Li-Jun

    2013-10-01

    Control over the assembly of molecules on a surface is of great importance for the fabrication of molecule-based miniature devices. Melamine (MA) and molecules with terminal MA units are promising candidates for supramolecular interfacial packing patterning, owing to their multiple hydrogen-bonding sites. Herein, we report the formation of self-assembled structures of MA-capped molecules through a simple on-surface synthetic route. MA terminal groups were successfully fabricated onto rigid molecular cores with 2-fold and 3-fold symmetry through interfacial Schiff-base reactions between MA and aldehyde groups. Sub-molecular scanning tunneling microscopy (STM) imaging of the resultant adlayer revealed the formation of nanoporous networks. Detailed structural analysis indicated that strong hydrogen-bonding interactions between the MA groups persistently drove the formation of nanoporous networks. Herein, we demonstrate that functional groups with strong hydrogen-bond-formation ability are promising building blocks for the guided assembly of nanoporous networks and other hierarchical 2D assemblies. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Reversible redox reaction and water configuration on a positively charged platinum surface: first principles molecular dynamics simulation.

    Science.gov (United States)

    Ikeshoji, Tamio; Otani, Minoru; Hamada, Ikutaro; Okamoto, Yasuharu

    2011-12-07

    The water dissociation reaction and water molecule configuration on a positively charged platinum (111) surface were investigated by means of first principles molecular dynamics under periodic boundary conditions. Water molecules on the Pt surface were mostly in the O-down orientation but some H-down structures were also found. OH(-) ion, generated by removing H from H(2)O in the bulk region, moved to the Pt surface, on which a positive charge is induced, by a Grotthuss-like proton-relay mechanism and adsorbed on it as OH(Pt). Hydrogen atom exchange between OH(Pt) and a near-by water molecule frequently occurred on the Pt surface and had a low activation energy of the same order as room temperature energy. When a positive charge (7 μC cm(-2)) was added to the Pt surface, H(3)O(+) and OH(Pt) were generated from 2H(2)O on the Pt. This may be coupled with an electron transfer to the Pt electrode [2H(2)O → H(3)O(+) + OH(Pt) + e(-)]. The opposite reaction was also observed on the same charged surface during a simulation of duration about 10 ps; it is a reversible redox reaction. When further positive charge (14 μC cm(-2)) was added, the reaction shifted to the right hand side completely. Thus, this one-electron transfer reaction, which is a part of the oxygen electrode reaction in fuel cells and water electrolysis, was confirmed to be a low activation energy process.

  14. Structural changes and molecular interactions of hydrophobin SC3 in solution and on a hydrophobic surface

    NARCIS (Netherlands)

    Wang, X.; Vocht, M.L. de; Poolman, B.; Robillard, G.T.; Wang, [No Value; Jonge, J. de

    2002-01-01

    The hydrophobin SC3 belongs to a class of small proteins functioning in the growth and development of fungi. Its unique amphipathic property and remarkable surface activity make it interesting not only for biological studies but also for medical and industrial applications. Biophysical studies have

  15. Molecular dimensions and surface diffusion assisted mechanically robust slippery perfluoropolyether impregnated mesoporous alumina interfaces

    Science.gov (United States)

    Rowthu, Sriharitha; Balic, Edin E.; Hoffmann, Patrik

    2017-12-01

    Accomplishing mechanically robust omniphobic surfaces is a long-existing challenge, and can potentially find applications in bioengineering, tribology and paint industries. Slippery liquid impregnated mesoporous α-Al2O3 interfaces are achieved with water, alkanes, water based and oil based high viscosity acrylic paints. Incredibly high abrasion-resistance (wear coefficients ≤10‑8 mm3 N‑1 m‑1) and ultra-low friction coefficients (≥0.025) are attained, attributing to the hard alumina matrix and continuous replenishment of perfluoropolyether aided by capillarity and surface diffusion processes. A variety of impregnating liquids employed suggest that large molecules, faster surface diffusion and lowest evaporation rate generate the rare combination of high wear-resistance and omniphobicity. It is noteworthy that these novel liquid impregnated Al2O3 composites exhibit outstanding load bearing capacity up to 350 MPa; three orders of magnitude higher than achievable by the state of the art omniphobic surfaces. Further, our developed thermodynamic calculations suggest that the relative thermodynamic stability of liquid impregnated composites is linearly proportional to the spreading coefficient (S) of the impregnating liquid with the matrix material and is an important tool for the selection of an appropriate matrix material for a given liquid.

