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.

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.

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 [...].

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

Science.gov (United States)

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

2011-06-17

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

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

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.

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.

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.

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

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.

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1982-06-01

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

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.)

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

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.

Molecular Contamination on Anodized Aluminum Components of the Genesis Science Canister

Science.gov (United States)

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

2005-01-01

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

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

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

Science.gov (United States)

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

2017-08-22

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

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

Science.gov (United States)

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

2017-06-12

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

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

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)

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.

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.

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

International Nuclear Information System (INIS)

Schiesser, Alexander; Schaefer, Rolf

2009-01-01

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

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.

Surface science and heterogeneous catalysis

International Nuclear Information System (INIS)

Somorjai, G.A.

1980-05-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Bargar, John R

1999-05-07

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

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

International Nuclear Information System (INIS)

Bargar, John R

1999-01-01

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

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.

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.

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

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.

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

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

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

Molecular tailoring of solid surfaces

Energy Technology Data Exchange (ETDEWEB)

Evenson, Simon Alan

1997-07-01

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

Molecular tailoring of solid surfaces

International Nuclear Information System (INIS)

Evenson, Simon Alan

1997-01-01

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

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

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

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

Marine molecular biology: An emerging field of biological sciences

Digital Repository Service at National Institute of Oceanography (India)

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

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

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

Molecular surface mesh generation by filtering electron density map.

Science.gov (United States)

Giard, Joachim; Macq, Benoît

2010-01-01

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

Molecular Surface Mesh Generation by Filtering Electron Density Map

Directory of Open Access Journals (Sweden)

Joachim Giard

2010-01-01

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

Deep Generative Models for Molecular Science

DEFF Research Database (Denmark)

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

2018-01-01

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

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

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-04-10

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

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)

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.

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.

Autonomous molecular cascades for evaluation of cell surfaces

Science.gov (United States)

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

2013-08-01

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

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

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.

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

Science.gov (United States)

Tibell, Lena A E; Rundgren, Carl-Johan

2010-01-01

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

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.

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 ...

Molecular environmental science and synchrotron radiation sources

Energy Technology Data Exchange (ETDEWEB)

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

1995-12-31

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

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...

Effect of polar surfaces on organic molecular crystals

Science.gov (United States)

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

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

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.

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...

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

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

On-Surface Synthesis by Click Chemistry Investigated by STM and XPS

DEFF Research Database (Denmark)

Vadapoo, Sundar Raja

2014-01-01

Molecular synthesis is essential in the bottom-up approach of achieving highly stable nanostructures. On-surface synthesis is highly interesting from the basic science of view to improve the understanding of molecular behavior adsorbed on metal surfaces, and has potential applications such as mol......Molecular synthesis is essential in the bottom-up approach of achieving highly stable nanostructures. On-surface synthesis is highly interesting from the basic science of view to improve the understanding of molecular behavior adsorbed on metal surfaces, and has potential applications...... such as molecular electronics and surface functionalization. In this thesis, a well-defined click chemistry approach is followed, with the study of azide-alkyne cycloaddition on Cu(111) surface in UHV environment. A successful achievement of the click reaction product via on-surface synthesis has been shown, which...

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

Science.gov (United States)

Jian, Huahua; Tour, James M

2003-06-27

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

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

Science.gov (United States)

Wang, Hong-Fei

2016-12-01

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

Learning surface molecular structures via machine vision

Science.gov (United States)

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

2017-08-01

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

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.

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

Science.gov (United States)

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

2017-11-23

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

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…

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.

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:

Surface Science at the Solid Liquid Interface

Science.gov (United States)

1993-10-06

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

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.

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.

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

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...

Atomic molecular and optical physics

International Nuclear Information System (INIS)

Anon.

1986-01-01

Laser-assisted manufacturing and fiber-optics communications are but two of the products of atomic, molecular, and optical physics, (AMO) research. AMO physics provides theoretical and experimental methods and essential data to neighboring areas of science such as chemistry, astrophysics, condensed-matter physics, plasma physics, surface science, biology, and medicine. This book addresses advances in atomic, molecular, and optical fields and provides recommendations for further research. It also looks at scientific applications in national security, manufacturing, medicine, and other fields

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.

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

International Nuclear Information System (INIS)

Meyerhof, W.E.

1981-01-01

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

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-...

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

NARCIS (Netherlands)

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

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

Structure of adsorbed monolayers. The surface chemical bond

International Nuclear Information System (INIS)

Somorjai, G.A.; Bent, B.E.

1984-06-01

This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table

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

Science.gov (United States)

Dlott, Dana

2008-03-01

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

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.

Integrated multiscale modeling of molecular computing devices

International Nuclear Information System (INIS)

Cummings, Peter T; Leng Yongsheng

2005-01-01

Molecular electronics, in which single organic molecules are designed to perform the functions of transistors, diodes, switches and other circuit elements used in current siliconbased microelecronics, is drawing wide interest as a potential replacement technology for conventional silicon-based lithographically etched microelectronic devices. In addition to their nanoscopic scale, the additional advantage of molecular electronics devices compared to silicon-based lithographically etched devices is the promise of being able to produce them cheaply on an industrial scale using wet chemistry methods (i.e., self-assembly from solution). The design of molecular electronics devices, and the processes to make them on an industrial scale, will require a thorough theoretical understanding of the molecular and higher level processes involved. Hence, the development of modeling techniques for molecular electronics devices is a high priority from both a basic science point of view (to understand the experimental studies in this field) and from an applied nanotechnology (manufacturing) point of view. Modeling molecular electronics devices requires computational methods at all length scales - electronic structure methods for calculating electron transport through organic molecules bonded to inorganic surfaces, molecular simulation methods for determining the structure of self-assembled films of organic molecules on inorganic surfaces, mesoscale methods to understand and predict the formation of mesoscale patterns on surfaces (including interconnect architecture), and macroscopic scale methods (including finite element methods) for simulating the behavior of molecular electronic circuit elements in a larger integrated device. Here we describe a large Department of Energy project involving six universities and one national laboratory aimed at developing integrated multiscale methods for modeling molecular electronics devices. The project is funded equally by the Office of Basic

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.

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

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.

Molecularly engineered graphene surfaces for sensing applications: A review

International Nuclear Information System (INIS)

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

2015-01-01

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

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.

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.

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

Science.gov (United States)

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

2018-04-11

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

Protein signatures using electrostatic molecular surfaces in harmonic space

Directory of Open Access Journals (Sweden)

C. Sofia Carvalho

2013-10-01

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

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.

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

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1994-10-01

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

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.

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

Probing gas-surface interactions with a molecular beam

International Nuclear Information System (INIS)

Spruit, M.E.M.

1988-01-01

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

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

Reaction dynamics of molecular hydrogen on silicon surfaces

DEFF Research Database (Denmark)

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

1996-01-01

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

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.

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.

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

KAUST Repository

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

2012-01-01

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

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.

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)

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-04-21

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

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

Science.gov (United States)

López-Moreno, S.; Romero, A. H.

2015-04-01

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

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

International Nuclear Information System (INIS)

López-Moreno, S.; Romero, A. H.

2015-01-01

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

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.

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.

Tuning the deposition of molecular graphene nanoribbons by surface functionalization

Science.gov (United States)

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

2015-07-01

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

Molecular ingredients of heterogeneous catalysis

International Nuclear Information System (INIS)

Somorjai, G.A.

1982-06-01

The purpose of this paper is to present a review and status report to those in theoretical chemistry of the rapidly developing surface science of heterogeneous catalysis. The art of catalysis is developing into science. This profound change provides one with opportunities not only to understand the molecular ingredients of important catalytic systems but also to develop new and improved catalyst. The participation of theorists to find answers to important questions is sorely needed for the sound development of the field. It is the authors hope that some of the outstanding problems of heterogeneous catalysis that are identified in this paper will be investigated. For this purpose the paper is divided into several sections. The brief Introduction to the methodology and recent results of the surface science of heterogeneous catalysis is followed by a review of the concepts of heterogeneous catalysis. Then, the experimental results that identified the three molecular ingredients of catalysis, structure, carbonaceous deposit and the oxidation state of surface atoms are described. Each section is closed with a summary and a list of problems that require theoretical and experimental scrutiny. Finally attempts to build new catalyst systems and the theoretical and experimental problems that appeared in the course of this research are described

Molecular ingredients of heterogeneous catalysis

Energy Technology Data Exchange (ETDEWEB)

Somorjai, G.A.

1982-06-01

The purpose of this paper is to present a review and status report to those in theoretical chemistry of the rapidly developing surface science of heterogeneous catalysis. The art of catalysis is developing into science. This profound change provides one with opportunities not only to understand the molecular ingredients of important catalytic systems but also to develop new and improved catalyst. The participation of theorists to find answers to important questions is sorely needed for the sound development of the field. It is the authors hope that some of the outstanding problems of heterogeneous catalysis that are identified in this paper will be investigated. For this purpose the paper is divided into several sections. The brief Introduction to the methodology and recent results of the surface science of heterogeneous catalysis is followed by a review of the concepts of heterogeneous catalysis. Then, the experimental results that identified the three molecular ingredients of catalysis, structure, carbonaceous deposit and the oxidation state of surface atoms are described. Each section is closed with a summary and a list of problems that require theoretical and experimental scrutiny. Finally attempts to build new catalyst systems and the theoretical and experimental problems that appeared in the course of this research are described.

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}

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

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.

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)

Multiresolution molecular mechanics: Surface effects in nanoscale materials

Energy Technology Data Exchange (ETDEWEB)

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

2017-05-01

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

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.

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

Directory of Open Access Journals (Sweden)

International Journal of Molecular Sciences Editorial Office

2016-03-01

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

Molecular recognition on a cavitand-functionalized silicon surface.

Science.gov (United States)

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

2009-06-03

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

Surface science models of CoMoS hydrodesulfurisation catalysts

NARCIS (Netherlands)

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

1997-01-01

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

Thermochemical Surface Engineering: A Playground for Science and Innovation

DEFF Research Database (Denmark)

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

2017-01-01

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

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

DEFF Research Database (Denmark)

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

2010-01-01

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

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

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

International Nuclear Information System (INIS)

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

1978-01-01

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

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.

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.

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

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

Science.gov (United States)

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

2015-09-01

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

A preliminary exploration of Advanced Molecular Bio-Sciences Research Center

International Nuclear Information System (INIS)

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

2000-01-01

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

Confinement properties of 2D porous molecular networks on metal surfaces

International Nuclear Information System (INIS)

Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

2016-01-01

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

Monitoring peptide-surface interaction by means of molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

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

2010-12-09

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

Molecular science solving global problems

International Nuclear Information System (INIS)

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

1995-01-01

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

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.

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

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

International Nuclear Information System (INIS)

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

2001-01-01

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

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

Science.gov (United States)

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

2018-06-01

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

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.

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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.

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.

Molecular dynamics for reactions of heterogeneous catalysis

NARCIS (Netherlands)

Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

1991-01-01

An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

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.

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

Science.gov (United States)

Ebbesen, Thomas W

2016-11-15

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

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.

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.

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.

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.

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

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.

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

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

Science.gov (United States)

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

2015-01-01

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

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.

Molecular beam scattering from clean surfaces of alkali halides

International Nuclear Information System (INIS)

Meyers, J.A.

1975-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-04-17

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

Revolution in Field Science: Apollo Approach to Inaccessible Surface Exploration

Science.gov (United States)

Clark, P. E.

2010-07-01

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

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

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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.

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

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)

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.

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

Science.gov (United States)

Sakk, Eric

2007-08-01

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

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

NARCIS (Netherlands)

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

2004-01-01

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

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

Science.gov (United States)

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

2018-05-01

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

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).

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.

Hydration of excess electrons trapped in charge pockets on molecular surfaces

Science.gov (United States)

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

2007-01-01

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

Surface science of single-site heterogeneous olefin polymerization catalysts

OpenAIRE

Kim, Seong H.; Somorjai, Gabor A.

2006-01-01

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

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

Science.gov (United States)

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

2015-03-01

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

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.

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.

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

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

Science.gov (United States)

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

2014-09-12

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

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

Interlocking Molecular Gear Chains Built on Surfaces.

Science.gov (United States)

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

2018-05-17

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

Surface tension and contact angles: Molecular origins and associated microstructure

Science.gov (United States)

Davis, H. T.

1982-01-01

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

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

CERN Document Server

Yates, John T

2015-01-01

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

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

Science.gov (United States)

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

2018-05-10

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

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.

Interplay of adsorbate-adsorbate and adsorbate-substrate interactions in self-assembled molecular surface nanostructures

DEFF Research Database (Denmark)

Schnadt, Joachim; Xu, Wei; Vang, Ronnie Thorbjørn

2010-01-01

a large tolerance to monatomic surface steps on the Ag(110) surface. The observed behaviour is explained in terms of strong intermolecular hydrogen bonding and a strong surface-mediated directionality, assisted by a sufficient degree of molecular backbone flexibility. In contrast, the same kind of step......-edge crossing is not observed when the molecules are adsorbed on the isotropic Ag(111) or more reactive Cu(110) surfaces. On Ag(111), similar 1-D assemblies are formed to those on Ag(110), but they are oriented along the step edges. On Cu(110), the carboxylic groups of NDCA are deprotonated and form covalent...... bonds to the surface, a situation which is also achieved on Ag(110) by annealing to 200 degrees C. These results show that the formation of particular self-assembled molecular nanostructures depends significantly on a subtle balance between the adsorbate-adsorbate and adsorbate-substrate interactions...

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

International Nuclear Information System (INIS)

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

2008-01-01

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

Progress in molecular precursors for electronic materials

Energy Technology Data Exchange (ETDEWEB)

Buhro, W.E. [Washington Univ., St. Louis, MO (United States)

1996-09-01

Molecular-precursor chemistry provides an essential underpinning to all electronic-materials technologies, including photovoltaics and related areas of direct interest to the DOE. Materials synthesis and processing is a rapidly developing field in which advances in molecular precursors are playing a major role. This article surveys selected recent research examples that define the exciting current directions in molecular-precursor science. These directions include growth of increasingly complex structures and stoichiometries, surface-selective growth, kinetic growth of metastable materials, growth of size-controlled quantum dots and quantum-dot arrays, and growth at progressively lower temperatures. Continued progress in molecular-precursor chemistry will afford precise control over the crystal structures, nanostructures, and microstructures of electronic materials.

Beam line 4: A dedicated surface science facility at Daresbury Laboratory

International Nuclear Information System (INIS)

Dhanak, V.R.; Robinson, A.W.; van der Laan, G.; Thornton, G.

1992-01-01

We describe a beam line currently under construction at the Daresbury Laboratory which forms part of a surface science research facility for the Interdisciplinary Research Centre in Surface Science. The beam line has three branches, two of which are described here. The first branch covers the high-energy range 640 eV≤hν≤10 keV, being equipped with a double-crystal monochromator and a novel multicoated premirror system. The second branch line is optimized for the energy range 15≤hν≤250 eV, using cylindrical focusing mirrors, a spherical diffraction grating and an ellipsoidal refocusing mirror to achieve high resolution with a small spot size

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

Science.gov (United States)

Reilly, Charles; Ingber, Donald E

2017-12-26

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2006-02-01

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

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

Energy Technology Data Exchange (ETDEWEB)

Doughty, Benjamin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Goverapet Srinivasan, Sriram [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Indian Inst. of Technology (IIT), Rajasthan (India); Bryantsev, Vyacheslav S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Dongkyu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Ho Nyung [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ma, Ying-Zhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lutterman, Daniel A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-06-12

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments, and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO₂ catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO₂ (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.

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

Science.gov (United States)

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

2011-03-01

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

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.

Implementation of surface hopping molecular dynamics using semiempirical methods

International Nuclear Information System (INIS)

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

2008-01-01

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

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

NARCIS (Netherlands)

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

2008-01-01

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

Major Successes of Theory-and-Experiment-Combined Studies in Surface Chemistry and Heterogeneous Catalysis.

Energy Technology Data Exchange (ETDEWEB)

Somorjai, Gabor A.; Li, Yimin

2009-11-21

Experimental discoveries followed by theoretical interpretations that pave the way of further advances by experimentalists is a developing pattern in modern surface chemistry and catalysis. The revolution of modern surface science started with the development of surface-sensitive techniques such as LEED, XPS, AES, ISS and SIMS, in which the close collaboration between experimentalists and theorists led to the quantitative determination of surface structure and composition. The experimental discovery of the chemical activity of surface defects and the trends in the reactivity of transitional metals followed by the explanations from the theoretical studies led to the molecular level understanding of active sites in catalysis. The molecular level knowledge, in turn, provided a guide for experiments to search for new generation of catalysts. These and many other examples of successes in experiment-and-theory-combined studies demonstrate the importance of the collaboration between experimentalists and theorists in the development of modern surface science.

An ab initio molecular

Indian Academy of Sciences (India)

mechanisms of two molecular crystals: An ab initio molecular dynamics ... for Computation in Molecular and Materials Science and Department of Chemistry, School of ..... NSAF Foundation of National Natural Science Foun- ... Matter 14 2717.

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

Science.gov (United States)

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

2010-01-01

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

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

DEFF Research Database (Denmark)

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

2010-01-01

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

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.

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

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.

Atomic and molecular beams production and collimation

CERN Document Server

Lucas, Cyril Bernard

2013-01-01

Atomic and molecular beams are employed in physics and chemistry experiments and, to a lesser extent, in the biological sciences. These beams enable atoms to be studied under collision-free conditions and allow the study of their interaction with other atoms, charged particles, radiation, and surfaces. Atomic and Molecular Beams: Production and Collimation explores the latest techniques for producing a beam from any substance as well as from the dissociation of hydrogen, oxygen, nitrogen, and the halogens.The book not only provides the basic expressions essential to beam design but also offers

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

Science.gov (United States)

Adib, Kaveh

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1993-12-01

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

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.

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

DEFF Research Database (Denmark)

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

2014-01-01

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

Molecular environmental geochemistry

Science.gov (United States)

O'Day, Peggy A.

1999-05-01

mineral surfaces and mineral-water interfaces. A review of recent studies employing molecular characterizations of soils, sediments, and biological samples from contaminated sites exemplifies the utility and benefits, as well as the challenge, of applying molecular probes to complicated natural materials. New techniques, technological advances, and the crossover of methods from other disciplines such as biochemistry and materials science promise better examination of environmental chemical processes in real time and at higher resolution, and will further the integration of molecular information into field-scale chemical and hydrologic models.

Surface science station of the infrared beamline at SPring-8

International Nuclear Information System (INIS)

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

2001-01-01

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

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

Data.gov (United States)

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

Solvation of excess electrons trapped in charge pockets on molecular surfaces

Science.gov (United States)

Jalbout, Abraham F.

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

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...

Probing Interactions in Complex Molecular Systems through Ordered Assembly

International Nuclear Information System (INIS)

De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

2002-01-01

Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

Molecular identification of a malaria merozoite surface sheddase.

Directory of Open Access Journals (Sweden)

Philippa K Harris

2005-11-01

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

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.

Advances in atomic, molecular, and optical physics

CERN Document Server

Walther, Herbert; Walther, Herbert

1999-01-01

This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics.

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).

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

International Nuclear Information System (INIS)

Sugiura, Hideo; Yamaguchi, Masafumi; Shibukawa, Atsushi

1983-01-01

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

Molecular approach of uranyl/mineral surfaces: theoretical approach

International Nuclear Information System (INIS)

Roques, J.

2009-01-01

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

Molecular dynamics simulation of wetting behaviors of Li on W surfaces

Energy Technology Data Exchange (ETDEWEB)

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

2017-04-15

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

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

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.

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.

Life Sciences Implications of Lunar Surface Operations

Science.gov (United States)

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

2010-01-01

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

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

Science.gov (United States)

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

2017-09-01

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

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.

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.

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

International Nuclear Information System (INIS)

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

2008-01-01

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

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.

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

Science.gov (United States)

Sanderson, R D; Bernfield, M

1988-12-01

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

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

Science.gov (United States)

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

2014-12-01

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

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)...

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)

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

Science.gov (United States)

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

2017-12-01

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

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

NARCIS (Netherlands)

JUFFER, AH; BERENDSEN, HJC

1993-01-01

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

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

Science.gov (United States)

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

2015-10-20

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

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

International Nuclear Information System (INIS)

Huang Guoliang; Yang Xiaoyong; Ma Li; Yang Xu

2011-01-01

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

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

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.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. AYOUB KANAANI. Articles written in Journal of Chemical Sciences. Volume 128 Issue 8 August 2016 pp 1211-1221 Regular Article. Synthesis, molecular structure, spectroscopic investigations and computational study of a potential molecular switch of 2-([1 ...

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

Nano Trek Beyond: Driving Nanocars/Molecular Machines at Interfaces.

Science.gov (United States)

Ariga, Katsuhiko; Mori, Taizo; Nakanishi, Waka

2018-03-09

In 2016, the Nobel Prize in Chemistry was awarded for pioneering work on molecular machines. Half a year later, in Toulouse, the first molecular car race, a "nanocar race", was held by using the tip of a scanning tunneling microscope as an electrical remote control. In this Focus Review, we discuss the current state-of-the-art in research on molecular machines at interfaces. In the first section, we briefly explain the science behind the nanocar race, followed by a selection of recent examples of controlling molecules on surfaces. Finally, motion synchronization and the functions of molecular machines at liquid interfaces are discussed. This new concept of molecular tuning at interfaces is also introduced as a method for the continuous modification and optimization of molecular structure for target functions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interactive Multimodal Molecular Set – Designing Ludic Engaging Science Learning Content

DEFF Research Database (Denmark)

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

2014-01-01

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

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.

Molecular dynamics simulations of the calcite/solution interface as a means to explore surface modifications induced by nitrate

Energy Technology Data Exchange (ETDEWEB)

Hofmann, Sascha; Schmidt, Moritz [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Surface Processes; Spijker, P. [Aalto Univ., Helsinki (Finland). Dept. of Applied Physics; Voitchovsky, K. [Durham Univ. (United Kingdom). Physics Dept.