  16. Nanoscale organization of biomimetic peptide motifs on polymer surfaces: a molecular printing approach

    Czech Academy of Sciences Publication Activity Database

    Rypáček, František; Chánová, Eliška; Popelka, Štěpán; Machová, Luďka; Proks, Vladimír; Bačáková, Lucie

    2008-01-01

    Roč. 14, č. 5 (2008), s. 759-760 ISSN 1937-3341 R&D Projects: GA AV ČR(CZ) 1QS500110564 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z50110509 Keywords : biomaterials * block copolymers * surface modification Subject RIV: CD - Macromolecular Chemistry

  17. Charge exchange, surface-induced dissociation and reactions of doubly charged molecular ions SF42+ upon impact on a stainless steel surface: A comparison with surface-induced dissociation of singly charged SF4+ molecular ions

    Czech Academy of Sciences Publication Activity Database

    Feketeová, L.; Grill, V.; Zappa, F.; Endstrasser, N.; Rasul, B.; Herman, Zdeněk; Scheier, P.; Märk, T. D.

    2008-01-01

    Roč. 276, č. 1 (2008), s. 37-42 ISSN 1387-3806 Institutional research plan: CEZ:AV0Z40400503 Keywords : doubly charged ion * surface-induced dissociations * surface-induced reaction * charge exchange Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.445, year: 2008

  18. The environmental and molecular sciences laboratory project: Continuous evolution in leadership

    International Nuclear Information System (INIS)

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

    1995-09-01

    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 abounds of toxic waste sites, including DOE sites, is estimated to exceed one trillion dollars. That level of expenditure contains no guarantee that the sites can be restored to their original condition, and no consensus on ''how clean is clean enough.'' ''Ultimately, the scientific challenge is to determine as accurately as possible each term in the path that links the source of the contaminant with the particular biological end points or health effects and to understand the mechanisms that connect them. However, the present state of scientific knowledge regarding the effects of exogenous chemicals on human biology is very limited. Understanding the connections at the molecular level is, at best, a blurred picture and often a black box.'' 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

  19. In situ surface/interface x-ray diffractometer for oxide molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J. H. [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA; Tung, I. C. [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA; Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA; Chang, S. -H. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Bhattacharya, A. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Fong, D. D. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Freeland, J. W. [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA; Hong, Hawoong [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA

    2016-01-01

    In situ studies of oxide molecular beam epitaxy by synchrotron x-ray scattering has been made possible by upgrading an existing UHV/molecular beam epitaxy (MBE) six-circle diffractometer system. For oxide MBE growth, pure ozone delivery to the chamber has been made available, and several new deposition sources have been made available on a new 12 in. CF (ConFlat, a registered trademark of Varian, Inc.) flange. X-ray diffraction has been used as a major probe for film growth and structures for the system. In the original design, electron diffraction was intended for the secondary diagnostics available without the necessity of the x-ray and located at separate positions. Deposition of films was made possible at the two diagnostic positions. And, the aiming of the evaporation sources is fixed to the point between two locations. Ozone can be supplied through two separate nozzles for each location. Also two separate thickness monitors are installed. Additional features of the equipment are also presented together with the data taken during typical oxide film growth to illustrate the depth of information available via in situ x-ray techniques.