2016-07-01

The reactivity of calcite, one of the most abundant minerals in the earth's crust, is determined by the molecular details of its interface with the contacting solution. Recently, it has been found that trace concentrations of NaNO{sub 3} severely affect calcite's (104) surface and its reactivity. Molecular dynamics (MD) simulations reveal density profiles of different ions near calcite's surface, with NO{sub 3}{sup -} able to reach closer to the surface than CO{sub 3}{sup 2-} and in higher concentrations. Additionally, incorporation of NO{sub 3}{sup -} into the surface significantly disturbs the water structure at the interface.

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

Science.gov (United States)

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

2017-11-01

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

A parametric study of surface roughness and bonding mechanisms of aluminum alloys with epoxies: a molecular dynamics simulation

Science.gov (United States)

Timilsina, Rajendra; Termaath, Stephanie

The marine environment is highly aggressive towards most materials. However, aluminium-magnesium alloys (Al-Mg, specifically, 5xxx series) have exceptionally long service life in such aggressive marine environments. For instance, an Al-Mg alloy, AA5083, is extensively used in naval structures because of its good mechanical strength, formability, seawater corrosion resistance and weldability. However, bonding mechanisms of these alloys with epoxies in a rough surface environment are not fully understood yet. It requires a rigorous investigation at molecular or atomic levels. We performed a molecular dynamics simulation to study an adherend surface preparation and surface bonding mechanisms of Al-Mg alloy (AA5083) with different epoxies by developing several computer models. Various distributions of surface roughness are introduced in the models and performed molecular dynamics simulations. Formation of a beta phase (Al3Mg2) , microstructures, bonding energies at the interface, bonding strengths and durability are investigated. Office of Naval Research.

A proposal to establish an international network in molecular microbiology and genetic engineering for scientific cooperation and prevention of misuse of biological sciences in the framework of science for peace

International Nuclear Information System (INIS)

Becker, Y.

1998-01-01

The conference on 'Science and Technology for Construction of Peace' which was organized by the Landau Network Coordination Center and A. Volta Center for Scientific Culture dealt with conversion of military and technological capacities into sustainable civilian application. The ideas regarding the conversion of nuclear warheads into nuclear energy for civilian-use led to the idea that the extension of this trend of thought to molecular biology and genetic engineering, will be a useful contribution to Science for Peace. This idea of developing a Cooperation Network in Molecular Biology and Genetic Engineering that will function parallel to and with the Landau Network Coordination in the 'A. Volta' Center was discussed in the Second International Symposium on Science for Peace, Jerusalem, January 1997. It is the reason for the inclusion of the biological aspects in the deliberations of our Forum. It is hoped that the establishment of an international network in molecular biology and genetic engineering, similar to the Landau Network in physics, will support and achieve the decommissioning of biological weapons. Such a network in microbiology and genetic engineering will contribute to the elimination of biological weapons and to contributions to Science for Peace and to Culture of Peace activities of UNESCO. (author)

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.

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

Science.gov (United States)

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

2006-07-01

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

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

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.

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...

Surface chemistry and growth mechanisms studies of homo epitaxial (1 0 0) GaAs by laser molecular beam epitaxy

International Nuclear Information System (INIS)

Yan Dawei; Wu Weidong; Zhang Hong; Wang Xuemin; Zhang Hongliang; Zhang Weibin; Xiong Zhengwei; Wang Yuying; Shen Changle; Peng Liping; Han Shangjun; Zhou Minjie

2011-01-01

In this paper, GaAs thin film has been deposited on thermally desorbed (1 0 0) GaAs substrate using laser molecular beam epitaxy. Scanning electron microscopy, in situ reflection high energy electron diffraction and in situ X-ray photoelectron spectroscopy are applied for evaluation of the surface morphology and chemistry during growth process. The results show that a high density of pits is formed on the surface of GaAs substrate after thermal treatment and the epitaxial thin film heals itself by a step flow growth, resulting in a smoother surface morphology. Moreover, it is found that the incorporation of As species into GaAs epilayer is more efficient in laser molecular beam epitaxy than conventional molecular beam epitaxy. We suggest the growth process is impacted by surface chemistry and morphology of GaAs substrate after thermal treatment and the growth mechanisms are discussed in details.

Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

Energy Technology Data Exchange (ETDEWEB)

Ylikantola, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Linnanto, J., E-mail: juha.m.linnanto@gmail.com [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); University of Tartu, Institute of Physics, Riia 142, EE-51014 Tartu (Estonia); Knuutinen, J.; Oravilahti, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Toivakka, M. [Åbo Akademi University, Laboratory of Paper Coating and Converting and Center for Functional Materials, FI-20500 Turku/Åbo (Finland)

2013-07-01

The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree–Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree–Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree–Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

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

Science.gov (United States)

Taylor, Amy; Jones, Gail

2009-01-01

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

Surface science models of CoMoS hydrodesulfurisation catalysts

Energy Technology Data Exchange (ETDEWEB)

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

1997-07-01

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

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.

Functionalized Surface Geometries Induce: “Bone: Formation by Autoinduction”

Directory of Open Access Journals (Sweden)

Ugo Ripamonti

2018-02-01

Full Text Available The induction of tissue formation, and the allied disciplines of tissue engineering and regenerative medicine, have flooded the twenty-first century tissue biology scenario and morphed into high expectations of a fulfilling regenerative dream of molecularly generated tissues and organs in assembling human tissue factories. The grand conceptualization of deploying soluble molecular signals, first defined by Turing as forms generating substances, or morphogens, stemmed from classic last century studies that hypothesized the presence of morphogens in several mineralized and non-mineralized mammalian matrices. The realization of morphogens within mammalian matrices devised dissociative extractions and chromatographic procedures to isolate, purify, and finally reconstitute the cloned morphogens, found to be members of the transforming growth factor-β (TGF-β supergene family, with insoluble signals or substrata to induce de novo tissue induction and morphogenesis. Can we however construct macroporous bioreactors per se capable of inducing bone formation even without the exogenous applications of the osteogenic soluble molecular signals of the TGF-β supergene family? This review describes original research on coral-derived calcium phosphate-based macroporous constructs showing that the formation of bone is independent of the exogenous application of the osteogenic soluble signals of the TGF-β supergene family. Such signals are the molecular bases of the induction of bone formation. The aim of this review is to primarily describe today's hottest topic of biomaterials' science, i.e., to construct and define osteogenetic biomaterials' surfaces that per se, in its own right, do initiate the induction of bone formation. Biomaterials are often used to reconstruct osseous defects particularly in the craniofacial skeleton. Edentulism did spring titanium implants as tooth replacement strategies. No were else that titanium surfaces require functionalized

Bulletin of Materials Science | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Bulletin of Materials Science. B P Singh. Articles written in Bulletin of Materials Science. Volume 23 Issue 1 February 2000 pp 11-16 Molecular Magnets. Synthesis and magnetic properties of one-dimensional metal oxalate networks as molecular-based magnets · B P Singh B Singh · More Details Abstract ...

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

Science.gov (United States)

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

2010-11-01

Established methods for cleaning and sterilising biomedical devices may achieve removal of bioburden only at the macroscopic level while leaving behind molecular levels of contamination (mainly proteinaceous). This is of particular concern if the residue might contain prions. We investigated at the molecular level the removal of model and real-life proteinaceous contamination from model and practical surfaces by air plasma (ionised air) treatment. The surface-sensitive technique of X-ray photoelectron spectroscopy (XPS) was used to assess the removal of proteinaceous contamination, with the nitrogen (N1s) photoelectron signal as its marker. Model proteinaceous contamination (bovine serum albumin) adsorbed on to a model surface (silicon wafer) and the residual proteinaceous contamination resulting from incubating surgical stainless steel (a practical biomaterial) in whole human blood exhibited strong N1s signals [16.8 and 18.5 atomic percent (at.%), respectively] after thorough washing. After 5min air plasma treatment, XPS detected no nitrogen on the sample surfaces, indicating complete removal of proteinaceous contamination, down to the estimated XPS detection limit 10ng/cm(2). Applying the same plasma treatment, the 7.7at.% nitrogen observed on a clinically cleaned dental bur was reduced to a level reflective of new, as-received burs. Contact angle measurements and atomic force microscopy also indicated complete molecular-level removal of the proteinaceous contamination upon air plasma treatment. This study demonstrates the effectiveness of air plasma treatment for removing proteinaceous contamination from both model and practical surfaces and offers a method for ensuring that no molecular residual contamination such as prions is transferred upon re-use of surgical and dental instruments. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

Selective Dispersive Solid Phase Extraction of Ser-traline Using Surface Molecularly Imprinted Polymer Grafted on SiO2/Graphene Oxide

Directory of Open Access Journals (Sweden)

Faezeh Khalilian

2017-01-01

Full Text Available A surface molecularly imprinted dispersive solid phase extraction coupled with liquid chromatography–ultraviolet detection is proposed as a selective and fast clean-up technique for the determination of sertraline in biological sample. Surface sertraline-molecular imprinted polymer was grafted and synthesized on the SiO2/graphene oxide surface. Firstly SiO2 was coated on synthesized graphene oxide sheet using sol-gel technique. Prior to polymerization, the vinyl group was incorporated on to the surface of SiO2/graphene oxide to direct selective polymerization on the surface. Methacrylic acid, ethylene glycol dimethacrylate and ethanol were used as monomer, cross-linker and progen, respectively. Non-imprinted polymer was also prepared for comparing purposes. The properties of the molecular imprinted polymer were characterized using field emission-scanning electron microscopy and Fourier transform infrared spectroscopy methods. The surface molecular imprinted polymer was utilized as an adsorbent of dispersive solid phase extraction for separation and preconcentration of sertraline. The effects of the different parameters influencing the extraction efficiency, such as sample pH were investigated and optimized. The specificity of the molecular imprinted polymer over the non-imprinted polymer was examined in absence and presence of competitive drugs. Sertraline calibration curve showed linearity in the ranges 1–500 µg L-1. The limits of detection and quantification under optimized conditions were obtained 0.2 and 0.5 µg L-1. The within-day and between-day relative standard deviations (n=3 were 4.3 and 7.1%, respectively. Furthermore, the relative recoveries for spiked biological samples were above 92%.

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

Science.gov (United States)

Gillams, Richard J; Jia, Tony Z

2018-05-08

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

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

Directory of Open Access Journals (Sweden)

Richard J. Gillams

2018-05-01

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

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

International Nuclear Information System (INIS)

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

1990-01-01

Resonantly enhanced multiphoton ionization (REMPI) laser spectroscopic and molecular beam-surface scattering techniques are coupled to study inelastic and reactive gas-surface scattering with state-to-state specificity. Rotational, vibrational, translational and angular distributions have been measured for the inelastic scattering of HCI and N 2 from Au(111). In both cases the scattering is direct-inelastic in nature and exhibits interesting dynamical features such as rotational rainbow scattering. In an effort to elucidate the dynamics of chemical reactions occurring on surfaces we have extended our quantum-resolved scattering studies to include the reactive scattering of a beam of gas phase H-atoms from a chlorinated metal surface M-CI. The nascent rotational and vibrational distributions of the HCI product are determined using REMPI. The thermochemistry for this reaction on Au indicates that the product formation proceeding through chemisorbed H-atoms is slightly endothermic while direct reaction of a has phase H-atom with M-CI is highly exothermic (ca. 50 kcal/mole). Details of the experimental techniques, results and implications regarding the scattering dynamics are discussed. 55 ref., 8 fig

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.

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.

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.

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

DEFF Research Database (Denmark)

Bohr, Adam; Wang, Yingya; Harmankaya, Necati

2017-01-01

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

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

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

International Nuclear Information System (INIS)

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

2004-01-01

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

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

Directory of Open Access Journals (Sweden)

Tao Ma

2017-03-01

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

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...

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.

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

NARCIS (Netherlands)

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

2003-01-01

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

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

Science.gov (United States)

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

2011-03-21

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

Isolate extended state in the DNA molecular transistor with surface interaction

Energy Technology Data Exchange (ETDEWEB)

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

2016-02-01

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

Switchable host-guest systems on surfaces.

Science.gov (United States)

Yang, Ying-Wei; Sun, Yu-Long; Song, Nan

2014-07-15

CONSPECTUS: For device miniaturization, nanotechnology follows either the "top-down" approach scaling down existing larger-scale devices or the "bottom-up' approach assembling the smallest possible building blocks to functional nanoscale entities. For synthetic nanodevices, self-assembly on surfaces is a superb method to achieve useful functions and enable their interactions with the surrounding world. Consequently, adaptability and responsiveness to external stimuli are other prerequisites for their successful operation. Mechanically interlocked molecules such as rotaxanes and catenanes, and their precursors, that is, molecular switches and supramolecular switches including pseudorotaxanes, are molecular machines or prototypes of machines capable of mechanical motion induced by chemical signals, biological inputs, light or redox processes as the external stimuli. Switching of these functional host-guest systems on surfaces becomes a fundamental requirement for artificial molecular machines to work, mimicking the molecular machines in nature, such as proteins and their assemblies operating at dynamic interfaces such as the surfaces of cell membranes. Current research endeavors in material science and technology are focused on developing either a new class of materials or materials with novel/multiple functionalities by shifting host-guest chemistry from solution phase to surfaces. In this Account, we present our most recent attempts of building monolayers of rotaxanes/pseudorotaxanes on surfaces, providing stimuli-induced macroscopic effects and further understanding on the switchable host-guest systems at interfaces. Biocompatible versions of molecular machines based on synthetic macrocycles, such as cucurbiturils, pillararenes, calixarenes, and cyclodextrins, have been employed to form self-assembled monolayers of gates on the surfaces of mesoporous silica nanoparticles to regulate the controlled release of cargo/drug molecules under a range of external stimuli

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

DEFF Research Database (Denmark)

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

2004-01-01

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

Assessment of environments for Mars Science Laboratory entry, descent, and surface operations

Science.gov (United States)

Vasavada, Ashwin R.; Chen, Allen; Barnes, Jeffrey R.; Burkhart, P. Daniel; Cantor, Bruce A.; Dwyer-Cianciolo, Alicia M.; Fergason, Robini L.; Hinson, David P.; Justh, Hilary L.; Kass, David M.; Lewis, Stephen R.; Mischna, Michael A.; Murphy, James R.; Rafkin, Scot C.R.; Tyler, Daniel; Withers, Paul G.

2012-01-01

The Mars Science Laboratory mission aims to land a car-sized rover on Mars' surface and operate it for at least one Mars year in order to assess whether its field area was ever capable of supporting microbial life. Here we describe the approach used to identify, characterize, and assess environmental risks to the landing and rover surface operations. Novel entry, descent, and landing approaches will be used to accurately deliver the 900-kg rover, including the ability to sense and "fly out" deviations from a best-estimate atmospheric state. A joint engineering and science team developed methods to estimate the range of potential atmospheric states at the time of arrival and to quantitatively assess the spacecraft's performance and risk given its particular sensitivities to atmospheric conditions. Numerical models are used to calculate the atmospheric parameters, with observations used to define model cases, tune model parameters, and validate results. This joint program has resulted in a spacecraft capable of accessing, with minimal risk, the four finalist sites chosen for their scientific merit. The capability to operate the landed rover over the latitude range of candidate landing sites, and for all seasons, was verified against an analysis of surface environmental conditions described here. These results, from orbital and model data sets, also drive engineering simulations of the rover's thermal state that are used to plan surface operations.

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

Science.gov (United States)

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

2017-05-01

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

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

Science.gov (United States)

Ito, Juri; Kajikawa, Kotaro

2016-02-01

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

A tight-binding model of the transmission probability through a molecular junction; a single molecule vs. a molecular layer

International Nuclear Information System (INIS)

Landau, A.; Nitzan, A.

2006-01-01

Full Text: Molecular electronics, one of the major fields of the current effort in nano-science, may be de ed as the study of electronic behaviors, devices and applications that depend on the properties of matter at the molecular scale. If the miniaturization trend of microelectronic devices is to continue, elements such as transistors and contacts will soon shrink to single molecules. The promise of these new technological breakthroughs has been major driving force in this ld. Moreover, the consideration of molecular systems as electronic devices has raised new fundamental questions. In particular, while traditional quantum chemistry deals with electronically closed systems, we now face problems involving molecular systems that are open to their electronic environment, moreover, function in far from equilibrium situations. A generic molecular junction is made of two electrodes connected by a molecular spacer that takes the form of a molecular chain of varying length or a molecular layer of varying thickness. We use a simple nearest-neighbors tight-biding model with the non-equilibrium Green's function (NEGF) method to investigate and compare between a self-assembled monolayer (SAM), finite molecular layer (FML), and single molecule (SM) chemisorption to a surface of a metal substrate. In addition, we examine the difference in the transmission probability through a SAM, FML and SM sandwiched between two metallic electrodes. Dramatic differences are observed between the SM, FML and SAM density of electronic states and transmission functions. In addition, we analyze the effects of changing different physical parameters such as molecule-substrate interaction, molecule-molecule interactions, etc; interesting effects that pertain to the conduction properties of single molecules and molecular layers are observed. Intriguing results are attained when we investigate the commensurability of the SAM with the metallic surface

Molecular adsorption of alkanes on platinum surfaces: A predictive theoretical model

International Nuclear Information System (INIS)

Stinnett, J.A.; Madix, R.J.

1996-01-01

The adsorption probabilities of methane and propane on Pt(111), and propane on Pt(110)-(1x2) have been successfully predicted for a wide range of incident energies and angles with classical stochastic trajectory simulations, using a pairwise additive Morse methyl endash platinum potential previously developed from the measured trapping probabilities of ethane on Pt(111). These predictions, along with those for ethane adsorption on Pt(110)endash(1x2), comprise a unified model for the molecular adsorption of alkanes on platinum surfaces. The simulations show the initial trapping probabilities of methane and propane on Pt(111) are determined to within approximately 10% by the fate of the first bounce. They also indicate that at normal incidence on Pt(111) energy conversions from perpendicular translational motion to both cartwheeling rotation and lattice phonons play increasingly important roles in increasing the trapping probability as the alkane increases in size and molecular weight. For methane itself excitation of parallel translational momentum after the first bounce serves as the most effective energy storage mechanism which facilitates trapping, whereas for propane cartwheel rotational motion plays the dominant role. Excessive excitation of these modes of motion, however, can cause scattering on subsequent bounces by reconversion of the energy into perpendicular translational energy. Collisions of methane with the hollow and bridge sites on the Pt(111) surface appear less effective in trapping than do atop sites. The simulations also suggest excitation of the C endash C endash C bending mode of propane has little effect on the trapping of propane on platinum surfaces for beam energies below 55 kJ/mol. copyright 1996 American Institute of Physics

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.

Sensor for the working surface cleanliness definition in vacuum

Science.gov (United States)

Deulin, E. A.; Mashurov, S. S.; Gatsenko, A. A.

2016-07-01

Modern development of nanotechnology as one of the modern science priority directions is impossible to imagine without the use of vacuum systems and technologies. And the better the vacuum (lower the pressure), the “cleaner” we get a surface, which is very important for nanotechnology. Determination of the cleanliness of the surface or the amount of molecular layers of adsorbed gases on the working surface of the products especially in industry, where the cleanliness of the working surface is a key parameter of the technological process and has a significant influence on the output parameters of the final product is the main goal of this work.

Sensor for the working surface cleanliness definition in vacuum

International Nuclear Information System (INIS)

Deulin, E A; Mashurov, S S; Gatsenko, A A

2016-01-01

Modern development of nanotechnology as one of the modern science priority directions is impossible to imagine without the use of vacuum systems and technologies. And the better the vacuum (lower the pressure), the “cleaner” we get a surface, which is very important for nanotechnology. Determination of the cleanliness of the surface or the amount of molecular layers of adsorbed gases on the working surface of the products especially in industry, where the cleanliness of the working surface is a key parameter of the technological process and has a significant influence on the output parameters of the final product is the main goal of this work. (paper)

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.

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

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

Science.gov (United States)

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

2012-12-03

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

Quantum state-resolved gas/surface reaction dynamics probed by reflection absorption infrared spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Chen Li [Department of Dynamics at Surfaces, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen (Germany); Ueta, Hirokazu; Beck, Rainer D. [Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Federale de Lausanne (Switzerland); Bisson, Regis [Aix-Marseille Universite, PIIM, CNRS, UMR 7345, 13397 Marseille (France)

2013-05-15

We report the design and characterization of a new molecular-beam/surface-science apparatus for quantum state-resolved studies of gas/surface reaction dynamics combining optical state-specific reactant preparation in a molecular beam by rapid adiabatic passage with detection of surface-bound reaction products by reflection absorption infrared spectroscopy (RAIRS). RAIRS is a non-invasive infrared spectroscopic detection technique that enables online monitoring of the buildup of reaction products on the target surface during reactant deposition by a molecular beam. The product uptake rate obtained by calibrated RAIRS detection yields the coverage dependent state-resolved reaction probability S({theta}). Furthermore, the infrared absorption spectra of the adsorbed products obtained by the RAIRS technique provide structural information, which help to identify nascent reaction products, investigate reaction pathways, and determine branching ratios for different pathways of a chemisorption reaction. Measurements of the dissociative chemisorption of methane on Pt(111) with this new apparatus are presented to illustrate the utility of RAIRS detection for highly detailed studies of chemical reactions at the gas/surface interface.

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.)

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

Science.gov (United States)

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

2013-01-01

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

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

Chemical bonding of water to metal surfaces studied with core-level spectroscopies

DEFF Research Database (Denmark)

Schiros, T.; Andersson, Klas Jerker; Pettersson, L.G.M.

2010-01-01

The nature of the contact layer of water on surfaces is of relevance for many practical fields, including corrosion, electrochemistry, environmental science and heterogeneous catalysis. Here we focus on the geometric and electronic structure of the water contact layer on transition metal surfaces......-specific information on the partial local density of states, local atomic structure, geometrical parameters and molecular orientation, allowing general principles for water-metal interaction to be derived....