  20. In situ surface/interface x-ray diffractometer for oxide molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J. H.; Freeland, J. W.; Hong, Hawoong, E-mail: hhong@aps.anl.gov [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Tung, I. C. [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Chang, S.-H.; Bhattacharya, A.; Fong, D. D. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2016-01-15

    In situ studies of oxide molecular beam epitaxy by synchrotron x-ray scattering has been made possible by upgrading an existing UHV/molecular beam epitaxy (MBE) six-circle diffractometer system. For oxide MBE growth, pure ozone delivery to the chamber has been made available, and several new deposition sources have been made available on a new 12 in. CF (ConFlat, a registered trademark of Varian, Inc.) flange. X-ray diffraction has been used as a major probe for film growth and structures for the system. In the original design, electron diffraction was intended for the secondary diagnostics available without the necessity of the x-ray and located at separate positions. Deposition of films was made possible at the two diagnostic positions. And, the aiming of the evaporation sources is fixed to the point between two locations. Ozone can be supplied through two separate nozzles for each location. Also two separate thickness monitors are installed. Additional features of the equipment are also presented together with the data taken during typical oxide film growth to illustrate the depth of information available via in situ x-ray techniques.

  1. Curcumin induced nanoscale CD44 molecular redistribution and antigen-antibody interaction on HepG2 cell surface

    International Nuclear Information System (INIS)

    Wang Mu; Ruan Yuxia; Xing Xiaobo; Chen Qian; Peng, Yuan; Cai Jiye

    2011-01-01

    Graphical abstract: Highlights: → In this study, we investigate the changes of CD44 expression and distribution on HepG2 cells after curcumin treatment. → We find curcumin is able to change the morphology and ultrastructure of HepG2 cells. → Curcumin can reduce the expression of CD44 molecules and induce the nanoscale molecular redistribution on cell surface. → The binding force between CD44-modified AFM tip and the HepG2 cell surface decreases after curcumin-treatment. - Abstract: The cell surface glycoprotein CD44 was implicated in the progression, metastasis and apoptosis of certain human tumors. In this study, we used atomic force microscope (AFM) to monitor the effect of curcumin on human hepatocellular carcinoma (HepG2) cell surface nanoscale structure. High-resolution imaging revealed that cell morphology and ultrastructure changed a lot after being treated with curcumin. The membrane average roughness increased (10.88 ± 4.62 nm to 129.70 ± 43.72 nm) and the expression of CD44 decreased (99.79 ± 0.16% to 75.14 ± 8.37%). Laser scanning confocal microscope (LSCM) imaging showed that CD44 molecules were located on the cell membrane. The florescence intensity in control group was weaker than that in curcumin treated cells. Most of the binding forces between CD44 antibodies and untreated HepG2 cell membrane were around 120-220 pN. After being incubated with curcumin, the major forces focused on 70-150 pN (10 μM curcumin-treated) and 50-120 pN (20 μM curcumin-treated). These results suggested that, as result of nanoscale molecular redistribution, changes of the cell surface were in response to external treatment of curcumin. The combination of AFM and LSCM could be a powerful method to detect the distribution of cell surface molecules and interactions between molecules and their ligands.

  2. Adsorption of Zn(II) on the kaolinite(001) surfaces in aqueous environment: A combined DFT and molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qiang; Kong, Xiang-Ping; Zhang, Bao-Hua; Wang, Juan, E-mail: juaner80@163.com

    2017-08-31

    Highlights: • Zn(II) adsorption on two types of neutral kaolinite(001) surfaces is investigated. • Surface “Ou” is found the preferred site for mono- and bi-dentate complexes. • Both Zn(II) and surface oxygen accept electrons from aqua oxygens. • Coupling of O 2p with Zn sp{sup 3}d{sup 2} (or sp{sup 3}) hybridization states is the bonding nature. - Abstract: Adsorption of Zn(II) on two types of neutral (001) surfaces of kaolinite, tetrahedral Si(t) and octahedral Al(o), was studied by means of DFT calculations and classical molecular dynamics simulations. The position and structure for both outer-sphere and mono-/bi-dentate inner-sphere complexes of Zn(II) in aqueous environment were examined, with binding energy and radial distribution function calculated. Outer-sphere complex on the Si(t) surface, monodentate inner-sphere complex of “O{sub u}” (surface oxygen with “upright” hydrogen) site and bidentate complex of “O{sub u}-O{sub u}” site of neighboring Al centers on the Al(o) surface are considered to be the dominant adsorption species. The outer-sphere complex is found six-coordinated with distorted octahedral geometry, while both the inner-sphere complexes exhibit the tetrahedral structure with coordination number of four. Hydrogen bonding interactions between oxygen or hydrogen of the kaolinite(001) surfaces and the aqua ligands of Zn(II) act as the key role for the structure and stability of adsorption complexes. Upon the Mulliken population analysis and partial density of states, both Zn(II) and surface oxygen accept electrons from aqua oxygens, and coupling of O 2p with the sp{sup 3}d{sup 2} or sp{sup 3} hybridization states of Zn(II) is the primary bonding nature of Zn(II) with oxygen in outer- and inner-sphere complexes, respectively.