Proceedings of the fifth Asian conference on colloid and interface science

International Nuclear Information System (INIS)

2013-01-01

Colloid and Interfacial (Surface) phenomena constitute a field of science which today embodies concepts that are fundamental to the understanding of both microscopic and macroscopic behaviors, and hence the design of a wide range of system of great potential interest. Now a days, this branch of science has entered a new era where modern development and knowledge of physics, chemistry, biology, material science, pharmacy, engineering, etc., have been extensively exploited and adopted. As a result, both fundamental and applied aspects of colloid and surface science have advanced over the years, for example, starting from tertiary oil recovery to nanotechnology to environmental science. These multifaceted fields also find applications in everyday life, and helps in understanding the intricacies of the life process. All these developments have enriched the field, which is considered to be the front-line/emerging area of research in the national and international scenario. Recent growth of modern colloid and interface science in Asian countries has encouraged the scientists to share in-depth discussions within the regional scientific community in Asia. Scientific topics covered by the conference were: Adsorption, Molecular Assemblies, Colloids and Dispersions, Gels, Surfaces and Interfaces, Thin Films, Membranes, Nanomaterials, Biomaterials, Devices and Applications etc. Papers relevant to INIS are indexed separately

SFG analysis of the molecular structures at the surfaces and buried interfaces of PECVD ultralow-dielectric constant pSiCOH

Science.gov (United States)

Zhang, Xiaoxian; Myers, John N.; Huang, Huai; Shobha, Hosadurga; Chen, Zhan; Grill, Alfred

2016-02-01

PECVD deposited porous SiCOH with ultralow dielectric constant has been successfully integrated as the insulator in advanced interconnects to decrease the RC delay. The effects of NH3 plasma treatment and the effectiveness of the dielectric repair on molecular structures at the surface and buried interface of a pSiCOH film deposited on top of a SiCNH film on a Si wafer were fully characterized using sum frequency generation vibrational spectroscopy (SFG), supplemented by X-ray photoelectron spectroscopy. After exposure to NH3 plasma for 18 s, about 40% of the methyl groups were removed from the pSiCOH surface, and the average orientation of surface methyl groups tilted more towards the surface. The repair method used here effectively repaired the molecular structures at the pSiCOH surface but did not totally recover the entire plasma-damaged layer. Additionally, simulated SFG spectra with various average orientations of methyl groups at the SiCNH/pSiCOH buried interface were compared with the experimental SFG spectra collected using three different laser input angles to determine the molecular structural information at the SiCNH/pSiCOH buried interface after NH3 plasma treatment and repair. The molecular structures including the coverage and the average orientation of methyl groups at the buried interface were found to be unchanged by NH3 plasma treatment and repair.

ISIS muons for materials and molecular science studies

International Nuclear Information System (INIS)

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

2013-01-01

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

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

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

Surface science studies of ethene containing model interstellar ices

Science.gov (United States)

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

2011-05-01

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

Enhancing the magnetic anisotropy of maghemite nanoparticles via the surface coordination of molecular complexes

Science.gov (United States)

Prado, Yoann; Daffé, Niéli; Michel, Aude; Georgelin, Thomas; Yaacoub, Nader; Grenèche, Jean-Marc; Choueikani, Fadi; Otero, Edwige; Ohresser, Philippe; Arrio, Marie-Anne; Cartier-dit-Moulin, Christophe; Sainctavit, Philippe; Fleury, Benoit; Dupuis, Vincent; Lisnard, Laurent; Fresnais, Jérôme

2015-01-01

Superparamagnetic nanoparticles are promising objects for data storage or medical applications. In the smallest—and more attractive—systems, the properties are governed by the magnetic anisotropy. Here we report a molecule-based synthetic strategy to enhance this anisotropy in sub-10-nm nanoparticles. It consists of the fabrication of composite materials where anisotropic molecular complexes are coordinated to the surface of the nanoparticles. Reacting 5 nm γ-Fe2O3 nanoparticles with the [CoII(TPMA)Cl2] complex (TPMA: tris(2-pyridylmethyl)amine) leads to the desired composite materials and the characterization of the functionalized nanoparticles evidences the successful coordination—without nanoparticle aggregation and without complex dissociation—of the molecular complexes to the nanoparticles surface. Magnetic measurements indicate the significant enhancement of the anisotropy in the final objects. Indeed, the functionalized nanoparticles show a threefold increase of the blocking temperature and a coercive field increased by one order of magnitude. PMID:26634987

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

Energy Technology Data Exchange (ETDEWEB)

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

2009-08-26

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

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

International Nuclear Information System (INIS)

Evangelakis, G.A.; Pontikis, V.

2009-01-01

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

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.

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

Acidic deposition: State of science and technology. Report 15. Liming acidic surface waters. Final report

International Nuclear Information System (INIS)

Olem, H.; Thornelof, E.; Sandoy, S.; Schreiber, R.K.

1990-09-01

The document describes the science and technology of aquatic liming--a method for improving the water quality of acidic surface waters to restore or enhance fisheries. The report is a comprehensive compilation of years of research in North America and Europe by dozens of scientists. Several mitigation technologies--including those that have only been proposed--are critically evaluated along with the effects of liming on water chemistry and aquatic biota. Through these evaluations, the state of the science and technology of aquatic liming is identified for the reader. Whole-lake liming is now recognized as a valuable management tool for acidic surface waters and their fisheries. However, some liming technologies are considered experimental and will need further evaluation. Distinctions between technologies are included--as is the distinction between liming acidic surface waters and reducing acidifying emissions

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

... Physics · Proceedings – Mathematical Sciences · Resonance – Journal of Science ... Home; Journals; Journal of Chemical Sciences; Special Issues ... 2nd International Symposium on Materials Chemistry (ISMC-2008) ... New Directions of Research in Molecules and Materials ... Theoretical Models for Molecular Structure.

EDITORIAL: Molecular Imaging Technology

Science.gov (United States)

Asai, Keisuke; Okamoto, Koji

2006-06-01

'Molecular Imaging Technology' focuses on image-based techniques using nanoscale molecules as sensor probes to measure spatial variations of various species (molecular oxygen, singlet oxygen, carbon dioxide, nitric monoxide, etc) and physical properties (pressure, temperature, skin friction, velocity, mechanical stress, etc). This special feature, starting on page 1237, contains selected papers from The International Workshop on Molecular Imaging for Interdisciplinary Research, sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan, which was held at the Sendai Mediatheque, Sendai, Japan, on 8 9 November 2004. The workshop was held as a sequel to the MOSAIC International Workshop that was held in Tokyo in 2003, to summarize the outcome of the 'MOSAIC Project', a five-year interdisciplinary project supported by Techno-Infrastructure Program, the Special Coordination Fund for Promotion of Science Technology to develop molecular sensor technology for aero-thermodynamic research. The workshop focused on molecular imaging technology and its applications to interdisciplinary research areas. More than 110 people attended this workshop from various research fields such as aerospace engineering, automotive engineering, radiotechnology, fluid dynamics, bio-science/engineering and medical engineering. The purpose of this workshop is to stimulate intermixing of these interdisciplinary fields for further development of molecular sensor and imaging technology. It is our pleasure to publish the seven papers selected from our workshop as a special feature in Measurement and Science Technology. We will be happy if this issue inspires people to explore the future direction of molecular imaging technology for interdisciplinary research.

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

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.

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.

The inhibition of methane hydrate formation by water alignment underneath surface adsorption of surfactants

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Ngoc N.; Nguyen, Anh V.; Dang, Liem X.

2017-06-01

Sodium dodecyl sulfate (SDS) has been widely shown to strongly promote the formation of methane hydrate. Here we show that SDS displays an extraordinary inhibition effect on methane hydrate formation when the surfactant is used in sub-millimolar concentration (around 0.3 mM). We have also employed Sum Frequency Generation vibrational spectroscopy (SFG) and molecular dynamics simulation (MDS) to elucidate the molecular mechanism of this inhibition. The SFG and MDS results revealed a strong alignment of water molecules underneath surface adsorption of SDS in its sub-millimolar solution. Interestingly, both the alignment of water and the inhibition effect (in 0.3 mM SDS solution) went vanishing when an oppositely-charged surfactant (tetra-n-butylammonium bromide, TBAB) was suitably added to produce a mixed solution of 0.3 mM SDS and 3.6 mM TBAB. Combining structural and kinetic results, we pointed out that the alignment of water underneath surface adsorption of dodecyl sulfate (DS-) anions gave rise to the unexpected inhibition of methane hydration formation in sub-millimolar solution of SDS. The adoption of TBAB mitigated the SDS-induced electrostatic field at the solution’s surface and, therefore, weakened the alignment of interfacial water which, in turn, erased the inhibition effect. We discussed this finding using the concept of activation energy of the interfacial formation of gas hydrate. The main finding of this work is to reveal the interplay of interfacial water in governing gas hydrate formation which sheds light on a universal molecular-scale understanding of the influence of surfactants on gas hydrate formation. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-01-29

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

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.

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.

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

DEFF Research Database (Denmark)

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

2010-01-01

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

Structure and dynamics at the liquid surface of benzyl alcohol

International Nuclear Information System (INIS)

Dietter, J.; Morgner, H.

1999-01-01

A molecular dynamics simulation of a liquid layer of benzyl alcohol has been performed in order to compare the results with those obtained in experimental studies of our group. The main result of the experimental work was a strong orientational ordering of the benzyl alcohol molecules in the surface as well as an exceptionally large surface potential of ca. 0.6 V. According to the experiments the surface molecules orientate in such a way that the benzene ring points toward the vapor phase while the CH 2 group and the OH group are directed towards the bulk of the liquid. The simulation confirms this orientation of the surface molecules. The surface potential resulting from the simulation is 350 mV. The simulation reveals that the rather large surface potential can be understood as a consequence of the mean orientation of the molecular dipole moment in the surface region. The mean orientation of the molecules themselves in the surface is due to the tendency of the system to maintain the hydrogen bonding structure of the bulk in the surface region as well. The preferential orientation of the surface molecules causes a change of the dynamics of the individual components of the molecules when switching from bulk to surface which depends on the separation of these components from the polar group. This becomes most obvious in case of the reorientation dynamics of the molecular axes, e.g. the reorientation of the benzene ring is faster than the reorientation of the OH group. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

... XIONG1 WEIHUA ZHU1 HEMING XIAO1. Institute for Computation in Molecular and Materials Science and Department of Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; School of Materials Science and Engineering, Nanjing Institute of Technology, ...

A study on EUV reticle surface molecular contamination under different storage conditions in a HVM foundry fab

Science.gov (United States)

Singh, SherJang; Yatzor, Brett; Taylor, Ron; Wood, Obert; Mangat, Pawitter

2017-03-01

The prospect of EUVL (Extreme Ultraviolet Lithography) insertion into HVM (High Volume Manufacturing) has never been this promising. As technology is prepared for "lab to fab" transition, it becomes important to comprehend challenges associated with integrating EUVL infrastructure within existing high volume chip fabrication processes in a foundry fab. The existing 193nm optical lithography process flow for reticle handling and storage in a fab atmosphere is well established and in-fab reticle contamination concerns are mitigated with the reticle pellicle. However EUVL reticle pellicle is still under development and if available, may only provide protection against particles but not molecular contamination. HVM fab atmosphere is known to be contaminated with trace amounts of AMC's (Atmospheric Molecular Contamination). If such contaminants are organic in nature and get absorbed on the reticle surface, EUV photon cause photo-dissociation resulting into carbon generation which is known to reduce multilayer reflectivity and also degrades exposure uniformity. Chemical diffusion and aggregation of other ions is also reported under the e-beam exposure of a EUV reticle which is known to cause haze issues in optical lithography. Therefore it becomes paramount to mitigate absorbed molecular contaminant concerns on EUVL reticle surface. In this paper, we have studied types of molecular contaminants that are absorbed on an EUVL reticle surface under HVM fab storage and handling conditions. Effect of storage conditions (gas purged vs atmospheric) in different storage pods (Dual pods, Reticle Clamshells) is evaluated. Absorption analysis is done both on ruthenium capping layer as well as TaBN absorber. Ru surface chemistry change as a result of storage is also studied. The efficacy of different reticle cleaning processes to remove absorbed contaminant is evaluated as well.

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

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Author Affiliations. Santanu Bhattacharya1 Raghavan Varadarajan2. Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012; Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 ...

Advances in atomic, molecular, and optical physics

CERN Document Server

Walther, Herbert; Walther, Herbert

2001-01-01

This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

Advances in atomic, molecular, and optical physics

CERN Document Server

Walther, Herbert; Walther, Herbert

2000-01-01

This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

Advances in atomic, molecular, and optical physics

CERN Document Server

Walther, Herbert; Walther, Herbert

2002-01-01

This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered include related applied areas, such as atmospheric science, astrophysics, surface physics and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

Opportunities and limitations related to the application of plant-derived lipid molecular proxies in soil science

Directory of Open Access Journals (Sweden)

B. Jansen

2017-11-01

Full Text Available The application of lipids in soils as molecular proxies, also often referred to as biomarkers, has dramatically increased in the last decades. Applications range from inferring changes in past vegetation composition, climate, and/or human presence to unraveling the input and turnover of soil organic matter (SOM. The molecules used are extractable and non-extractable lipids, including ester-bound lipids. In addition, the carbon or hydrogen isotopic composition of such molecules is used. While holding great promise, the application of soil lipids as molecular proxies comes with several constraining factors, the most important of which are (i variability in the molecular composition of plant-derived organic matter both internally and between individual plants, (ii variability in (the relative contribution of input pathways into the soil, and (iii the transformation and/or (selective degradation of (some of the molecules once present in the soil. Unfortunately, the information about such constraining factors and their impact on the applicability of molecular proxies is fragmented and scattered. The purpose of this study is to provide a critical review of the current state of knowledge with respect to the applicability of molecular proxies in soil science, specifically focusing on the factors constraining such applicability. Variability in genetic, ontogenetic, and environmental factors influences plant n-alkane patterns in such a way that no unique compounds or specific molecular proxies pointing to, for example, plant community differences or environmental influences, exist. Other components, such as n-alcohols, n-fatty acids, and cutin- and suberin-derived monomers, have received far less attention in this respect. Furthermore, there is a high diversity of input pathways offering both opportunities and limitations for the use of molecular proxies at the same time. New modeling approaches might offer a possibility to unravel such mixed input

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.

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.

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

Molecular Modeling

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-05-01

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

Surface properties of poly(acrylonitrile) (PAN) precipitation polymerized in supercritical CO2 and the influence of the molecular weight.

Science.gov (United States)

Shen, Qing; Gu, Qing-Feng; Hu, Jian-Feng; Teng, Xin-Rong; Zhu, Yun-Feng

2003-11-15

In this paper, the surface properties, e.g., the total surface free energy and the related Lifshitz-van der Waals and Lewis acid-base components, of polyacrylonitrile (PAN) precipitation polymerized in supercritical CO(2) have been characterized. Moreover, the influence of molecular weight varying has been also investigated. Results show that the surface properties of PAN resulting from supercritical CO(2) are different from those obtained by the conventional method. Of these data, one important finding is that the supercritical CO(2) PAN seems to decrease the surface free energy with the increased molecular weight. Based on previous recorded NMR spectra of this PAN and especially compared to commercial PAN, such phenomena are discussed and ascribed to an increase of the H-bonds and a reduction of the isotacticity in the supercritical CO(2) condition for PAN.

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.

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.

Energy harvesting through gas dynamics in the free molecular flow regime between structured surfaces at different temperatures

DEFF Research Database (Denmark)

Baier, Tobias; Dölger, Julia; Hardt, Steffen

2014-01-01

For a gas confined between surfaces held at different temperatures the velocity distribution shows a significant deviation from the Maxwell distribution when the mean free path of the molecules is comparable to or larger than the channel dimensions. If one of the surfaces is suitably structured...... from the thermal creep flow that has gained more attention so far. This situation is studied in the limit of free-molecular flow for the case that an unstructured surface is allowed to move tangentially with respect to a structured surface. Parameter studies are conducted, and configurations...

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

International Nuclear Information System (INIS)

Soberon, Felipe

2014-01-01

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

Digitotalar dysmorphism: Molecular elucidation

African Journals Online (AJOL)

obtained for molecular studies. Since the distal arthrogryposes (DAs) are genetically heterogeneous, an unbiased approach to mutation ... Diseases and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa, with an interest in molecular genetics of connective ...

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.

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.

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;

Nanofins science and applications

CERN Document Server

Singh, Navdeep

2014-01-01

Nanofins Science and Technology describes the heat transfer effectiveness of polymer coolants and their fundamental interactions with carbon nanotube coatings that act as nanofins. Heat transfer at micro/nano-scales has attracted significant attention in contemporary literature. This has been primarily driven by industrial requirements where significant decrease in the size of electronic devices/chips with concomitant enhancement in the heat flux have caused challenging needs for cooling of these platforms. With quantum effects kicking in, traditional cooling techniques need to be replaced with more effective technologies. A promising technique is to enhance heat transfer by surface texturing using nanoparticle coatings or engineered nanostructures. These nanostructures are termed as nanofins because they augment heat transfer by a combination of surface area enhancement as well as liquid-solid interactions at the molecular scale.

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.

Advances in atomic, molecular, and optical physics

CERN Document Server

Walther, Herbert; Walther, Herbert

1998-01-01

This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material as well as detailed descriptions of important recent developments.

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

Colloquium on Atomic, Molecular and Optical Physics of the French Physics Society. Days of Molecular Spectroscopy, Lille, 7-10 July 2008

International Nuclear Information System (INIS)

Balcou, Philippe; Aspect, Alain; Merkt, Frederic; Haroche, Serge; Hendecourt, Louis d'; Dereux, Alain; Bloch, Daniel; Courty, Jean-Michel; Demaison, Jean; Hynes, James T.; Lievin, Jacky; Billy, J.; Josse, V.; Zuo, Z.; Bernard, A.; Hambrecht, B.; Lugan, P.; Clement, D.; Sanchez-Palencia, L.; Bouyer, P.; Aspect, A.; Garreau, Jean-Claude; Chabe, Julien; Szriftgiser, Pascal; Lemarie, Gabriel; Gremaud, Benoit; Delande, Dominique; Simoni, Andrea; Browaeys, Antoine; Kasparian, Jerome; Boutou, Veronique; Guyon, Laurent; Courvoisier, Francois; Roth, Matthias; Roslund, Jon; Rabitz, Herschel; Bonacina, Luigi; Rondi, Ariana; Extermann, Jerome; Wolf, Jean-Pierre; Maitre, Philippe; Zehnacker, Anne; Le Barbu-Debus, Katia; Sidis, Victor; Aguillon, Francois; Sizun, Muriel; Rougeau, Nathalie; Teillet-Billy, Dominique; Bachellerie, Damien; Jeloaica, Leonard; Morisset, Sabine; Picaud, Sylvain; Cacciani, Patrice; Grosliere, Marie-Christine; Joly, Gilles; Joly, Nicolas; Kudlinsky, Alexandre; Martinelli, Gilbert; Buchard, Virginie; Tudorie, Marcela; Khelkhal, Mohamed; Cosleou, Jean; Hennequin, Daniel; Beaugeois, Maxime; Lebrun, Nathalie; Droz, Daniel; El Aydam, Mohamed; Gama, Marie-Jose; Ferri, Sandrine; Schyns, Bernadette; Courty, Jean Michel

2008-07-01

This colloquium of the French Physics Society on atomic, molecular and optical physics (and more particularly on molecular spectroscopy) comprised several mini-colloquia: methane and its applications in planetology, moving mirrors and Casimir, atoms and molecules in interaction with surfaces, electronic properties of small molecules, molecular spectroscopy for atmospheric applications, quantum memories in atomic sets, methods and applications of reaction dynamics, dynamics of super-excited molecular statuses, mass spectrometry, quantum spectroscopy and chemistry, spectroscopy and reactivity of of confined molecules, electronic and molecular dynamics, dipolar quantum gases. It also comprised plenary sessions: atto-second optics, the atomic Hanbury-Brown-Twiss effect with fermions and bosons, atom and molecule slowing down by Zeeman effect and by Stark effect on Rydberg levels, non destructive counting of photons trapped in a cavity, interstellar chemistry, atom-surface van der Waals interaction noticed in the exotic regime of short distances, communication, vulgarisation and education (the multiple lives of a scientific result), the actual precision of molecular parameters, towards the formation of an amine acid precursor in the interstellar medium via proton transfer, prediction of the ionized and excited molecular electronic structure by Quantum Chemistry (from bi-atomic to bio-molecules), direct observation of Anderson location of matter waves in a controlled disordered potential, experimental observation of the Anderson transition of cold atoms, ultra-cold collisions as a key towards the quantum world, Quantum physics with a single atom, Teramobile or plasma filaments to study the atmosphere, optimal control or how to discriminate two almost identical bio-molecules, infrared spectroscopy as a new dimension for mass spectrometry, chiral recognition in gaseous phase, interactions and reactions between H atoms and graphite surfaces, modelling of gas

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

Lifescience Database Archive (English)

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

Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

International Nuclear Information System (INIS)

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

2016-01-01

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

A guide to synchrotron radiation science

CERN Document Server

Sato, Shigeru; Munro, Ian; Lodha, G S

2015-01-01

Synchrotron Radiation (SR), as a light source is now in use around the world to provide brilliant radiation from the infrared into the soft and hard X-ray regions. It is an indispensible and essential tool to establish the physic-chemical characteristics of materials and surfaces from an atomic and molecular view point. It is being applied to topics which range from mineralogy to protein crystallography, embracing research in areas from the physical to the life sciences. This new guide is a concise yet comprehensive and easily readable introduction to an expanding area of science. It presents in a readily assimilable form the basic concepts of SR science from its generation principles, through source design and operation to the principles of instruments for SR exploitation followed by a survey of its actual applications in selected research fields, including spectroscopy, diffractometry, microanalysis and chemical processing.

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.

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

DEFF Research Database (Denmark)

Kneipp, Harald; Møbjerg, Nadja; Jørgensen, Aslak

2013-01-01

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

Surface properties of heat-induced soluble soy protein aggregates of different molecular masses.