  3. Molecular analysis of long-term biofilm formation on PVC and cast iron surfaces in drinking water distribution system.

    Science.gov (United States)

    Liu, Ruyin; Zhu, Junge; Yu, Zhisheng; Joshi, DevRaj; Zhang, Hongxun; Lin, Wenfang; Yang, Min

    2014-04-01

    To understand the impacts of different plumbing materials on long-term biofilm formation in water supply system, we analyzed microbial community compositions in the bulk water and biofilms on faucets with two different materials-polyvinyl chloride (PVC) and cast iron, which have been frequently used for more than10 years. Pyrosequencing was employed to describe both bacterial and eukaryotic microbial compositions. Bacterial communities in the bulk water and biofilm samples were significantly different from each other. Specific bacterial populations colonized on the surface of different materials. Hyphomicrobia and corrosion associated bacteria, such as Acidithiobacillus spp., Aquabacterium spp., Limnobacter thiooxidans, and Thiocapsa spp., were the most dominant bacteria identified in the PVC and cast iron biofilms, respectively, suggesting that bacterial colonization on the material surfaces was selective. Mycobacteria and Legionella spp. were common potential pathogenic bacteria occurred in the biofilm samples, but their abundance was different in the two biofilm bacterial communities. In contrast, the biofilm samples showed more similar eukaryotic communities than the bulk water. Notably, potential pathogenic fungi, i.e., Aspergillus spp. and Candida parapsilosis, occurred in similar abundance in both biofilms. These results indicated that microbial community, especially bacterial composition was remarkably affected by the different pipe materials (PVC and cast iron). Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

  4. The experimental teaching reform in biochemistry and molecular biology for undergraduate students in Peking University Health Science Center.

    Science.gov (United States)

    Yang, Xiaohan; Sun, Luyang; Zhao, Ying; Yi, Xia; Zhu, Bin; Wang, Pu; Lin, Hong; Ni, Juhua

    2015-01-01

    Since 2010, second-year undergraduate students of an eight-year training program leading to a Doctor of Medicine degree or Doctor of Philosophy degree in Peking University Health Science Center (PKUHSC) have been required to enter the "Innovative talent training project." During that time, the students joined a research lab and participated in some original research work. There is a critical educational need to prepare these students for the increasing accessibility of research experience. The redesigned experimental curriculum of biochemistry and molecular biology was developed to fulfill such a requirement, which keeps two original biochemistry experiments (Gel filtration and Enzyme kinetics) and adds a new two-experiment component called "Analysis of anti-tumor drug induced apoptosis." The additional component, also known as the "project-oriented experiment" or the "comprehensive experiment," consists of Western blotting and a DNA laddering assay to assess the effects of etoposide (VP16) on the apoptosis signaling pathways. This reformed laboratory teaching system aims to enhance the participating students overall understanding of important biological research techniques and the instrumentation involved, and to foster a better understanding of the research process all within a classroom setting. Student feedback indicated that the updated curriculum helped them improve their operational and self-learning capability, and helped to increase their understanding of theoretical knowledge and actual research processes, which laid the groundwork for their future research work. © 2015 The International Union of Biochemistry and Molecular Biology.

  5. Surface-water quality-assurance plan for the U.S. Geological Survey Washington Water Science Center

    Science.gov (United States)

    Mastin, Mark C.

    2016-02-19

    This Surface-Water Quality-Assurance Plan documents the standards, policies, and procedures used by the U.S. Geological Survey Washington Water Science Center (WAWSC) for activities related to the collection, processing, storage, analysis, and publication of surface-water data. This plan serves as a guide to all WAWSC personnel involved in surface-water data activities, and changes as the needs and requirements of the WAWSC change. Regular updates to this plan represent an integral part of the quality-assurance process. In the WAWSC, direct oversight and responsibility by the hydrographer(s) assigned to a surface-water station, combined with team approaches in all work efforts, assure highquality data, analyses, reviews, and reports for cooperating agencies and the public.

  6. Science literacy and meaningful learning: status of public high school students from Rio de Janeiro face to molecular biology concepts

    Directory of Open Access Journals (Sweden)

    Daniel Alves Escodino

    2013-12-01

    Full Text Available In this work we aimed to determine the level of Molecular Biology (MB science literacy of students from two Brazilian public schools which do not consider the rogerian theory for class planning and from another institution, Cap UERJ, which favours this theory. We applied semiclosed questionnaires specific to the different groups of science literacy levels. Besides, we have asked them to perform conceptual maps with MB concepts in order to observe if they have experienced meaningful learning. Finally, we prepared MB classes for students of the three schools, considering their conceptual maps and tried to evaluate, through a second map execution, if the use of alternative didactics material, which consider meaningful learning process, would have any effect over the appropriation of new concepts. We observed that most students are placed at Functional literacy level. Nonetheless, several students from CAp were also settled at the higher Conceptual and Procedural levels. We found that most students have not experienced meaningful learning and that the employment of didactic material and implementation of proposals which consider the cognitive structure of the students had a significant effect on the appropriation of several concepts.

  7. Targeting and molecular imaging of HepG2 cells using surface-functionalized gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Rathinaraj, Pierson [Auckland University of Technology, Institute of Biomedical Technologies (New Zealand); Lee, Kyubae; Choi, Yuri; Park, Soo-Young [Kyungpook National University, School of Applied Chemical Engineering, Graduate School (Korea, Republic of); Kwon, Oh Hyeong [Kumoh National Institute of Technology, Department of Polymer Science and Engineering (Korea, Republic of); Kang, Inn-Kyu, E-mail: ikkang@knu.ac.kr [Kyungpook National University, School of Applied Chemical Engineering, Graduate School (Korea, Republic of)

    2015-07-15

    Mercaptosuccinic acid (M)-conjugated gold nanoparticles (GM) were prepared and characterized by transmission electron microscope and dynamic light scattering. M was used to improve the monodispersity and non-specific intracellular uptake of nanoparticles. Lactobionic acid (L) was subsequently conjugated to the GM to target preferentially HepG2 cells (liver cancer cells) that express asialoglycoprotein receptors (ASGPR) on their membrane surfaces and facilitate the transit of nanoparticles across the cell membrane. The mean size of lactobionic acid-conjugated gold nanoparticle (GL) was approximately 10 ± 0.2 nm. Finally, the Atto 680 dye (A6) was coupled to the nanoparticles to visualize their internalization into HepG2 cells. The interaction of surface-modified gold nanoparticles with HepG2 cells was studied after culturing cells in media containing the GM or L-conjugated GM (GL)

  8. Surface-Assisted Laser Desorption Ionization of Low Molecular Organic Substances on Oxidized Porous Silicon

    Science.gov (United States)

    Shmigol, I. V.; Alekseev, S. A.; Lavrynenko, O. Yu.; Zaitsev, V. N.; Barbier, D.; Pokrovskiy, V. A.

    Desorption/ionization on silicon (DIOS) mass spectra of methylene blue (MB+Cl-) were studied using p+-type oxidized monofunctional porous silicon (PS-OX mono ) free layers. Reduction/protonation processes of methylene blue (MB) dye were investigated. It was shown that SiH x terminal sites on oxidized surface of porous silicon (PS-OX) are not the rate-determining factor for the reduction/protonation in DIOS. Tunneling of electron through the dielectric layer of nanostructures on silicon surface under effect of local electrostatic and electromagnetic fields is considered to be the most significant factor of adsorbate-adsorbent electron exchange and further laser-induced ion formation.

  9. Comparative surface and molecular investigations of the sandfish’s epidermis (Squamata: Scincidae: Scincus scincus)

    OpenAIRE

    Staudt, Konrad

    2012-01-01

    The sandfish (Scincidae: Scincus scincus) is a lizard capable of moving through desert sand in a swimming-like fashion. The epidermis of this lizard shows a low friction to sand as an adaption to a subterranean life below the desert’s surface. Caused by material properties of ß-keratin proteins forming the outer epidermis, this low friction reduces further adhesive wear. Both skin effects, the friction reduction and abrasion resistance outperform even steel. A possible explanation for these p...

  10. First principles study of NH3 molecular adsorption on LiH (100) surfaces

    International Nuclear Information System (INIS)

    Lu Xiaoxia; Chen Yuhong; Dong Xiao

    2012-01-01

    The adsorption of NH 3 on LiH (100) crystal surfaces was studied by first principles method. The preferred adsorption sites, adsorption energy, dissociation energy and electronic structure of the LiH (100)/NH 3 systems were calculated separately. It is found that chemical adsorption happened mainly when NH 3 molecules are on the LiH (100) crystal surfaces. When NH 3 is adsorbed on the Li top site, NH 2 is formed on the LiH (100) crystal surfaces after loss of H atom, the calculated adsorption energy, 0.511 eV, belongs to strong chemical adsorption, then the interaction is strongest. The interaction between NH 2 and the neighboring Li, H are ionic. The covalent bonds are formed between N and H atoms in NH 2 . One H 2 molecule is formed by another H atom in NH 3 and H atom from LiH (100) crystal sur- faces. The covalent bonds are formed between H and H atoms in H 2 . (authors)

  11. Surface-Engineered Nanocontainers Based on Molecular Self-Assembly and Their Release of Methenamine

    Directory of Open Access Journals (Sweden)

    Minghui Zhang

    2018-02-01

    Full Text Available The mixing of polymers and nanoparticles is opening pathways for engineering flexible composites that exhibit advantageous functional properties. To fabricate controllable assembling nanocomposites for efficiently encapsulating methenamine and releasing them on demand, we functionalized the surface of natural halloysite nanotubes (HNTs selectively with polymerizable gemini surfactant which has peculiar aggregation behavior, aiming at endowing the nanomaterials with self-assembly and stimulative responsiveness characteristics. The micromorphology, grafted components and functional groups were identified using transmission electron microscopy (TEM, thermogravimetric analysis (TGA, Fourier transform infrared (FTIR spectroscopy, and X-ray photoelectron spectroscopy (XPS. The created nanocomposites presented various characteristics of methenamine release with differences in the surface composition. It is particularly worth mentioning that the controlled release was more efficient with the increase of geminized monomer proportion, which is reasonably attributed to the fact that the amphiphilic geminized moieties with positive charge and obvious hydrophobic interactions interact with the outer and inner surface in different ways through fabricating polymeric shell as release stoppers at nanotube ends and forming polymer brush into the nanotube lumen for guest immobilization. Meanwhile, the nanocomposites present temperature and salinity responsive characteristics for the release of methenamine. The combination of HNTs with conjugated functional polymers will open pathways for engineering flexible composites which are promising for application in controlled release fields.

  12. Spatiotemporal control over molecular delivery and cellular encapsulation from electropolymerized micro- and nanopatterned surfaces.

    Science.gov (United States)

    Stern, Eric; Jay, Steven M; Demento, Stacey L; Murelli, Ryan P; Reed, Mark A; Malinski, Tadeusz; Spiegel, David A; Mooney, David J; Fahmy, Tarek M

    2009-07-13

    Bioactive, patterned micro- and nanoscale surfaces that can be spatially engineered for three-dimensional ligand presentation and sustained release of signaling molecules represent a critical advance for the development of next-generation diagnostic and therapeutic devices. Lithography is ideally suited to patterning such surfaces due to its precise, easily scalable, high-throughput nature; however, to date polymers patterned by these techniques have not demonstrated the capacity for sustained release of bioactive agents. We demonstrate here a class of lithographically-defined, electropolymerized polymers with monodisperse micro- and nanopatterned features capable of sustained release of bioactive drugs and proteins. We show that precise control can be achieved over the loading capacity and release rates of encapsulated agents and illustrate this aspect using a fabricated surface releasing a model antigen (ovalbumin) and a cytokine (interleukin-2) for induction of a specific immune response. We further demonstrate the ability of this technique to enable three-dimensional control over cellular encapsulation. The efficacy of the described approach is buttressed by its simplicity, versatility, and reproducibility, rendering it ideally suited for biomaterials engineering.

  13. science

    International Development Research Centre (IDRC) Digital Library (Canada)

    David Spurgeon

    green revolution". — seemed to confirm the value of science and technology to international development. Yet studies showed that, at that time, only about two percent of ... gap in science and technology between the Third World and the industrial- ..... Finance; Treasury Board; Industry, Trade and Commerce; Agriculture;.

  14. DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces

    Science.gov (United States)

    Szymonik, M.; Davies, A. G.; Wälti, C.

    2016-09-01

    We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces—demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable.

  15. Surface-enhanced Raman scattering (SERS) of riboflavin on nanostructured Ag surfaces: The role of excitation wavelength, plasmon resonance and molecular resonance

    Science.gov (United States)

    Šubr, Martin; Kuzminova, Anna; Kylián, Ondřej; Procházka, Marek

    2018-05-01

    Optimization of surface-enhanced Raman scattering (SERS)-based sensors for (bio)analytical applications has received much attention in recent years. For optimum sensitivity, both the nanostructure fabrication process and the choice of the excitation wavelength used with respect to the specific analyte studied are of crucial importance. In this contribution, detailed SERS intensity profiles were measured using gradient nanostructures with the localized surface-plasmon resonance (LSPR) condition varying across the sample length and using riboflavin as the model biomolecule. Three different excitation wavelengths (633 nm, 515 nm and 488 nm) corresponding to non-resonance, pre-resonance and resonance excitation with respect to the studied molecule, respectively, were tested. Results were interpreted in terms of a superposition of the enhancement provided by the electromagnetic mechanism and intrinsic properties of the SERS probe molecule. The first effect was dictated mainly by the degree of spectral overlap between the LSPR band, the excitation wavelength along with the scattering cross-section of the nanostructures, while the latter was influenced by the position of the molecular resonance with respect to the excitation wavelength. Our experimental findings contribute to a better understanding of the SERS enhancement mechanism.

  16. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    Directory of Open Access Journals (Sweden)

    Bingjie Hu

    2014-08-01

    Full Text Available Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer. PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD. We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets.

  17. Development of self-assembled molecular structures on polymeric surfaces and their applications as ultrasonically responsive barrier coatings for on-demand, pulsatile drug delivery

    Science.gov (United States)

    Kwok, Connie Sau-Kuen

    Nature in the form of DNA, proteins, and cells has the remarkable ability to interact with its environment by processing biological information through specific molecular recognition at the interface. As such, materials that are capable of triggering an appropriate biological response need to be engineered at the biomaterial surface. Chemically and structurally well-defined self-assembled monolayers (SAMs), biomimetics of the lipid bilayer in cell membranes, have been created and studied mostly on rigid metallic surfaces. This dissertation is motivated by the lack of methods to generate a molecularly designed surface for biomedical polymers and thus provides an enabling technology to engineer a polymeric surface precisely at a molecular and cellular level. To take this innovation one step further, we demonstrated that such self-assembled molecular structure coated on drug-containing polymeric devices could act as a stimulus-responsive barrier for controlled drug delivery. A simple, one-step procedure for generating ordered, crystalline methylene chains on polymeric surfaces via urethane linkages was successfully developed. The self-assemblies and molecular structures of these crystalline methylene chains are comparable to the SAM model surfaces, as evidenced by various surface characterization techniques (XPS, TOF-SIMS, and FTIR-ATR). For the first time, these self-assembled molecular structures are shown to function collectively as an ultrasound-responsive barrier membrane for pulsatile drug delivery, including delivery of low-molecular-weight ciprofloxacin and high-molecular-weight insulin. Encouraging results, based on the insulin-activated deoxyglucose uptakes in adipocytes, indicate that the released insulin remained biologically active. Both chemical and acoustic analyses suggest that the ultrasound-assisted release mechanism is primarily induced by transient cavitation, which causes temporary disruption of the self-assembled overlayer, and thus allows

  18. In situ monitoring of the surface reconstructions on InP(001) prepared by molecular beam epitaxy

    Science.gov (United States)

    Ozanyan, K. B.; Parbrook, P. J.; Hopkinson, M.; Whitehouse, C. R.; Sobiesierski, Z.; Westwood, D. I.

    1997-07-01

    Reflection anisotropy spectroscopy (RAS) and reflection high-energy electron diffraction (RHEED) were applied to study clean InP(001) surfaces prepared by molecular beam epitaxy (MBE). At phosphorus beam equivalent pressures (BEPs) between 3.5×10-7 and 3.5×10-6 mbar and substrate temperature (Ts) falling from 590 to 150 °C, (2×4), (2×1), (2×2), and c(4×4) RHEED patterns are observed. The main RAS features, observed at 1.7-1.9 and 2.6-2.9 eV are assigned to In and P dimers, respectively. The above reconstruction sequence is associated closely with transformations identified in RAS signatures that are induced by progressively increasing the P surface coverage. The RAS results also imply the existence of (2×4)α and (2×4)β phases. A surface-phase diagram for MBE-grown (001) InP, in the whole range of Ts and phosphorus BEPs is proposed.

  19. A Comparative Study of Molecular Structure, pKa, Lipophilicity, Solubility, Absorption and Polar Surface Area of Some Antiplatelet Drugs

    Directory of Open Access Journals (Sweden)

    Milan Remko

    2016-03-01

    Full Text Available Theoretical chemistry methods have been used to study the molecular properties of antiplatelet agents (ticlopidine, clopidogrel, prasugrel, elinogrel, ticagrelor and cangrelor and several thiol-containing active metabolites. The geometries and energies of most stable conformers of these drugs have been computed at the Becke3LYP/6-311++G(d,p level of density functional theory. Computed dissociation constants show that the active metabolites of prodrugs (ticlopidine, clopidogrel and prasugrel and drugs elinogrel and cangrelor are completely ionized at pH 7.4. Both ticagrelor and its active metabolite are present at pH = 7.4 in neutral undissociated form. The thienopyridine prodrugs ticlopidine, clopidogrel and prasugrel are lipophilic and insoluble in water. Their lipophilicity is very high (about 2.5–3.5 logP values. The polar surface area, with regard to the structurally-heterogeneous character of these antiplatelet drugs, is from very large interval of values of 3–255 Å2. Thienopyridine prodrugs, like ticlopidine, clopidogrel and prasugrel, with the lowest polar surface area (PSA values, exhibit the largest absorption. A high value of polar surface area (PSA of cangrelor (255 Å2 results in substantial worsening of the absorption in comparison with thienopyridine drugs.

  20. Metaproteomic characterization of high molecular weight dissolved organic matter in surface seawaters in the South China Sea

    Science.gov (United States)

    Dong, Hong-Po; Wang, Da-Zhi; Xie, Zhang-Xian; Dai, Min-Han; Hong, Hua-Sheng

    2013-05-01

    Dissolved organic matter (DOM) is an important reservoir of carbon and energy in the marine environment and plays a key role in regulating the global carbon cycle. This study characterized proteins of high-molecular-weight DOM (size between 5 kDa and classification and function dominated the dissolved protein pool (43-53%) while the remaining proteins presented close similarity in biological origin among the four sampling sites. Rhodospirillaceae, Prochlorococcus, SAR11 clade and viruses were the major contributors to dissolved proteins in the HMW-DOM from surface seawaters while very few proteins were from the eukaryotic phytoplankton and no archaeal proteins were detected. Transporters with substrate specificities for nitrogen- and carbon-containing compounds (1.5% of the total spectra for each) were highly detected while no phosphate transporters were found, suggesting that carbon and nitrogen might be more limiting than phosphorus in the surface seawater. Viral proteins were assigned into three families: Myoviridae, Podoviridae and Siphoviridae, and the Myoviridae proteins were the most abundant. Among them, structure proteins were the most abundant viral proteins. This study indicated that the dissolved proteins of HMW-DOM presented compositional and biologically original homogeneity in the surface seawaters of the South China Sea, and bacteria and viruses dominated the dissolved protein pool.