Science.gov (United States)

Guo, Fengxian; Xiong, Youling L; Qin, Fang; Jian, Huajun; Huang, Xiaolin; Chen, Jie

2015-02-01

Suspensions (2% and 5%, w/v) of soy protein isolate (SPI) were heated at 80, 90, or 100 °C for different time periods to produce soluble aggregates of different molecular sizes to investigate the relationship between particle size and surface properties (emulsions and foams). Soluble aggregates generated in these model systems were characterized by gel permeation chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Heat treatment increased surface hydrophobicity, induced SPI aggregation via hydrophobic interaction and disulfide bonds, and formed soluble aggregates of different sizes. Heating of 5% SPI always promoted large-size aggregate (LA; >1000 kDa) formation irrespective of temperature, whereas the aggregate size distribution in 2% SPI was temperature dependent: the LA fraction progressively rose with temperature (80→90→100 °C), corresponding to the attenuation of medium-size aggregates (MA; 670 to 1000 kDa) initially abundant at 80 °C. Heated SPI with abundant LA (>50%) promoted foam stability. LA also exhibited excellent emulsifying activity and stabilized emulsions by promoting the formation of small oil droplets covered with a thick interfacial protein layer. However, despite a similar influence on emulsion stability, MA enhanced foaming capacity but were less capable of stabilizing emulsions than LA. The functionality variation between heated SPI samples is clearly related to the distribution of aggregates that differ in molecular size and surface activity. The findings may encourage further research to develop functional SPI aggregates for various commercial applications. © 2015 Institute of Food Technologists®

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

Dual analyzer system for surface analysis dedicated for angle-resolved photoelectron spectroscopy at liquid surfaces and interfaces

Energy Technology Data Exchange (ETDEWEB)

Niedermaier, Inga; Kolbeck, Claudia; Steinrück, Hans-Peter; Maier, Florian, E-mail: florian.maier@fau.de [Lehrstuhl für Physikalische Chemie II, FAU Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058 Erlangen (Germany)

2016-04-15

The investigation of liquid surfaces and interfaces with the powerful toolbox of ultra-high vacuum (UHV)-based surface science techniques generally has to overcome the issue of liquid evaporation within the vacuum system. In the last decade, however, new classes of liquids with negligible vapor pressure at room temperature—in particular, ionic liquids (ILs)—have emerged for surface science studies. It has been demonstrated that particularly angle-resolved X-ray Photoelectron Spectroscopy (ARXPS) allows for investigating phenomena that occur at gas-liquid and liquid-solid interfaces on the molecular level. The results are not only relevant for IL systems but also for liquids in general. In all of these previous ARXPS studies, the sample holder had to be tilted in order to change the polar detection angle of emitted photoelectrons, which restricted the liquid systems to very thin viscous IL films coating a flat solid support. We now report on the concept and realization of a new and unique laboratory “Dual Analyzer System for Surface Analysis (DASSA)” which enables fast ARXPS, UV photoelectron spectroscopy, imaging XPS, and low-energy ion scattering at the horizontal surface plane of macroscopically thick non-volatile liquid samples. It comprises a UHV chamber equipped with two electron analyzers mounted for simultaneous measurements in 0° and 80° emission relative to the surface normal. The performance of DASSA on a first macroscopic liquid system will be demonstrated.

Dual analyzer system for surface analysis dedicated for angle-resolved photoelectron spectroscopy at liquid surfaces and interfaces

International Nuclear Information System (INIS)

Niedermaier, Inga; Kolbeck, Claudia; Steinrück, Hans-Peter; Maier, Florian

2016-01-01

The investigation of liquid surfaces and interfaces with the powerful toolbox of ultra-high vacuum (UHV)-based surface science techniques generally has to overcome the issue of liquid evaporation within the vacuum system. In the last decade, however, new classes of liquids with negligible vapor pressure at room temperature—in particular, ionic liquids (ILs)—have emerged for surface science studies. It has been demonstrated that particularly angle-resolved X-ray Photoelectron Spectroscopy (ARXPS) allows for investigating phenomena that occur at gas-liquid and liquid-solid interfaces on the molecular level. The results are not only relevant for IL systems but also for liquids in general. In all of these previous ARXPS studies, the sample holder had to be tilted in order to change the polar detection angle of emitted photoelectrons, which restricted the liquid systems to very thin viscous IL films coating a flat solid support. We now report on the concept and realization of a new and unique laboratory “Dual Analyzer System for Surface Analysis (DASSA)” which enables fast ARXPS, UV photoelectron spectroscopy, imaging XPS, and low-energy ion scattering at the horizontal surface plane of macroscopically thick non-volatile liquid samples. It comprises a UHV chamber equipped with two electron analyzers mounted for simultaneous measurements in 0° and 80° emission relative to the surface normal. The performance of DASSA on a first macroscopic liquid system will be demonstrated.

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

Energy Technology Data Exchange (ETDEWEB)

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

2013-12-14

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

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.

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)

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

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

Life sciences and environmental sciences

Energy Technology Data Exchange (ETDEWEB)

1992-02-01

The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER's mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.

Life sciences and environmental sciences

Energy Technology Data Exchange (ETDEWEB)

1992-02-01

The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER`s mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.

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

Molecular Theory of the Living Cell Concepts, Molecular Mechanisms, and Biomedical Applications

CERN Document Server

Ji, Sungchul

2012-01-01

This book presents a comprehensive molecular theory of the living cell based on over thirty concepts, principles and laws imported from thermodynamics, statistical mechanics, quantum mechanics, chemical kinetics, informatics, computer science, linguistics, semiotics, and philosophy. The author formulates physically, chemically and enzymologically realistic molecular mechanisms to account for the basic living processes such as ligand-receptor interactions, protein folding, single-molecule enzymic catalysis, force-generating mechanisms in molecular motors, signal transduction, regulation of the genome-wide RNA metabolism, morphogenesis, the micro-macro coupling in coordination dynamics, the origin of life, and the mechanisms of biological evolution itself. Possible solutions to basic and practical problems facing contemporary biology and biomedical sciences have been suggested, including pharmacotheragnostics and personalized medicine.

Molecular Basis of Clay Mineral Structure and Dynamics in Subsurface Engineering Applications

Science.gov (United States)

Cygan, R. T.

2015-12-01

Clay minerals and their interfaces play an essential role in many geochemical, environmental, and subsurface engineering applications. Adsorption, dissolution, precipitation, nucleation, and growth mechanisms, in particular, are controlled by the interplay of structure, thermodynamics, kinetics, and transport at clay mineral-water interfaces. Molecular details of these processes are typically beyond the sensitivity of experimental and analytical methods, and therefore require accurate models and simulations. Also, basal surfaces and interlayers of clay minerals provide constrained interfacial environments to facilitate the evaluation of these complex processes. We have developed and used classical molecular and quantum methods to examine the complex behavior of clay mineral-water interfaces and dynamics of interlayer species. Bulk structures, swelling behavior, diffusion, and adsorption processes are evaluated and compared to experimental and spectroscopic findings. Analysis of adsorption mechanisms of radionuclides on clay minerals provides a scientific basis for predicting the suitability of engineered barriers associated with nuclear waste repositories and the fate of contaminants in the environment. Similarly, the injection of supercritical carbon dioxide into geological reservoirs—to mitigate the impact of climate change—is evaluated by molecular models of multi-fluid interactions with clay minerals. Molecular dynamics simulations provide insights into the wettability of different fluids—water, electrolyte solutions, and supercritical carbon dioxide—on clay surfaces, and which ultimately affects capillary fluid flow and the integrity of shale caprocks. This work is supported as part of Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science and by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Geosciences Research Program

Fellowship | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Fellowship. Fellow Profile. Elected: 2007 Section: Plant Sciences. Grover, Prof. Anil Ph.D. (IARI), FNASc, FNAAS, FNA. Date of birth: 15 August 1958. Specialization: Plant Abiotic Stress Responses, Plant Biotechnology, Molecular Biology and Crop Sciences Address: Professor, Department of Plant Molecular Biology, ...

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

Energy Technology Data Exchange (ETDEWEB)

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

2008-01-01

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

Behind adhesion of uranyl onto montmorillonite surface: A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Yang, W.; Zaoui, A., E-mail: azaoui@polytech-lille.fr

2013-10-15

Highlights: • We investigated the adsorption of uranyl onto Montmorillonite surface. • We studied the surface energy between layered Montmorillonite sheets. • We studied the work of adhesion between radionuclide and charged Montmorillonite. -- Abstract: We have performed molecular dynamics simulations to investigate the adsorption of radionuclide elements species onto substituted Montmorillonite (001) surface in the presence of different counterions. The structure and the dynamics of uranyl ion as well as its aquo, chloride ion, and carbonate complexes are analyzed. In addition, we have studied the surface energy between layered Montmorillonite sheets and the work of adhesion between radionuclide and charged Montmorillonite. The clay model used here is a Wyoming-type Montmorillonite with 0.75e negative charge per unit cell resulting from substitutions in Octahedral and Tetrahedral sheets. The system model was constructed based on CLAYFF force field potential model. To evaluate the thermodynamic work of adhesion, each surface and clay layer regions are converted to a thin film model. One and two species of radionuclide elements (UO{sub 2}(H{sub 2}O){sub 5},UO{sub 2}CO{sub 3}(H{sub 2}O){sub 5}, and UO{sub 2}Cl{sub 2}(H{sub 2}O){sub 5}) were deposited near the clay surface in a pseudo-two-dimensional periodic cell. Analysis shows that the uranyl ion structure is preserved with two axial oxygen atoms detected at 1.8 Å. Radial distribution functions results indicate that average U-O{sub w} distances are 2.45–2.61 Å, and 2.29–2.40 Å for U-O{sub c} distance. Average U-Cl distances are 2.78–3.08 Å, which is relatively larger than that of Uranium atom-Oxygen atom because of electrostatic factors.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

National Engineering Research Center for Integrated Utilization of Salt Lake Resource, East China University of Science and Technology, Meilong Road 130, Shanghai 200237, China; Van 't Hoff Institute for Molecular Sciences & Amsterdam Center for Multiscale Modeling, University of Amsterdam, 1098 XH Amsterdam, ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. M PRASANTHI. Articles written in Journal of Chemical Sciences. Volume 129 Issue 5 May 2017 pp 515-531 Regular Article. Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDS) · ANAMIKA SINGH GAUR ANSHU ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. SRIDHARA JANARDHAN. Articles written in Journal of Chemical Sciences. Volume 129 Issue 5 May 2017 pp 515-531 Regular Article. Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDS) · ANAMIKA SINGH GAUR ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Kishalay Bhar. Articles written in Journal of Chemical Sciences. Volume 125 Issue 4 July 2013 pp 715-721. Syntheses, molecular and crystalline architectures, and luminescence behaviour of terephthalate bridged heptacoordinated dinuclear lead(II) complexes containing a ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. DIPU SUTRADHAR. Articles written in Journal of Chemical Sciences. Volume 128 Issue 9 September 2016 pp 1377-1384 Regular Article. Two new hexacoordinated coordination polymers of cadmium(II) containing bridging units only: Syntheses, structures and molecular ...

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

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

Adsorption of molecular brushes with polyelectrolyte backbones onto oppositely charged surfaces: A self-consistent field theory

NARCIS (Netherlands)

Feuz, L.; Leermakers, F.A.M.; Textor, M.; Borisov, O.V.

2008-01-01

The two-gradient version of the Scheutjens¿Fleer self-consistent field (SF-SCF) theory is employed to model the interaction between a molecular bottle brush with a polyelectrolyte backbone and neutral hydrophilic side chains and an oppositely charged surface. Our system mimics graft-copolymers with

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)

Surface vibrational spectroscopy

International Nuclear Information System (INIS)

Erskine, J.L.

1984-01-01

A brief review of recent studies which combine measurements of surface vibrational energies with lattice dynamical calculations is presented. These results suggest that surface vibrational spectroscopy offers interesting prospects for use as a molecular-level probe of surface geometry, adsorbate bond distances and molecular orientations

Interfacially enhancement of PBO/epoxy composites by grafting MWCNTs onto PBO surface through melamine as molecular bridge

Science.gov (United States)

Lv, Junwei; Wang, Bin; Ma, Qi; Wang, Wenjing; Xiang, Dong; Li, Mengyao; Zeng, Lan; Li, Hui; Li, Yuntao; Zhao, Chunxia

2018-06-01

Melamine and multi-walled carbon nanotubes (MWCNTs) were grafted onto Poly-p-phenylene benzobisoxazole (PBO) fiber surface effectively via layer-by-layer method. Both of them have been chemically bonded as fourier transform infrared spectroscopy (FTIR) confirmed. Grafting melamine overcame the inertness of PBO surface. Ammoniation was processed on PBO surface through grafting melamine so that the MWCNTs could be grafted onto PBO surface. Scanning electron microscopy (SEM) images indicated that melamine used as molecular bridge could increase MWCNTs’ quantity on PBO surface. X-ray photoelectron spectroscopy (XPS) results revealed the variation of chemical composition of PBO surface. Test of interfacial shear strength (IFSS) and tensile strength indicated the great mechanical properties of modified PBO fibers when combining with epoxy resin. Furthermore, whole reaction was processed under a simple condition. Results in this research also promised a potential method to modify PBO surface.

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

International Nuclear Information System (INIS)

Vree, C; Mayr, S G

2010-01-01

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

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

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.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. M RAM VIVEK. Articles written in Journal of Chemical Sciences. Volume 129 Issue 5 May 2017 pp 515-531 Regular Article. Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDS) · ANAMIKA SINGH GAUR ANSHU ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Asim Bhaumik. Articles written in Journal of Chemical Sciences. Volume 114 Issue 4 August 2002 pp 451-460. Mesoporous titanium phosphates and related molecular sieves: Synthesis, characterization and applications · Asim Bhaumik · More Details Abstract Fulltext PDF.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Charusita Chakravarty. Articles written in Journal of Chemical Sciences. Volume 121 Issue 5 September 2009 pp 913-919. Evaluation of collective transport properties of ionic melts from molecular dynamics simulations · Manish Agarwal Charusita Chakravarty · More Details ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. T SHANMUGANATHAN. Articles written in Journal of Chemical Sciences. Volume 129 Issue 1 January 2017 pp 117-130 Regular Article. Synthesis, in vitro anti-inflammatory activity and molecular docking studies of novel 4,5-diarylthiophene-2-carboxamide derivatives.

Quantum molecular dynamics study on energy transfer to the secondary electron in surface collision process of an ion

International Nuclear Information System (INIS)

Shibahara, M; Satake, S; Taniguchi, J

2008-01-01

In the present study the quantum molecular dynamics method was applied to an energy transfer problem to an electron during ionic surface collision process in order to elucidate how energy of ionic collision transfers to the emitted electrons. Effects of various physical parameters, such as the collision velocity and interaction strength between the observed electron and the classical particles on the energy transfer to the electron were investigated by the quantum molecular dynamics method when the potassium ion was collided with the surface so as to elucidate the energy path to the electron and the predominant factor of energy transfer to the electron. Effects of potential energy between the ion and the electron and that between the surface molecule and the electron on the electronic energy transfer were shown in the present paper. The energy transfer to the observed secondary electron through the potential energy term between the ion and the electron was much dependent on the ion collision energy although the energy increase to the observed secondary electron was not monotonous through the potential energy between the ion and surface molecules with the change of the ion collision energy

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

International Nuclear Information System (INIS)

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

2011-01-01

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

Molecular Beam Epitaxy on Gas Cluster Ion Beam Prepared GaSb Substrates: Towards Improved Surfaces and Interfaces

National Research Council Canada - National Science Library

Krishnaswami, Kannan; Vangala, Shivashankar R; Dauplaise, Helen M; Allen, Lisa P; Dallas, Gordon; Bakken, Daniel; Bliss, David F; Goodhue, WIlliam D

2007-01-01

... at temperatures ranging 530 degrees C to 560 degrees C. Cross-sectional transmission electron microscopy of molecular beam epitaxy grown GaSb/AlGaSb layers showed that the HBr-GCIB surface produced a smooth dislocation-free substrate-to-epi transition...

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

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. SABIHA FATIMA. Articles written in Journal of Chemical Sciences. Volume 128 Issue 7 July 2016 pp 1163-1173 Regular Article. Molecular docking, MM/GBSA and 3D-QSAR studies on EGFR inhibitors · RAJU BATHINI SREE KANTH SIVAN SABIHA FATIMA VIJJULATHA ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Tapta Kanchan Roy. Articles written in Journal of Chemical Sciences. Volume 121 Issue 5 September 2009 pp 805-810. Effective harmonic oscillator description of anharmonic molecular vibrations · Tapta Kanchan Roy M Durga Prasad · More Details Abstract Fulltext PDF.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. RAJU BATHINI. Articles written in Journal of Chemical Sciences. Volume 128 Issue 7 July 2016 pp 1163-1173 Regular Article. Molecular docking, MM/GBSA and 3D-QSAR studies on EGFR inhibitors · RAJU BATHINI SREE KANTH SIVAN SABIHA FATIMA VIJJULATHA ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Navneet Kaur. Articles written in Journal of Chemical Sciences. Volume 126 Issue 1 January 2014 pp 49-54. Anthraquinone-based demultiplexer and other multiple operations at the molecular level · Navneet Kaur Subodh Kumar · More Details Abstract Fulltext PDF.

Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer.

Science.gov (United States)

Zhang, Yue; Barnes, George L; Yan, Tianying; Hase, William L

2010-05-07

Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Science, 2007, 317, 787). Different models are considered to determine how they affect the heat transfer dynamics. They include temperature equilibrated (TE) and temperature gradient (TG) thermostat models for the Au(s) surface, and soft and stiff S/Au(s) models for bonding of the S-atoms to the Au(s) surface. A detailed analysis of the non-equilibrium heat transfer at the heterogeneous interface is presented. There is a short time temperature gradient within the top layers of the Au(s) surface. The S-atoms heat rapidly, much faster than do the C-atoms in the alkylthiolate chains. A high thermal conductivity in the H-SAM, perpendicular to the interface, results in nearly identical temperatures for the CH(2) and CH(3) groups versus time. Thermal-induced disorder is analyzed for the Au(s) substrate, the S/Au(s) interface and the H-SAM. Before heat transfer occurs from the hot Au(s) substrate to the H-SAM, there is disorder at the S/Au(s) interface and within the alkylthiolate chains arising from heat-induced disorder near the surface of hot Au(s). The short-time rapid heating of the S-atoms enhances this disorder. The increasing disorder of H-SAM chains with time results from both disorder at the Au/S interface and heat transfer to the H-SAM chains.

Comparison of gas-solid chromatography and MM2 force field molecular binding energies for greenhouse gases on a carbonaceous surface.

Science.gov (United States)

Rybolt, Thomas R; Bivona, Kevin T; Thomas, Howard E; O'Dell, Casey M

2009-10-01

Gas-solid chromatography was used to determine B(2s) (gas-solid virial coefficient) values for eight molecular adsorbates interacting with a carbon powder (Carbopack B, Supelco). B(2s) values were determined by multiple size variant injections within the temperature range of 313-553 K. The molecular adsorbates included: carbon dioxide (CO(2)); tetrafluoromethane (CF(4)); hexafluoroethane (C(2)F(6)); 1,1-difluoroethane (C(2)H(4)F(2)); 1-chloro-1,1-difluoroethane (C(2)H(3)ClF(2)); dichlorodifluoromethane (CCl(2)F(2)); trichlorofluoromethane (CCl(3)F); and 1,1,1-trichloroethane (C(2)H(3)Cl(3)). Two of these molecules are of special interest because they are "super greenhouse gases". The global warming potential, GWP, for CF(4) is 6500 and for C(2)F(6) is 9200 relative to the reference value of 1 for CO(2). The GWP index considers both radiative blocking and molecular lifetime. For these and other industrial greenhouse gases, adsorptive trapping on a carbonaceous solid, which depends on molecule-surface binding energy, could avoid atmospheric release. The temperature variations of the gas-solid virial coefficients in conjunction with van't Hoff plots were used to find the experimental adsorption energy or binding energy values (E(*)) for each adsorbate. A molecular mechanics based, rough-surface model was used to calculate the molecule-surface binding energy (Ecal(*)) using augmented MM2 parameters. The surface model consisted of parallel graphene layers with two separated nanostructures each containing 17 benzene rings arranged in linear strips. The separation of the parallel nanostructures had been optimized in a prior study to appropriately represent molecule-surface interactions for Carbopack B. Linear regressions of E(*) versus Ecal(*) for the current data set of eight molecules and the same surface model gave E(*)=0.926 Ecal(*) and r(2)=0.956. A combined set of the current and prior Carbopack B adsorbates studied (linear alkanes, branched alkanes, cyclic alkanes

Molecular insight into nanoscale water films dewetting on modified silica surfaces.

Science.gov (United States)

Zhang, Jun; Li, Wen; Yan, Youguo; Wang, Yefei; Liu, Bing; Shen, Yue; Chen, Haixiang; Liu, Liang

2015-01-07

In this work, molecular dynamics simulations are adopted to investigate the microscopic dewetting mechanism of nanoscale water films on methylated silica surfaces. The simulation results show that the dewetting process is divided into two stages: the appearance of dry patches and the quick contraction of the water film. First, the appearance of dry patches is due to the fluctuation in the film thickness originating from capillary wave instability. Second, for the fast contraction of water film, the unsaturated electrostatic and hydrogen bond interactions among water molecules are the driving forces, which induce the quick contraction of the water film. Finally, the effect of film thickness on water films dewetting is studied. Research results suggest that upon increasing the water film thickness from 6 to 8 Å, the final dewetting patterns experience separate droplets and striation-shaped structures, respectively. But upon further increasing the water film thickness, the water film is stable and there are no dry patches. The microscopic dewetting behaviors of water films on methylated silica surfaces discussed here are helpful in understanding many phenomena in scientific and industrial processes better.

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.

Molecular interactions with ice: Molecular embedding, adsorption, detection, and release

Energy Technology Data Exchange (ETDEWEB)

Gibson, K. D.; Langlois, Grant G.; Li, Wenxin; Sibener, S. J., E-mail: s-sibener@uchicago.edu [The James Franck Institute and Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637 (United States); Killelea, Daniel R. [Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Ave., Chicago, Illinois 60660 (United States)

2014-11-14

The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF{sub 4} molecules with high translational energies (≥3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF{sub 4} embedding probability is much less than for Xe. In addition, a larger molecule, SF{sub 6}, did not embed at the same translational energies that both CF{sub 4} and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF{sub 4} > SF{sub 6}. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF{sub 4}. Tentatively, this order suggests that for Xe and CF{sub 4}, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF{sub 6} molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas