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

PubMed

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.

Nanoarchitectonics of molecular aggregates: science and technology.

PubMed

Ramanathan, Muruganathan; Hong, Kunlun; Ji, Qingmin; Yonamine, Yusuke; Hill, Jonathan P; Ariga, Katsuhiko

2014-01-01

The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review, we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

Nanoarchitectonics of Molecular Aggregates: Science and Technology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanathan, Nathan Muruganathan; Hong, Kunlun; Ji, Dr. Qingmin

2014-01-01

The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

Studying Two-Dimensional Zeolites with the Tools of Surface Science: MFI Nanosheets on Au(111)

DOE PAGES

J. D. Kestell; Zhong, J. Q.; Shete, M.; ...

2016-07-26

While surface science has provided fundamental insights into a variety a materials, the most used catalysts in the industry, namely zeolites, still remain a challenge. The recent preparation of two-dimensional versions of MFI zeolite frameworks and the possibility of their deposition on electrically conductive supports provides for the first time a viable strategy to perform detailed studies on industrially relevant zeolites using the vast toolkit of surface science. In this work we demonstrate the use of infrared reflection absorption spectroscopy (IRRAS) and synchrotron-based x-ray photoelectron spectroscopy (XPS) to study these materials. Furthermore, polarization modulation IRRAS is used to study themore » adsorption of methanol and its effect in phonon vibrations of the zeolite framework. The possibility of using surface science methods, in particular under ambient pressure conditions, for the study of well-defined zeolites and other microporous structures opens new avenues to understand structural and mechanistic aspects of these materials as catalysts, adsorbents and molecular sieves.« less

Studying Two-Dimensional Zeolites with the Tools of Surface Science: MFI Nanosheets on Au(111)

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. D. Kestell; Zhong, J. Q.; Shete, M.

While surface science has provided fundamental insights into a variety a materials, the most used catalysts in the industry, namely zeolites, still remain a challenge. The recent preparation of two-dimensional versions of MFI zeolite frameworks and the possibility of their deposition on electrically conductive supports provides for the first time a viable strategy to perform detailed studies on industrially relevant zeolites using the vast toolkit of surface science. In this work we demonstrate the use of infrared reflection absorption spectroscopy (IRRAS) and synchrotron-based x-ray photoelectron spectroscopy (XPS) to study these materials. Furthermore, polarization modulation IRRAS is used to study themore » adsorption of methanol and its effect in phonon vibrations of the zeolite framework. The possibility of using surface science methods, in particular under ambient pressure conditions, for the study of well-defined zeolites and other microporous structures opens new avenues to understand structural and mechanistic aspects of these materials as catalysts, adsorbents and molecular sieves.« less

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

PubMed

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.

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

NASA Astrophysics Data System (ADS)

Costa, Dominique; Pradier, Claire-Marie; Tielens, Frederik; Savio, Letizia

2015-12-01

Understanding the bio-physical-chemical interactions at nanostructured biointerfaces and the assembly mechanisms of so-called hybrid nano-composites is nowadays a key issue for nanoscience in view of the many possible applications foreseen. The contribution of surface science in this field is noteworthy since, using a bottom-up approach, it allows the investigation of the fundamental processes at the basis of complex interfacial phenomena and thus it helps to unravel the elementary mechanisms governing them. Nowadays it is well demonstrated that a wide variety of different molecular assemblies can form upon adsorption of small biomolecules at surfaces. The geometry of such self-organized structures can often be tuned by a careful control of the experimental conditions during the deposition process. Indeed an impressive number of studies exists (both experimental and - to a lesser extent - theoretical), which demonstrates the ability of molecular self-assembly to create different structural motifs in a more or less predictable manner, by tuning the molecular building blocks as well as the metallic substrate. In this frame, amino acids and small peptides at surfaces are key, basic, systems to be studied. The amino acids structure is simple enough to serve as a model for the chemisorption of biofunctional molecules, but their adsorption at surfaces has applications in surface functionalization, in enantiospecific catalysis, biosensing, shape control of nanoparticles or in emerging fields such as "green" corrosion inhibition. In this paper we review the most recent advances in this field. We shall start from the adsorption of amino acids at metal surfaces and we will evolve then in the direction of more complex systems, in the light of the latest improvements of surface science techniques and of computational methods. On one side, we will focus on amino acids adsorption at oxide surfaces, on the other on peptide adsorption both at metal and oxide substrates. Particular attention will be drawn to the added value provided by the combination of several experimental surface science techniques and to the precious contribution of advanced complementary computational methods to resolve the details of systems of increased complexity. Finally, some hints on experiments performed in presence of water and then characterized in UHV and on the related theoretical work will be presented. This is a further step towards a better approximation of real biological systems. However, since the methods employed are often not typical of surface science, this topic is not developed in detail.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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)more » 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.« less

Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2015-06-01

In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficientmore » layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. 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 the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.« less

Plasmonic nanoparticles for bioanalytics and therapy at the limit

NASA Astrophysics Data System (ADS)

Schneider, T.; Wirth, J.; Garwe, F.; Csáki, A.; Fritzsche, W.

2011-12-01

Noble metal nanoparticles interacting with electromagnetic waves exhibit the effect of localized surface plasmon resonance (LSPR) based on the collective oscillation of their conduction electrons. Local refractive index changes by a (bio) molecular layer surrounding the nanoparticle are important for a variety of research areas like optics and life sciences. In this work we demonstrate the potential of two applications in the field of molecular plasmonics, single nanoparticle sensors and nanoantennas, situated between plasmonics effects and the molecular world.

National Synchrotron Light Source annual report 1991

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hulbert, S.L.; Lazarz, N.M.

1992-04-01

This report discusses the following research conducted at NSLS: atomic and molecular science; energy dispersive diffraction; lithography, microscopy and tomography; nuclear physics; UV photoemission and surface science; x-ray absorption spectroscopy; x-ray scattering and crystallography; x-ray topography; workshop on surface structure; workshop on electronic and chemical phenomena at surfaces; workshop on imaging; UV FEL machine reviews; VUV machine operations; VUV beamline operations; VUV storage ring parameters; x-ray machine operations; x-ray beamline operations; x-ray storage ring parameters; superconducting x-ray lithography source; SXLS storage ring parameters; the accelerator test facility; proposed UV-FEL user facility at the NSLS; global orbit feedback systems; and NSLSmore » computer system.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruski, Marek; Sadow, Aaron D.; Slowing, Igor I.

Here the catalysis research at the U.S. Department of Energy's (DOE's) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/molecular catalysis, biocatalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE's mission to ensure America's security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions.

Shapes of embedded minimal surfaces

PubMed Central

Colding, Tobias H.; Minicozzi, William P.

2006-01-01

Surfaces that locally minimize area have been extensively used to model physical phenomena, including soap films, black holes, compound polymers, protein folding, etc. The mathematical field dates to the 1740s but has recently become an area of intense mathematical and scientific study, specifically in the areas of molecular engineering, materials science, and nanotechnology because of their many anticipated applications. In this work, we show that all minimal surfaces are built out of pieces of the surfaces in Figs. 1 and 2. PMID:16847265

Fundamental insights into interfacial catalysis.

PubMed

Gong, Jinlong; Bao, Xinhe

2017-04-03

Surface and interfacial catalysis plays a vital role in chemical industries, electrochemistry and photochemical reactions. The challenges of modern chemistry are to optimize the chemical reaction processes and understand the detailed mechanism of chemical reactions. Since the early 1960s, the foundation of surface science systems has allowed the study of surface and interfacial phenomena on atomic/molecular level, and thus brought a number of significant developments to fundamental and technological processes, such as catalysis, material science and biochemistry, just to name a few. This themed issue describes the recent advances and developments in the fundamental understanding of surface and interfacial catalysis, encompassing areas of knowledge from metal to metal oxide, carbide, graphene, hexagonal boron nitride, and transition metal dichalcogenides under ultrahigh vacuum conditions, as well as under realistic reaction conditions.

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives.

PubMed

Lacher, Sebastian; Matsuo, Yutaka; Nakamura, Eiichi

2011-10-26

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.

National Synchrotron Light Source annual report 1991. Volume 1, October 1, 1990--September 30, 1991

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hulbert, S.L.; Lazarz, N.M.

1992-04-01

This report discusses the following research conducted at NSLS: atomic and molecular science; energy dispersive diffraction; lithography, microscopy and tomography; nuclear physics; UV photoemission and surface science; x-ray absorption spectroscopy; x-ray scattering and crystallography; x-ray topography; workshop on surface structure; workshop on electronic and chemical phenomena at surfaces; workshop on imaging; UV FEL machine reviews; VUV machine operations; VUV beamline operations; VUV storage ring parameters; x-ray machine operations; x-ray beamline operations; x-ray storage ring parameters; superconducting x-ray lithography source; SXLS storage ring parameters; the accelerator test facility; proposed UV-FEL user facility at the NSLS; global orbit feedback systems; and NSLSmore » computer system.« less

Evidence of a molecular boundary lubricant at snakeskin surfaces

PubMed Central

Spinner, Marlene; Jaye, Cherno; Fischer, Daniel A.; Gorb, Stanislav N.; Weidner, Tobias

2015-01-01

During slithering locomotion the ventral scales at a snake's belly are in direct mechanical interaction with the environment, while the dorsal scales provide optical camouflage and thermoregulation. Recent work has demonstrated that compared to dorsal scales, ventral scales provide improved lubrication and wear protection. While biomechanic adaption of snake motion is of growing interest in the fields of material science and robotics, the mechanism for how ventral scales influence the friction between the snake and substrate, at the molecular level, is unknown. In this study, we characterize the outermost surface of snake scales using sum frequency generation (SFG) spectra and near-edge X-ray absorption fine structure (NEXAFS) images collected from recently shed California kingsnake (Lampropeltis californiae) epidermis. SFG's nonlinear optical selection rules provide information about the outermost surface of materials; NEXAFS takes advantage of the shallow escape depth of the electrons to probe the molecular structure of surfaces. Our analysis of the data revealed the existence of a previously unknown lipid coating on both the ventral and dorsal scales. Additionally, the molecular structure of this lipid coating closely aligns to the biological function: lipids on ventral scales form a highly ordered layer which provides both lubrication and wear protection at the snake's ventral surface. PMID:26655468

Evidence of a molecular boundary lubricant at snakeskin surfaces.

PubMed

Baio, Joe E; Spinner, Marlene; Jaye, Cherno; Fischer, Daniel A; Gorb, Stanislav N; Weidner, Tobias

2015-12-06

During slithering locomotion the ventral scales at a snake's belly are in direct mechanical interaction with the environment, while the dorsal scales provide optical camouflage and thermoregulation. Recent work has demonstrated that compared to dorsal scales, ventral scales provide improved lubrication and wear protection. While biomechanic adaption of snake motion is of growing interest in the fields of material science and robotics, the mechanism for how ventral scales influence the friction between the snake and substrate, at the molecular level, is unknown. In this study, we characterize the outermost surface of snake scales using sum frequency generation (SFG) spectra and near-edge X-ray absorption fine structure (NEXAFS) images collected from recently shed California kingsnake (Lampropeltis californiae) epidermis. SFG's nonlinear optical selection rules provide information about the outermost surface of materials; NEXAFS takes advantage of the shallow escape depth of the electrons to probe the molecular structure of surfaces. Our analysis of the data revealed the existence of a previously unknown lipid coating on both the ventral and dorsal scales. Additionally, the molecular structure of this lipid coating closely aligns to the biological function: lipids on ventral scales form a highly ordered layer which provides both lubrication and wear protection at the snake's ventral surface. © 2015 The Author(s).

Materials and Manufacturing Technology Directorate Thermal Sciences and Materials Branch (Overview)

DTIC Science & Technology

2010-09-01

Molecular Mechanics for thermo-mechanical response Materials Characterization • CNT modified durable thermal interface ( DTI ) • MEMS-based RTD micro...stabilization. Surface Characterization by Atomic Force Microscopy: Probing Thermal, Electrical, and Mechanical Properties Heater Current Path Anchor Leg 50 µm

Chiral selection on inorganic crystalline surfaces

NASA Technical Reports Server (NTRS)

Hazen, Robert M.; Sholl, David S.

2003-01-01

From synthetic drugs to biodegradable plastics to the origin of life, the chiral selection of molecules presents both daunting challenges and significant opportunities in materials science. Among the most promising, yet little explored, avenues for chiral molecular discrimination is adsorption on chiral crystalline surfaces - periodic environments that can select, concentrate and possibly even organize molecules into polymers and other macromolecular structures. Here we review experimental and theoretical approaches to chiral selection on inorganic crystalline surfaces - research that is poised to open this new frontier in understanding and exploiting surface-molecule interactions.

Analysis of Molecular Contamination on Genesis Collectors Through Spectroscopic Ellipsometry

NASA Technical Reports Server (NTRS)

McNamara, K. M.; Stansbery, Eileen K.

2005-01-01

Before the spacecraft returned to Earth in September, the Genesis mission had a preliminary assessment plan in place for the purpose of providing information on the condition and availability of collector materials to the science community as a basis for allocation requests. One important component of that plan was the evaluation of collector surfaces for molecular contamination. Sources of molecular contamination might be the on-orbit outgassing of spacecraft and science canister components, the condensation of thruster by-products during spacecraft maneuvers, or the condensation of volatile species associated with reentry. Although the non-nominal return of the Genesis spacecraft introduced particulate contamination to the collectors, such as dust and heatshield carbon-carbon, it is unlikely to have caused any molecular deposition. The contingency team's quick action in returning the damaged payload the UTTR cleanroom by 6 PM the evening of recovery help to ensure that exposure to weather conditions and the environment were kept to a minimum.

Effect of surface roughness on liquid property measurements using mechanically oscillating sensors

NASA Technical Reports Server (NTRS)

Jain, Mahaveer K.; Grimes, Craig A.

2002-01-01

The resonant frequency and quality factor Q of a liquid immersed magnetoelastic sensor are shown to shift linearly with the liquid viscosity and density product. Measurements using different grade oils, organic chemicals, and glycerol-water mixtures show that the surface roughness of the sensor in combination with the molecular size of the liquid play important roles in determining measurement sensitivity, which can be controlled through adjusting the surface roughness of the sensor surface. A theoretical model describing the sensor resonant frequency and quality factor Q as a function of liquid properties is developed using a novel equivalent circuit approach. Experimental results are in agreement with theory when the liquid molecule size is larger than the average surface roughness. However, when the molecular size of the liquid is small relative to the surface roughness features molecules are trapped, and the trapped molecules act both as a mass load and viscous load; the result is higher viscous damping of the sensor than expected. c2002 Elsevier Science B.V. All rights reserved.

Binding energies of benzene on coinage metal surfaces: Equal stability on different metals

NASA Astrophysics Data System (ADS)

Maaß, Friedrich; Jiang, Yingda; Liu, Wei; Tkatchenko, Alexandre; Tegeder, Petra

2018-06-01

Interfaces between organic molecules and inorganic solids adapt a prominent role in fundamental science, catalysis, molecular sensors, and molecular electronics. The molecular adsorption geometry, which is dictated by the strength of lateral and vertical interactions, determines the electronic structure of the molecule/substrate system. In this study, we investigate the binding properties of benzene on the noble metal surfaces Au(111), Ag(111), and Cu(111), respectively, using temperature-programmed desorption and first-principles calculations that account for non-locality of both electronic exchange and correlation effects. In the monolayer regime, we observed for all three systems a decrease of the binding energy with increasing coverage due to repulsive adsorbate/adsorbate interactions. Although the electronic properties of the noble metal surfaces are rather different, the binding strength of benzene on these surfaces is equal within the experimental error (accuracy of 0.05 eV), in excellent agreement with our calculations. This points toward the existence of a universal trend for the binding energy of aromatic molecules resulting from a subtle balance between Pauli repulsion and many-body van der Waals attraction.

Cleaning Surface Particle Contamination with Ultrapure Water (UPW) Megasonic Flow on Genesis Array Collectors

NASA Technical Reports Server (NTRS)

Allton, J. H.; Calaway, Michael J.; Hittle, J. D.; Rodriquez, M. C.; Stansbery, E. K.; McNamara, K. M.

2006-01-01

The hard landing experienced by the Genesis sample return capsule breached the science canister containing the solar wind collectors. This impact into the damp lakebed contaminated collector surfaces with pulverized collector and spacecraft materials and Utah sediment and brine residue. The gold foil, polished aluminum, and bulk metallic glass remained intact, but the solar wind bulk and regime-specific array collectors were jarred loose from their frames and fractured into greater than 10,000 specimens. After a year of investigation and cleaning experimentation, the Genesis Science Team determined that array collectors had 4 classes of contaminants: particles, molecular film, submicron inorganic particulate ("aerosol"), and pre-launch surface contamination. We discuss here use of megasonically energized ultrapure water (UPW) for removing particulate debris from array collector fragments.

Coherent Control About a Conical Intersection

NASA Astrophysics Data System (ADS)

Liekhus-Schmaltz, Chelsea; McCracken, Gregory; Kaldun, Andreas; Cryan, James P.; Bucksbaum, Philip H.

2017-04-01

Conical intersections (CIs) are degeneracies between molecular potential energy surfaces that occur in essentially all molecules with more than three atoms. Many studies have established that CIs allow for non-Born-Oppenheimer (non-adiabatic) molecular dynamics. In addition, CIs have many useful attributes for coherent control that have not been fully studied. Here we demonstrate two modes of control around a CI that make use of these properties. The first method uses a continuous light field, resonant absorption, and stimulated emission to control the population on two intersecting electronic states. The second method uses a pulsed light field and the geometric phase accumulated by a wavepacket traversing a CI to control the shape of the wavepacket. This work was supported by the National Science Foundation under Grant No. PHY-0649578, the DOE SCGSR fellowship program, and the DOE, Office of Science, BES, Chemical Sciences, Geosciences, and Biosciences Division.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, Michael A.; Lyubinetsky, Igor

The field of heterogeneous photocatalysis has grown considerably in the decades since Fujishima and Honda's ground-breaking publications of photoelectrochemistry on TiO2. Numerous review articles continue to point to both progress made in the use of heterogeneous materials (such as TiO2) to perform photoconversion processes, and the many opportunities and challenges in heterogeneous photocatalysis research such as solar energy conversion and environmental remediation. The past decade has also seen an increase in the use of molecular-level approaches applied to model single crystal surfaces in an effort to obtain new insights into photocatalytic phenomena. In particular, scanning probe techniques (SPM) have enabledmore » researchers to take a ‘nanoscale’ approach to photocatalysis that includes interrogation of the reactivities of specific sites and adsorbates on a model photocatalyst surface. The rutile TiO2(110) surface has become the prototypical oxide single crystal surface for fundamental studies of many interfacial phenomena. In particular, TiO2(110) has become an excellent model surface for probing photochemical and photocatalytic reactions at the molecular level. A variety of experimental approaches have emerged as being ideally suited for studying photochemical reactions on TiO2(110), including desorption-oriented approaches and electronic spectroscopies, but perhaps the most promising techniques for evaluating site-specific properties are those of SPM. In this review, we highlight the growing use of SPM techniques in providing molecular-level insights into surface photochemistry on the model photocatalyst surface of rutile TiO2(110). Our objective is to both illustrate the unique knowledge that scanning probe techniques have already provided the field of photocatalysis, and also to motivate a new generation of effort into the use of such approaches to obtain new insights into the molecular level details of photochemical events occurring at interfaces. Discussion will start with an examination of how scanning probe techniques are being used to characterize the TiO2(110) surface in ways that are relevant to photocatalysis. We will then discuss specific classes of photochemical reaction on TiO2(110) for which SPM has proven indispensible in providing unique molecular-level insights, and conclude with discussion of future areas in which SPM studies may prove valuable to photocatalysis on TiO2. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. I.L. was partially supported by a Pacific Northwest National Laboratory (PNNL) Chemical Imaging Initiative project. PNNL is a multiprogram national laboratory operated for DOE by Battelle.« less

Virtual special issue on catalysis at the U.S. Department of Energy's National Laboratories

DOE PAGES

Pruski, Marek; Sadow, Aaron D.; Slowing, Igor I.; ...

2016-04-21

Here the catalysis research at the U.S. Department of Energy's (DOE's) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/molecular catalysis, biocatalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE's mission to ensure America's security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions.

Characterization of anti-theft devices directly from the surface of banknotes via easy ambient sonic spray ionization mass spectrometry.

PubMed

Schmidt, Eduardo Morgado; Franco, Marcos Fernando; Cuelbas, Claudio José; Zacca, Jorge Jardim; de Carvalho Rocha, Werickson Fortunato; Borges, Rodrigo; de Souza, Wanderley; Sawaya, Alexandra Christine Helena Frankland; Eberlin, Marcos Nogueira; Correa, Deleon Nascimento

2015-09-01

Using Brazilian banknotes as a test case, forensic examination and identification of Rhodamine B dye anti-theft device (ATD) staining on banknotes were performed. Easy ambient sonic spray ionization mass spectrometry (EASI-MS) was used since it allows fast and simple analysis with no sample preparation providing molecular screening of the surface with direct desorption and ionization of the security dye. For a more accurate molecular characterization of the ATD dye, Q Exactive Orbitrap™ Fourier transform (tandem) mass spectrometry using eletrospray ionization (ESI-HRMS/MS) was also applied. Copyright © 2015 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

On the Reaction Mechanism of Acetaldehyde Decomposition on Mo(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Donghai; Karim, Ayman M.; Wang, Yong

2012-02-16

The strong Mo-O bond strength provides promising reactivity of Mo-based catalysts for the deoxygenation of biomass-derived oxygenates. Combining the novel dimer saddle point searching method with periodic spin-polarized density functional theory calculations, we investigated the reaction pathways of a acetaldehyde decomposition on the clean Mo(110) surface. Two reaction pathways were identified, a selective deoxygenation and a nonselective fragmentation pathways. We found that acetaldehyde preferentially adsorbs at the pseudo 3-fold hollow site in the η2(C,O) configuration on Mo(110). Among four possible bond (β-C-H, γ-C-H, C-O and C-C) cleavages, the initial decomposition of the adsorbed acetaldehyde produces either ethylidene via the C-Omore » bond scission or acetyl via the β-C-H bond scission while the C-C and the γ-C-H bond cleavages of acetaldehyde leading to the formation of methyl (and formyl) and formylmethyl are unlikely. Further dehydrogenations of ethylidene into either ethylidyne or vinyl are competing and very facile with low activation barriers of 0.24 and 0.31 eV, respectively. Concurrently, the formed acetyl would deoxygenate into ethylidyne via the C-O cleavage rather than breaking the C-C or the C-H bonds. The selective deoxygenation of acetaldehyde forming ethylene is inhibited by relatively weaker hydrogenation capability of the Mo(110) surface. Instead, the nonselective pathway via vinyl and vinylidene dehydrogenations to ethynyl as the final hydrocarbon fragment is kinetically favorable. On the other hand, the strong interaction between ethylene and the Mo(110) surface also leads to ethylene decomposition instead of desorption into the gas phase. This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). The EMSL is a U.S. Department of Energy (DOE) national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and supported by the DOE Office of Biological and Environmental Research. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Effect of Aging and Surface Interactions on the Diffusion of Endogenous Compounds in Latent Fingerprints Studied by Mass Spectrometry Imaging.

PubMed

O'Neill, Kelly C; Lee, Young Jin

2018-05-01

The ability to determine the age of fingerprints would be immeasurably beneficial in criminal investigations. We explore the possibility of determining the age of fingerprints by analyzing various compounds as they diffuse from the ridges to the valleys of fingerprints using matrix-assisted laser desorption/ionization mass spectrometry imaging. The diffusion of two classes of endogenous fingerprint compounds, fatty acids and triacylglycerols (TGs), was studied in fresh and aged fingerprints on four surfaces. We expected higher molecular weight TGs would diffuse slower than fatty acids and allow us to determine the age of older fingerprints. However, we found interactions between endogenous compounds and the surface have a much stronger impact on diffusion than molecular weight. For example, diffusion of TGs is faster on hydrophilic plain glass or partially hydrophilic stainless steel surfaces, than on a hydrophobic Rain-x treated surface. This result further complicates utilizing a diffusion model to age fingerprints. © 2017 American Academy of Forensic Sciences.

Next Generation LOCAD-PTS Cartridge Development

NASA Technical Reports Server (NTRS)

Morris, H.; Nutter, D.; Weite, E.; Wells, M.; Maule, J.; Damon, M.; Monaco, L.; Steele, A.; Wainwright, N.

2008-01-01

Future astrobiology exploration missions will require rapid, point-of-use techniques for surface science experiments and contamination monitoring. The Lab-On-a-Chip Application Development (LOCAD) team is developing operational instruments that advance spaceflight technologies to molecular-based methods. Currently, LOCAD-Portable Test System (PTS) is quantifying levels of the bacterial molecule endotoxin onboard the Internatioal Space Station. Future research and development will focus on more sensitive molecular techniques that expand the number of compounds detected to include beta-glucan from fungal cell walls.

Sensor for the working surface cleanliness definition in vacuum

NASA Astrophysics Data System (ADS)

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.

Plasmon Resonance Methods in GPCR Signaling and Other Membrane Events

PubMed Central

Alves, I.D.; Park, C.K.; Hruby, V.J.

2005-01-01

The existence of surface guided electromagnetic waves has been theoretically predicted from Maxwell’s equations and investigated during the first decades of the 20th century. However, it is only since the late 1960’s that they have attracted the interest of surface physicists and earned the moniker of “surface plasmon”. With the advent of commercially available instruments and well established theories, the technique has been used to study a wide variety of biochemical and biotechnological phenomena. Spectral response of the resonance condition serves as a sensitive indicator of the optical properties of thin films immobilized within a wavelength of the surface. This enhanced surface sensitivity has provided a boon to the surface sciences, and fosters collaboration between surface chemistry, physics and the ongoing biological and biotechnological revolution. Since then, techniques based on surface plasmons such as Surface Plasmon Resonance (SPR), SPR Imaging, Plasmon Waveguide Resonance (PWR) and others, have been increasingly used to determine the affinity and kinetics of a wide variety of real time molecular interactions such as protein-protein, lipid-protein and ligand-protein, without the need for a molecular tag or label. The physical-chemical methodologies used to immobilize membranes at the surface of these optical devices are reviewed, pointing out advantages and limitations of each method. The paper serves to summarize both historical and more recent developments of these technologies for investigating structure-function aspects of these molecular interactions, and regulation of specific events in signal transduction by G-protein coupled receptors (GPCRs). PMID:16101432

Reactivity of Hydrogen and Methanol on (001) Surfaces of WO3, ReO3, WO3/ReO3 and ReO3/WO3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ling, Sanliang; Mei, Donghai; Gutowski, Maciej S.

2011-05-16

Bulk tungsten trioxide (WO3) and rhenium trioxide (ReO3) share very similar structures but display different electronic properties. WO3 is a wide bandgap semiconductor while ReO3 is an electronic conductor. With the advanced molecular beam epitaxy techniques, it is possible to make heterostructures comprised of layers of WO3 and ReO3. These heterostructures might display reactivity different than pure WO3 and ReO3. The interactions of two probe molecules (hydrogen and methanol) with the (001) surfaces of WO3, ReO3, and two heterostructures ReO3/WO3 and WO3/ReO3 were investigated at the density functional theory level. Atomic hydrogen prefers to adsorb at the terminal O1C sitesmore » forming a surface hydroxyl on four surfaces. Dissociative adsorption of a hydrogen molecule at the O1C site leads to formation of a water molecule adsorbed at the surface M5C site. This is thermodynamically the most stable state. A thermodynamically less stable dissociative state involves two surface hydroxyl groups O1CH and O2CH. The interaction of molecular hydrogen and methanol with pure ReO3 is stronger than with pure WO3 and the strength of the interaction substantially changes on the WO3/ReO3 and ReO3/WO3 heterostructures. The reaction barriers for decomposition and recombination reactions are sensitive to the nature of heterostructure. The calculated adsorption energy of methanol on WO3(001) of -65.6 kJ/mol is consistent with the previous experimental estimation of -67 kJ/mol. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.« less

Molecular origin of contact line stick-slip motion during droplet evaporation

PubMed Central

Wang, FengChao; Wu, HengAn

2015-01-01

Understanding and controlling the motion of the contact line is of critical importance for surface science studies as well as many industrial engineering applications. In this work, we elucidate the molecular origin of contact line stick-slip motion during the evaporation of liquid droplets on flexible nano-pillared surfaces using molecular dynamics simulations. We demonstrate that the evaporation-induced stick-slip motion of the contact line is a consequence of competition between pinning and depinning forces. Furthermore, the tangential force exerted by the pillared substrate on the contact line was observed to have a sawtooth-like oscillation. Our analysis also establishes that variations in the pinning force are accomplished through the self-adaptation of solid-liquid intermolecular distances, especially for liquid molecules sitting directly on top of the solid pillar. Consistent with our theoretical analysis, molecular dynamics simulations also show that the maximum pinning force is quantitatively related to both solid-liquid adhesion strength and liquid-vapor surface tension. These observations provide a fundamental understanding of contact line stick-slip motion on pillared substrates and also give insight into the microscopic interpretations of contact angle hysteresis, wetting transitions and dynamic spreading. PMID:26628084

Interpreting Vibrational Sum-frequency Spectra of Sulfur Dioxide at the Air/Water Interface: A Comprehensive Molecular Dynamics Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baer, Marcel; Mundy, Christopher J.; Chang, Tsun-Mei

We investigated the solvation and spectroscopic properties of SO2 at the air/water interface using molecular simulation techniques. Molecular interactions from both Kohn-Sham (KS) density functional theory (DFT) and classical polarizable models were utilized to understand the properties of SO2:(H2O)x complexes in the vicinity of the air/water interface. The KS-DFT was included to allow comparisons with sum-frequency generation spectroscopy through the identification of surface SO2:(H2O)x complexes. Using our simulation results, we were able to develop a much more detailed picture for the surface structure of SO2 that is consistent with the spectroscopic data obtained Richmond and coworkers (J. Am. Chem. Soc.more » 127, 16806 (2005)). We also found many similarities and differences between to the two interaction potentials, including a noticeable weakness of the classical potential model in reproducing the asymmetric hydrogen bonding of water with SO2 due to its inability to account for SO2 resonance structures. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

What Controls Thermo-osmosis? Molecular Simulations Show the Critical Role of Interfacial Hydrodynamics

NASA Astrophysics Data System (ADS)

Fu, Li; Merabia, Samy; Joly, Laurent

2017-11-01

Thermo-osmotic and related thermophoretic phenomena can be found in many situations from biology to colloid science, but the underlying molecular mechanisms remain largely unexplored. Using molecular dynamics simulations, we measure the thermo-osmosis coefficient by both mechanocaloric and thermo-osmotic routes, for different solid-liquid interfacial energies. The simulations reveal, in particular, the crucial role of nanoscale interfacial hydrodynamics. For nonwetting surfaces, thermo-osmotic transport is largely amplified by hydrodynamic slip at the interface. For wetting surfaces, the position of the hydrodynamic shear plane plays a key role in determining the amplitude and sign of the thermo-osmosis coefficient. Finally, we measure a giant thermo-osmotic response of the water-graphene interface, which we relate to the very low interfacial friction displayed by this system. These results open new perspectives for the design of efficient functional interfaces for, e.g., waste-heat harvesting.

What Controls Thermo-osmosis? Molecular Simulations Show the Critical Role of Interfacial Hydrodynamics.

PubMed

Fu, Li; Merabia, Samy; Joly, Laurent

2017-11-24

Thermo-osmotic and related thermophoretic phenomena can be found in many situations from biology to colloid science, but the underlying molecular mechanisms remain largely unexplored. Using molecular dynamics simulations, we measure the thermo-osmosis coefficient by both mechanocaloric and thermo-osmotic routes, for different solid-liquid interfacial energies. The simulations reveal, in particular, the crucial role of nanoscale interfacial hydrodynamics. For nonwetting surfaces, thermo-osmotic transport is largely amplified by hydrodynamic slip at the interface. For wetting surfaces, the position of the hydrodynamic shear plane plays a key role in determining the amplitude and sign of the thermo-osmosis coefficient. Finally, we measure a giant thermo-osmotic response of the water-graphene interface, which we relate to the very low interfacial friction displayed by this system. These results open new perspectives for the design of efficient functional interfaces for, e.g., waste-heat harvesting.

Use of radiation in biomaterials science

NASA Astrophysics Data System (ADS)

Benson, Roberto S.

2002-05-01

Radiation is widely used in the biomaterials science for surface modification, sterilization and to improve bulk properties. Radiation is also used to design of biochips, and in situ photopolymerizable of bioadhesives. The energy sources most commonly used in the irradiation of biomaterials are high-energy electrons, gamma radiation, ultraviolet (UV) and visible light. Surface modification involves placement of selective chemical moieties on the surface of a material by chemical reactions to improve biointeraction for cell adhesion and proliferation, hemocompatibility and water absorption. The exposure of a polymer to radiation, especially ionizing radiation, can lead to chain scission or crosslinking with changes in bulk and surface properties. Sterilization by irradiation is designed to inactivate most pathogens from the surface of biomedical devices. An overview of the use of gamma and UV radiation to improve surface tissue compatibility, bulk properties and surface properties for wear resistance, formation of hydrogels and curing dental sealants and bone adhesives is presented. Gamma and vacuum ultraviolet (VUV) irradiated ultrahigh molecular weight polyethylene (UHMWPE) exhibit improvement in surface modulus and hardness. The surface modulus and hardness of UHMWPE showed a dependence on type of radiation, dosage and processing. VUV surface modified e-PTFE vascular grafts exhibit increases in hydrophilicity and improvement towards adhesion of fibrin glue.

Gas/Surface Interaction Study Applied to Si-based Materials Used in Driven Micro- and Nano-scale Devices

DTIC Science & Technology

2010-01-01

science and engineering. For example, by measuring the frequency shift of sensor oscillations, one can measure gas adsorption on the sensor surface...free-molecular regime with varied gas pressure. The measurement path of the experimental setup is schematically shown in Fig. 3.1. The sensor is...excited by the electric field between the sensor and fixed electrode by means of a specially designed system of self-induced oscillations. The

First-principles characterization of formate and carboxyl adsorption on the stoichiometric CeO2(111) and CeO2(110) surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Donghai

2013-05-20

Molecular adsorption of formate and carboxyl on the stoichiometric CeO2(111) and CeO2(110) surfaces was studied using periodic density functional theory (DFT+U) calculations. Two distinguishable adsorption modes (strong and weak) of formate are identified. The bidentate configuration is more stable than the monodentate adsorption configuration. Both formate and carboxyl bind at the more open CeO2(110) surface are stronger. The calculated vibrational frequencies of two adsorbed species are consistent with experimental measurements. Finally, the effects of U parameters on the adsorption of formate and carboxyl over both CeO2 surfaces were investigated. We found that the geometrical configurations of two adsorbed species aremore » not affected by using different U parameters (U=0, 5, and 7). However, the calculated adsorption energy of carboxyl pronouncedly increases with the U value while the adsorption energy of formate only slightly changes (<0.2 eV). The Bader charge analysis shows the opposite charge transfer occurs for formate and carboxyl adsorption where the adsorbed formate is negatively charge whiled the adsorbed carboxyl is positively charged. Interestingly, with the increasing U parameter, the amount of charge is also increased. This work was supported by the Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL) and by a Cooperative Research and Development Agreement (CRADA) with General Motors. The computations were performed using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington. Part of the computing time was also granted by the National Energy Research Scientific Computing Center (NERSC)« less

Experimental methods of molecular matter-wave optics.

PubMed

Juffmann, Thomas; Ulbricht, Hendrik; Arndt, Markus

2013-08-01

We describe the state of the art in preparing, manipulating and detecting coherent molecular matter. We focus on experimental methods for handling the quantum motion of compound systems from diatomic molecules to clusters or biomolecules.Molecular quantum optics offers many challenges and innovative prospects: already the combination of two atoms into one molecule takes several well-established methods from atomic physics, such as for instance laser cooling, to their limits. The enormous internal complexity that arises when hundreds or thousands of atoms are bound in a single organic molecule, cluster or nanocrystal provides a richness that can only be tackled by combining methods from atomic physics, chemistry, cluster physics, nanotechnology and the life sciences.We review various molecular beam sources and their suitability for matter-wave experiments. We discuss numerous molecular detection schemes and give an overview over diffraction and interference experiments that have already been performed with molecules or clusters.Applications of de Broglie studies with composite systems range from fundamental tests of physics up to quantum-enhanced metrology in physical chemistry, biophysics and the surface sciences.Nanoparticle quantum optics is a growing field, which will intrigue researchers still for many years to come. This review can, therefore, only be a snapshot of a very dynamical process.

3D metamaterial absorber for attomole molecular detection (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tanaka, Takuo; Ishikawa, Atsushi

2016-09-01

3D Metamaterial absorber was used for a background-suppressed surface-enhanced molecular detection technique. By utilizing the resonant coupling of plasmonic modes of a metamaterial absorber and infrared (IR) vibrational modes of a self-assembled monolayer (SAM), attomole level molecular sensitivity was experimentally demonstrated. IR absorption spectroscopy of molecular vibrations is of importance in chemical, material, medical science and so on, since it provides essential information of the molecular structure, composition, and orientation. In the vibrational spectroscopic techniques, in addition to the weak signals from the molecules, strong background degrades the signal-to-noise ratio, and suppression of the background is crucial for the further improvement of the sensitivity. Here, we demonstrate low-background resonant Surface enhanced IR absorption (SEIRA) by using the metamaterial IR absorber that offers significant background suppression as well as plasmonic enhancement. The fabricated metamaterial consisted of 1D array of Au micro-ribbons on a thick Au film separated by a transparent gap layer made of MgF2. The surface structures were designed to exhibit an anomalous IR absorption at 3000 cm-1, which spectrally overlapped with C-H stretching vibrational modes. 16-Mercaptohexadecanoic acid (16-MHDA) was used as a test molecule, which formed a 2-nm thick SAM with their thiol head-group chemisorbed on the Au surface. In the FTIR measurements, the symmetric and asymmetric C-H stretching modes were clearly observed as reflection peaks within a broad plasmonic absorption of the metamaterial.

Promotional effect of surface hydroxyls on electrochemical reduction of CO2 over SnOx/Sn electrode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Chaonan; Han, Jinyu; Zhu, Xinli

Tin oxide (SnOx) formation on tin-based electrode surfaces during CO2 electrochemical reduction can have a significant impact on the activity and selectivity of the reaction. In the present study, density functional theory (DFT) calculations have been performed to understand the role of SnOx in CO2 reduction using a SnO monolayer on the Sn(112) surface as a model for SnOx. Water molecules have been treated explicitly and considered actively participating in the reaction. The results showed that H2O dissociates on the perfect SnO monolayer into two hydroxyl groups symmetrically on the surface. CO2 energetically prefers to react with the hydroxyl, formingmore » a bicarbonate (HCO3(t)*) intermediate, which can then be reduced to either formate (HCOO*) by hydrogenating the carbon atom or carboxyl (COOH*) by protonating the oxygen atom. Both steps involve a simultaneous C-O bond breaking. Further reduction of HCOO* species leads to the formation of formic acid in the acidic solution at pH < 4, while the COOH* will decompose to CO and H2O via protonation. Whereas the oxygen vacancy (VO) in the monolayer maybe formed by the reduction of the monolayer, it can be recovered by H2O dissociation, resulting in two embedded hydroxyl groups. However, the hydroxylated surface with two symmetric hydroxyls is energetically more favorable for CO2 reduction than the hydroxylated VO surface with two embedded hydroxyls. The reduction potential for the former has a limiting-potential of -0.20 V (RHE), lower than that for the latter (-0.74 V (RHE)). Compared to the pure Sn electrode, the formation of SnOx monolayer on the electrode under the operating conditions promotes CO2 reduction more effectively by forming surface hydroxyls, thereby, providing a new channel via COOH* to the CO formation, although formic acid is still the major reduction product. The work was supported in part by National Natural Sciences Foundation of China (Grant #21373148 and #21206117). The High Performance Computing Center of Tianjin University is acknowledged for providing services to the computing cluster. CC acknowledges the support of 24 China Scholarship Council (CSC). QG acknowledges the support of NSF-CBET program (Award no. CBET-1438440). DM was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. The computations were performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory (PNNL) in Richland, Washington.« less

Preface to the Surface Science Topical Issue on Chirality at Surfaces

NASA Astrophysics Data System (ADS)

2014-11-01

This Topical Issue of Surface Science focuses on the rapidly growing interest in the structure and enantioselective properties of chiral surfaces and chiral organic layers on surfaces. Chirality has intrigued scientists since the time of Pasteur and his 1848 [1] demonstration of the relationship between the optical rotation of light and the atomic structure of the compounds through which it propagates. The origin of optical rotation in the structure of organic molecules and the tetrahedral nature of the carbon atom was first appreciated and articulated by van't Hoff in 1874 [2]. In biochemistry, the importance of molecular chirality arises from the fact that most naturally occurring chiral biomolecules exist in homochiral form. For example, the fundamental building blocks of proteins are the amino acids which all appear in the L-enantiomeric form in nature. The implications of biomolecular homochirality were not truly appreciated until the late 1950s [3] when the stereochemistry of the artificially produced drug thalidomide was implicated in the physical defects observed in thousands of children born to mothers who had used the drug during pregnancy. This then sparked an explosion in asymmetric synthesis and enantioselective chemical processing in general, as regulations required that chiral pharmaceuticals be manufactured in enantiomerically pure form. The development of heterogenous catalysts for industrial-scale production of enantiomerically pure molecules is still a huge challenge. Many of the studies in this Topical Issue are aimed at developing a molecular level understanding of the surface processes which direct enantioselective reactions at gas-solid and liquid-solid interfaces.

Momentum-Space Imaging of the Dirac Band Structure in Molecular Graphene via Quasiparticle Interference

NASA Astrophysics Data System (ADS)

Stephenson, Anna; Gomes, Kenjiro K.; Ko, Wonhee; Mar, Warren; Manoharan, Hari C.

2014-03-01

Molecular graphene is a nanoscale artificial lattice composed of carbon monoxide molecules arranged one by one, realizing a dream of exploring exotic quantum materials by design. This assembly is done by atomic manipulation with a scanning tunneling microscope (STM) on a Cu(111) surface. To directly probe the transformation of normal surface state electrons into massless Dirac fermions, we map the momentum space dispersion through the Fourier analysis of quasiparticle scattering maps acquired at different energies with the STM. The Fourier analysis not only bridges the real-space and momentum-space data but also reveals the chiral nature of those quasiparticles, through a set of selection rules of allowed scattering involving the pseudospin and valley degrees of freedom. The graphene-like band structure can be reshaped with simple alterations to the lattice, such as the addition of a strain. We analyze the effect on the momentum space band structure of multiple types of strain on our system. Supported by DOE, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under contract DE-AC02-76SF00515.

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prakash, Arushi; Baer, Marcel D.; Mundy, Christopher J.

Peptoids are peptide-mimetic biopolymers that are easy-to-synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semi-empirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with amore » hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids towards these conformations. ACKNOWLEDGMENT: MD simulations and manuscript preparation were supported by the MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory (PNNL), a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. CJM was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by the US Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. Computing resources were generously allocated by University of Washington's IT department and PNNL's Institutional Computing program. The authors greatly acknowledge conversations with Dr. Kayla Sprenger, Josh Smith, and Dr. Yeneneh Yimer.« less

Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems.

PubMed

Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; Kestell, John D; Boscoboinik, Alejandro M; Kim, Taejin; Stacchiola, Dario J; Lu, Deyu; Boscoboinik, J Anibal

2017-07-17

The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. In this work, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, the permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. These findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.

Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems

DOE PAGES

Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; ...

2017-07-17

The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. Here, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, themore » permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. Our findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.« less

Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin

The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. Here, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, themore » permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. Our findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.« less

Recent advances on polyoxometalate-based molecular and composite materials.

PubMed

Song, Yu-Fei; Tsunashima, Ryo

2012-11-21

Polyoxometalates (POMs) are a subset of metal oxides with unique physical and chemical properties, which can be reliably modified through various techniques and methods to develop sophisticated materials and devices. In parallel with the large number of new crystal structures reported in the literature, the application of these POMs towards multifunctional materials has attracted considerable attention. This critical review summarizes recent progress on POM-based molecular and composite materials, and particularly highlights the emerging areas that are closely related to surface, electronic, energy, environment, life science, etc. (171 references).

Effects of Hydration and Oxygen Vacancy on CO2 Adsorption and Activation on β-Ga2O3(100)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Yunxiang; Liu, Chang-jun; Mei, Donghai

The effects of hydration and oxygen vacancy on CO2 adsorption on the β-Ga2O3(100) surface have been studied using density functional theory slab calculations. Adsorbed CO2 is activated on the dry perfect β-Ga2O3(100) surface, resulting in a carbonate species. This adsorption is slightly endothermic, with an adsorption energy of 0.07 eV. Water is preferably adsorbed molecularly on the dry perfect β-Ga2O3(100) surface with an adsorption energy of -0.56 eV, producing a hydrated perfect β-Ga2O3(100) surface. Adsorption of CO2 on the hydrated surface as a carbonate species is also endothermic, with an adsorption energy of 0.14 eV, indicating a slight repulsive interactionmore » when H2O and CO2 are coadsorbed. The carbonate species on the hydrated perfect surface can be protonated by the co-adsorbed H2O to a bicarbonate species, making the overall process exothermic with an adsorption energy of -0.13 eV. The effect of defects on CO2 adsorption and activation has been examined by creating an oxygen vacancy on the dry β-Ga2O3(100) surface. The formation of an oxygen vacancy is endothermic, by 0.34 eV, with respect to a free O2 molecule in the gas phase. Presence of the oxygen vacancy promoted the adsorption and activation of CO2. In the most stable CO2 adsorption configuration on the dry defective β-Ga2O3(100) surface with an oxygen vacancy, one of the oxygen atoms of the adsorbed CO2 occupies the oxygen vacancy site and the CO2 adsorption energy is -0.31 eV. Water favors dissociative adsorption at the oxygen vacancy site on the defective surface. This process is instantaneous with an adsorption energy of -0.62 eV. These results indicate that, when water and CO2 are both present in the adsorption system simultaneously, the water molecule will compete with CO2 for the oxygen vacancy sites and impact CO2 adsorption and conversion negatively. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy. A portion of the computing time was granted by the scientific user projects using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). The EMSL is a DOE national scientific user facility located at PNNL, and supported by the DOE’s Office of Science, Biological and Environmental Research.« less

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

PubMed

Serna, Pedro; Gates, Bruce C

2014-08-19

Recent advances in the synthesis and characterization of small, essentially molecular metal complexes and metal clusters on support surfaces have brought new insights to catalysis and point the way to systematic catalyst design. We summarize recent work unraveling effects of key design variables of site-isolated catalysts: the metal, metal nuclearity, support, and other ligands on the metals, also considering catalysts with separate, complementary functions on supports. The catalysts were synthesized with the goal of structural simplicity and uniformity to facilitate incisive characterization. Thus, they are essentially molecular species bonded to porous supports chosen for their high degree of uniformity; the supports are crystalline aluminosilicates (zeolites) and MgO. The catalytic species are synthesized in reactions of organometallic precursors with the support surfaces; the precursors include M(L)2(acetylacetonate)1-2, with M = Ru, Rh, Ir, or Au and the ligands L = C2H4, CO, or CH3. Os3(CO)12 and Ir4(CO)12 are used as precursors of supported metal clusters, and some such catalysts are made by ship-in-a-bottle syntheses to trap the clusters in zeolite cages. The simplicity and uniformity of the supported catalysts facilitate precise structure determinations, even in reactive atmospheres and during catalysis. The methods of characterizing catalysts in reactive atmospheres include infrared (IR), extended X-ray absorption fine structure (EXAFS), X-ray absorption near edge structure (XANES), and nuclear magnetic resonance (NMR) spectroscopies, and complementary methods include density functional theory and atomic-resolution aberration-corrected scanning transmission electron microscopy for imaging of individual metal atoms. IR, NMR, XANES, and microscopy data demonstrate the high degrees of uniformity of well-prepared supported species. The characterizations determine the compositions of surface metal complexes and clusters, including the ligands and the metal-support bonding and structure, which identify the supports as ligands with electron-donor properties that influence reactivity and catalysis. Each of the catalyst design variables has been varied independently, illustrated by mononuclear and tetranuclear iridium on zeolite HY and on MgO and by isostructural rhodium and iridium (diethylene or dicarbonyl) complexes on these supports. The data provide examples resolving the roles of the catalyst design variables and place the catalysis science on a firm foundation of organometallic chemistry linked with surface science. Supported molecular catalysts offer the advantages of characterization in the absence of solvents and with surface-science methods that do not require ultrahigh vacuum. Families of supported metal complexes have been made by replacement of ligands with others from the gas phase. Spectroscopically identified catalytic reaction intermediates help to elucidate catalyst performance and guide design. The methods are illustrated for supported complexes and clusters of rhodium, iridium, osmium, and gold used to catalyze reactions of small molecules that facilitate identification of the ligands present during catalysis: alkene dimerization and hydrogenation, H-D exchange in the reaction of H2 with D2, and CO oxidation. The approach is illustrated with the discovery of a highly active and selective MgO-supported rhodium carbonyl dimer catalyst for hydrogenation of 1,3-butadiene to give butenes.

Sliding friction between polymer surfaces: A molecular interpretation

NASA Astrophysics Data System (ADS)

Allegra, Giuseppe; Raos, Guido

2006-04-01

For two contacting rigid bodies, the friction force F is proportional to the normal load and independent of the macroscopic contact area and relative velocity V (Amonton's law). With two mutually sliding polymer samples, the surface irregularities transmit deformation to the underlying material. Energy loss along the deformation cycles is responsible for the friction force, which now appears to depend strongly on V [see, e.g., N. Maeda et al., Science 297, 379 (2002)]. We base our theoretical interpretation on the assumption that polymer chains are mainly subjected to oscillatory "reptation" along their "tubes." At high deformation frequencies—i.e., with a large sliding velocity V—the internal viscosity due to the rotational energy barriers around chain bonds hinders intramolecular mobility. As a result, energy dissipation and the correlated friction force strongly diminish at large V. Derived from a linear differential equation for chain dynamics, our results are basically consistent with the experimental data by Maeda et al. [Science 297, 379 (2002)] on modified polystyrene. Although the bulk polymer is below Tg, we regard the first few chain layers below the surface to be in the liquid state. In particular, the observed maximum of F vs V is consistent with physically reasonable values of the molecular parameters. As a general result, the ratio F /V is a steadily decreasing function of V, tending to V-2 for large velocities. We evaluate a much smaller friction for a cross-linked polymer under the assumption that the junctions are effectively immobile, also in agreement with the experimental results of Maeda et al. [Science 297, 379 (2002)].

The Composition of Titan's Lower Atmosphere and Simple Surface Volatiles as Measured by the Cassini-Huygens Probe Gas Chromatograph Mass Spectrometer Experiment

NASA Technical Reports Server (NTRS)

Niemann, H. B.; Atreya, S. K.; Demick, J. E.; Gautier, D.; Haberman, J. A.; Harpold, D. N.; Kasprzak, W. T.; Lunine, J. I.; Owen, T. C.; Raulin, F.

2010-01-01

The Cassini-Huygens Probe Gas Chromatograph Mass Spectrometer (GCMS) determined the composition of the Titan atmosphere from 140km altitude to the surface. After landing, it returned composition data of gases evaporated from the surface. Height profiles of molecular nitrogen (N2), methane (CH4) and molecular hydrogen (H2) were determined. Traces were detected on the surface of evaporating methane, ethane (C2H6), acetylene (C2H2), cyanogen (C2N2) and carbon dioxide (CO2). The methane data showed evidence that methane precipitation occurred recently. The methane mole fraction was (1.48+/-0.09) x 10(exp -2) in the lower stratosphere (139.8 km to 75.5 km) and (5.65+/-0.18) x 10(exp -2) near the surface (6.7 km to the surface). The molecular hydrogen mole fraction was (1.01+/-0.16) x 10(exp -3) in the atmosphere and (9.90+/-0.17) x 10(exp -4) on the surface. Isotope ratios were 167.7+/-0.6 for N-14/N-15 in molecular nitrogen, 91.1+/-1.4 for C-12/C-13 in methane and (1.35+/-0.30) x 10(exp -4) for D/H in molecular hydrogen. The mole fractions of Ar-36 and radiogenic Ar-40 are (2.1+/-0.8) x 10(exp -7) and (3.39 +/-0.12) x 10(exp -5) respectively. Ne-22 has been tentatively identified at a mole fraction of (2.8+/-2.1) x 10(exp -7) Krypton and xenon were below the detection threshold of 1 x 10(exp -8) mole fraction. Science data were not retrieved from the gas chromatograph subsystem as the abundance of the organic trace gases in the atmosphere and on the ground did not reach the detection threshold. Results previously published from the GCMS experiment are superseded by this publication.

High-Resolution Structural and Electronic Properties of Epitaxial Topological Crystalline Insulator Films

NASA Astrophysics Data System (ADS)

Dagdeviren, Omur; Zhou, Chao; Zou, Ke; Simon, Georg; Albright, Stephen; Mandal, Subhasish; Morales-Acosta, Mayra; Zhu, Xiaodong; Ismail-Beigi, Sohrab; Walker, Frederick; Ahn, Charles; Schwarz, Udo; Altman, Eric

Revealing the local electronic properties of surfaces and their link to structural properties is an important problem for topological crystalline insulators (TCI) in which metallic surface states are protected by crystal symmetry. The microstructure and electronic properties of TCI SnTe film surfaces grown by molecular beam epitaxy were characterized using scanning probe microscopy. These results reveal the influence of various defects on the electronic properties: tilt boundaries leading to dislocation arrays that serve as periodic nucleation sites for pit growth; screw dislocations, and point defects. These features have varying length scale and display variations in the electronic structure of the surface, which are mapped with scanning tunneling microscopy images as standing waves superimposed on atomic scale images of the surface topography that consequently shape the wave patterns. Since the growth process results in symmetry breaking defects that patterns the topological states, we propose that the scanning probe tip can pattern the surface and electronic structure and enable the fabrication of topological devices on the SnTe surface. Financial support from the National Science Foundation through the Yale Materials Research Science and Engineering Center (Grant No. MRSEC DMR-1119826) and FAME.

Computer-aided design of polymers and composites

NASA Technical Reports Server (NTRS)

Kaelble, D. H.

1985-01-01

This book on computer-aided design of polymers and composites introduces and discusses the subject from the viewpoint of atomic and molecular models. Thus, the origins of stiffness, strength, extensibility, and fracture toughness in composite materials can be analyzed directly in terms of chemical composition and molecular structure. Aspects of polymer composite reliability are considered along with characterization techniques for composite reliability, relations between atomic and molecular properties, computer aided design and manufacture, polymer CAD/CAM models, and composite CAD/CAM models. Attention is given to multiphase structural adhesives, fibrous composite reliability, metal joint reliability, polymer physical states and transitions, chemical quality assurance, processability testing, cure monitoring and management, nondestructive evaluation (NDE), surface NDE, elementary properties, ionic-covalent bonding, molecular analysis, acid-base interactions, the manufacturing science, and peel mechanics.

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

PubMed

Ströhle, Alexander; Döring, Frank

2010-10-01

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

Workshop on High-Field NMR and Biological Applications

NASA Astrophysics Data System (ADS)

Scientists at the Pacific Northwest Laboratory have been working toward the establishment of a new Molecular Science Research Center (MSRC). The primary scientific thrust of this new research center is in the areas of theoretical chemistry, chemical dynamics, surface and interfacial science, and studies on the structure and interactions of biological macromolecules. The MSRC will provide important new capabilities for studies on the structure of biological macromolecules. The MSRC program includes several types of advanced spectroscopic techniques for molecular structure analysis, and a theory and modeling laboratory for molecular mechanics/dynamics calculations and graphics. It is the goal to closely integrate experimental and theoretical studies on macromolecular structure, and to join these research efforts with those of the molecular biological programs to provide new insights into the structure/function relationships of biological macromolecules. One of the areas of structural biology on which initial efforts in the MSRC will be focused is the application of high field, 2-D NMR to the study of biological macromolecules. First, there is interest in obtaining 3-D structural information on large proteins and oligonucleotides. Second, one of the primary objectives is to closely link theoretical approaches to molecular structure analysis with the results obtained in experimental research using NMR and other spectroscopies.

Supramolecular chemistry at interfaces: host-guest interactions for fabricating multifunctional biointerfaces.

PubMed

Yang, Hui; Yuan, Bin; Zhang, Xi; Scherman, Oren A

2014-07-15

CONSPECTUS: Host-guest chemistry can greatly improve the selectivity of biomolecule-ligand binding on account of recognition-directed interactions. In addition, functional structures and the actuation of supramolecular assemblies in molecular systems can be controlled efficiently through various host-guest chemistry. Together, these highly selective, strong yet dynamic interactions can be exploited as an alternative methodology for applications in the field of programmable and controllable engineering of supramolecular soft materials through the reversible binding between complementary components. Many processes in living systems such as biotransformation, transportation of matter, and energy transduction begin with interfacial molecular recognition, which is greatly influenced by various external stimuli at biointerfaces. Detailed investigations about the molecular recognition at interfaces can result in a better understanding of life science, and further guide us in developing new biomaterials and medicines. In order to mimic complicated molecular-recognition systems observed in nature that adapt to changes in their environment, combining host-guest chemistry and surface science is critical for fabricating the next generation of multifunctional biointerfaces with efficient stimuli-responsiveness and good biocompatibility. In this Account, we will summarize some recent progress on multifunctional stimuli-responsive biointerfaces and biosurfaces fabricated by cyclodextrin- or cucurbituril-based host-guest chemistry and highlight their potential applications including drug delivery, bioelectrocatalysis, and reversible adsorption and resistance of peptides, proteins, and cells. In addition, these biointerfaces and biosurfaces demonstrate efficient response toward various external stimuli, such as UV light, pH, redox chemistry, and competitive guests. All of these external stimuli can aid in mimicking the biological stimuli evident in complex biological environments. We begin by reviewing the current state of stimuli-responsive supramolecular assemblies formed by host-guest interactions, discussing how to transfer host-guest chemistry from solution onto surfaces required for fabricating multifunctional biosurfaces and biointerfaces. Then, we present different stimuli-responsive biosurfaces and biointerfaces, which have been prepared through a combination of cyclodextrin- or cucurbituril-based host-guest chemistry and various surface technologies such as self-assembled monolayers or layer-by-layer assembly. Moreover, we discuss the applications of these biointerfaces and biosurfaces in the fields of drug release, reversible adsorption and release of some organic molecules, peptides, proteins, and cells, and photoswitchable bioelectrocatalysis. In addition, we summarize the merits and current limitations of these methods for fabricating multifunctional stimuli-responsive biointerfaces in a dynamic noncovalent manner. Finally, we present possible strategies for future designs of stimuli-responsive multifunctional biointerfaces and biosurfaces by combining host-guest chemistry with surface science, which will lead to further critical development of supramolecular chemistry at interfaces.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruski, Marek; Sadow, Aaron D.; Slowing, Igor I.

Catalysis research at the U.S. Department of Energy's (DOE's) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/molecular catalysis, biocatalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE's mission to ensure America's security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. The catalysis research carried out at the DOE National Laboratories ranges from very fundamental catalysis science, funded by DOE's Office of Basic Energy Sciences (BES), to applied research and development (R&D)more » in areas such as biomass conversion to fuels and chemicals, fuel cells, and vehicle emission control with primary funding from DOE's Office of Energy Efficiency and Renewable Energy.« less

Introduction

NASA Astrophysics Data System (ADS)

2014-12-01

This special issue of Applied Surface Science is a compilation of papers inspired by the symposium on "Surface/Interfaces Characterization and Renewable Energy" held at the 2013 MRS Fall Meeting. Practical uses of renewable energy are one of the greatest technical challenges today. The symposium explored a number of surface and interface-related questions relevant to this overarching theme. Topics from fuel cells to photovoltaics, from water splitting to fundamental and practical issues in charge generation and storage were discussed. The work presented included the use of novel experimental spectroscopic and microscopic analytical techniques, theoretical and computational understanding of interfacial phenomena, characterization of intricate behavior of charged species, as well as molecules and molecular fragments at surfaces and interfaces. It emphasized fundamental understanding of underlying processes, as well as practical devices design and applications of surface and interfacial phenomena related to renewable energy. These subjects are complicated by the transport of photons, electrons, ions, heat, and almost any other form of energy. Given the current concerns of climate change, energy independence and national security, this work is important and of interest to the field of Applied Surface Science. The sixteen papers published in this special issue have all been refereed.

Elementary photocatalytic chemistry on TiO2 surfaces.

PubMed

Guo, Qing; Zhou, Chuanyao; Ma, Zhibo; Ren, Zefeng; Fan, Hongjun; Yang, Xueming

2016-07-07

Photocatalytic hydrogen production and pollutant degradation provided both great opportunities and challenges in the field of sustainable energy and environmental science. Over the past few decades, we have witnessed fast growing interest and efforts in developing new photocatalysts, improving catalytic efficiency and exploring the reaction mechanism at the atomic and molecular levels. Owing to its relatively high efficiency, nontoxicity, low cost and high stability, TiO2 becomes one of the most extensively investigated metal oxides in semiconductor photocatalysis. Fundamental studies on well characterized single crystals using ultrahigh vacuum based surface science techniques could provide key microscopic insight into the underlying mechanism of photocatalysis. In this review, we have summarized recent progress in the photocatalytic chemistry of hydrogen, water, oxygen, carbon monoxide, alcohols, aldehydes, ketones and carboxylic acids on TiO2 surfaces. We focused this review mainly on the rutile TiO2(110) surface, but some results on the rutile TiO2(011), anatase TiO2(101) and (001) surfaces are also discussed. These studies provided fundamental insights into surface photocatalysis as well as stimulated new investigations in this exciting field. At the end of this review, we have discussed how these studies can help us to develop new photocatalysis models.

Gain Coupling VECSELs (POSTPRINT)

DTIC Science & Technology

2013-01-01

International Conference on Molecular Beam Epitaxy (MBE-XV). 10. A. Siegman , Lasers , University Sciences Books, 1986. 11. C. Hessenius, N. Terry, M...Clearance Date 28 December 2012. Report contains color. 14. ABSTRACT Vertical external cavity surface emitting lasers (VECSELs) provide a flexible...platform in order to explore curious laser designs and systems as their high-power, high-brightness make them attractive for many applications, and their

Stanford MFEL and Near Infrared Science Center

DTIC Science & Technology

2011-01-28

guiding procedures for restoration of hearing— cochlear implants. Multifaceted approaches have been taken to understand the molecular and cellular...accompanying phenomena of cavitation, liquid flow and heat transfer in various biological tissues. In the field of laser surgery with ultrashort pulses...using yeast cell surface display, the Cochran group has generated EGF mutant libraries and have screened them by flow cytometry using fluorescently

Structure, dynamics and stability of water/scCO 2/mineral interfaces from ab initio molecular dynamics simulations

DOE PAGES

Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; ...

2015-10-12

Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO 2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca 2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO 2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences (R.R.), and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle. Computational resources were provided by PNNL’s Platform for Institutional Computing (PIC), the W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory.« less

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

NASA Astrophysics Data System (ADS)

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.

Interactions of Deuterium Plasma with Lithiated and Boronized Surfaces in NSTX-U

NASA Astrophysics Data System (ADS)

Krstic, Predrag

2015-09-01

The main research goal of the presented research has been to understand the changes in surface composition and chemistry at the nanoscopic temporal and spatial scales for long pulse Plasma Facing Components (PFCs) and link these to the overall machine performance of the National Spherical Torus Experiment Upgrade (NSTX-U). A study is presented of the lithium surface science, with atomic spatial and temporal resolutions. The dynamic surface responds and evolves in a mixed material environments (D, Li, C, B, O, Mo, W) with impingement of plasma particles in the energy range below 100 eV. The results, obtained by quantum-classical molecular dynamics, include microstructure changes, erosion, surface chemistry, deuterium implantation and permeation. Main objectives of the research are i) a comparison of Li and B deposition on carbon, ii) the role of oxygen and other impurities e.g. boron, carbon in the lithium performance, and iii) how this performance will change when lithium is applied to a high-Z refractory metal substrate (Mo, W). In addition to predicting and understanding the phenomenology of the processes, we will show plasma induced erosion of PFCs, including chemical and physical sputtering yields at various temperatures (300-700 K) as well as deuterium uptake/recycling. This work is supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Science, Award Number DE-SC0013752.

Metamaterial absorber for molecular detection and identification (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tanaka, Takuo

2017-03-01

Metamaterial absorber was used for a background-suppressed surface-enhanced molecular detection technique. By utilizing the resonant coupling between plasmonic modes of a metamaterial absorber and infrared (IR) vibrational modes of a self-assembled monolayer (SAM), attomole level molecular sensitivity was experimentally demonstrated. IR absorption spectroscopy of molecular vibrations is of importance in chemical, material, medical science and so on, since it provides essential information of the molecular structure, composition, and orientation. In the vibrational spectroscopic techniques, in addition to the weak signals from the molecules, strong background degrades the signal-to-noise ratio, and suppression of the background is crucial for the further improvement of the sensitivity. Here, we demonstrate low-background resonant Surface enhanced IR absorption (SEIRA) by using the metamaterial IR absorber that offers significant background suppression as well as plasmonic enhancement. By using mask-less laser lithography technique, metamaterial absorber which consisted of 1D array of Au micro-ribbons on a thick Au film separated by a transparent gap layer made of MgF2 was fabricated. This metamaterial structure was designed to exhibit an anomalous IR absorption at 3000 cm-1, which spectrally overlapped with C-H stretching vibrational modes. 16-Mercaptohexadecanoic acid (16-MHDA) was used as a test molecule, which formed a 2-nm thick SAM with their thiol head-group chemisorbed on the Au surface. In the FTIR measurements, the symmetric and asymmetric C-H stretching modes were clearly observed as reflection peaks within a broad plasmonic absorption of the metamaterial, and 1.8 attomole molecular sensitivity was experimentally demonstrated.

Ozone Production in Irradiated Laboratory Ices Relevant to Europa and Ganymede

NASA Astrophysics Data System (ADS)

Cooper, P. D.; Moore, M. H.; Hudson, R. L.

2005-08-01

Observations suggest ozone (O3) is present on the icy surfaces of Ganymede (1), and Rhea and Dione (2). Molecular oxygen (O2) has also been observed on Europa (3) and Ganymede (4). The formation and trapping of such molecules in ice and their subsequent transportation to a sub-surface ocean may be potentially important for sustaining astrobiological life (5). It is assumed that ozone is produced in these icy surfaces by the addition of an oxygen atom to molecular oxygen, with the latter formed by prior irradiation of the water ice. The infrared absorption band of ozone in ice at 1037 cm-1 is strong and thus makes ozone a good tracer for the presence of molecular oxygen which is difficult to detect. We will present results of water/oxygen ices irradiated with 800 keV protons and show the band position and growth of ozone with increasing radiation dose. The thermal stability of this radiolytically-produced ozone has also been measured and comparisons made to the Jovian satellites. P. Cooper is grateful for the support from the National Academies Research Associateship Program. (1) Noll, K.S., Johnson, R.E., Lane, A.L., Domingue, D.L., Weaver, H.A., Science, 273, 341-343, (1996). (2) Noll, K.S., Roush, T.L., Cruikshank, D.P., Johnson, R.E., Pendleton, Y.J., Nature, 388, 45-47, (1997). (3) Spencer, J.R., Calvin, W.M., Astron. J., 124, 3400-3403, (2002). (4) Spencer, J.R., Calvin, W.M., Person, M. J., J. Geo. Res. 100 (E9), 19049-19056 (1995). (5) Chyba, C.F., Hand, K.P., Science, 292, 2026-2027, (2001).

Plasmon-mediated chemical surface functionalization at the nanoscale

NASA Astrophysics Data System (ADS)

Nguyen, Mai; Lamouri, Aazdine; Salameh, Chrystelle; Lévi, Georges; Grand, Johan; Boubekeur-Lecaque, Leïla; Mangeney, Claire; Félidj, Nordin

2016-04-01

Controlling the surface grafting of species at the nanoscale remains a major challenge, likely to generate many opportunities in materials science. In this work, we propose an original strategy for chemical surface functionalization at the nanoscale, taking advantage of localized surface plasmon (LSP) excitation. The surface functionalization is demonstrated through aryl film grafting (derived from a diazonium salt), covalently bonded at the surface of gold lithographic nanostripes. The aryl film is specifically grafted in areas of maximum near field enhancement, as confirmed by numerical calculation based on the discrete dipole approximation method. The energy of the incident light and the LSP wavelength are shown to be crucial parameters to monitor the aryl film thickness of up to ~30 nm. This robust and versatile strategy opens up exciting prospects for the nanoscale confinement of functional layers on surfaces, which should be particularly interesting for molecular sensing or nanooptics.Controlling the surface grafting of species at the nanoscale remains a major challenge, likely to generate many opportunities in materials science. In this work, we propose an original strategy for chemical surface functionalization at the nanoscale, taking advantage of localized surface plasmon (LSP) excitation. The surface functionalization is demonstrated through aryl film grafting (derived from a diazonium salt), covalently bonded at the surface of gold lithographic nanostripes. The aryl film is specifically grafted in areas of maximum near field enhancement, as confirmed by numerical calculation based on the discrete dipole approximation method. The energy of the incident light and the LSP wavelength are shown to be crucial parameters to monitor the aryl film thickness of up to ~30 nm. This robust and versatile strategy opens up exciting prospects for the nanoscale confinement of functional layers on surfaces, which should be particularly interesting for molecular sensing or nanooptics. Electronic supplementary information (ESI) available: Additional figures are displayed (from Fig. SI1-SI6) to illustrate the content of the paper, including the proposed mechanisms of diazonium-derived aryl film grafting, the AFM measurements of the aryl film thickness and the calculation by the DDA method. See DOI: 10.1039/C6NR00744A

Application of atomic force microscopy as a nanotechnology tool in food science.

PubMed

Yang, Hongshun; Wang, Yifen; Lai, Shaojuan; An, Hongjie; Li, Yunfei; Chen, Fusheng

2007-05-01

Atomic force microscopy (AFM) provides a method for detecting nanoscale structural information. First, this review explains the fundamentals of AFM, including principle, manipulation, and analysis. Applications of AFM are then reported in food science and technology research, including qualitative macromolecule and polymer imaging, complicated or quantitative structure analysis, molecular interaction, molecular manipulation, surface topography, and nanofood characterization. The results suggested that AFM could bring insightful knowledge on food properties, and the AFM analysis could be used to illustrate some mechanisms of property changes during processing and storage. However, the current difficulty in applying AFM to food research is lacking appropriate methodology for different food systems. Better understanding of AFM technology and developing corresponding methodology for complicated food systems would lead to a more in-depth understanding of food properties at macromolecular levels and enlarge their applications. The AFM results could greatly improve the food processing and storage technologies.

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.

PubMed

Guerette, Paul A; Hoon, Shawn; Seow, Yiqi; Raida, Manfred; Masic, Admir; Wong, Fong T; Ho, Vincent H B; Kong, Kiat Whye; Demirel, Melik C; Pena-Francesch, Abdon; Amini, Shahrouz; Tay, Gavin Z; Ding, Dawei; Miserez, Ali

2013-10-01

Efforts to engineer new materials inspired by biological structures are hampered by the lack of genomic data from many model organisms studied in biomimetic research. Here we show that biomimetic engineering can be accelerated by integrating high-throughput RNA-seq with proteomics and advanced materials characterization. This approach can be applied to a broad range of systems, as we illustrate by investigating diverse high-performance biological materials involved in embryo protection, adhesion and predation. In one example, we rapidly engineer recombinant squid sucker ring teeth proteins into a range of structural and functional materials, including nanopatterned surfaces and photo-cross-linked films that exceed the mechanical properties of most natural and synthetic polymers. Integrating RNA-seq with proteomics and materials science facilitates the molecular characterization of natural materials and the effective translation of their molecular designs into a wide range of bio-inspired materials.

Surface Science and the Advancement of Direct Olefin Epoxidation A Perspective on the Article, ‘‘Partial Oxidation of Higher Olefins on Ag(111) and Ag(110): Conversion of Styrene to Styrene Oxide, Benzene, and Benzoic Acid’’, by Andreas Klust and Robert J. Madix.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barteau, Mark A.

2006-10-04

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Few reactions are as conceptually simple or as devilishly difficult as the epoxidation of ethylene to form ethylene oxide:

Detection of the plant parasite Cuscuta reflexa by a tomato cell surface receptor.

PubMed

Hegenauer, Volker; Fürst, Ursula; Kaiser, Bettina; Smoker, Matthew; Zipfel, Cyril; Felix, Georg; Stahl, Mark; Albert, Markus

2016-07-29

Parasitic plants are a constraint on agriculture worldwide. Cuscuta reflexa is a stem holoparasite that infests most dicotyledonous plants. One exception is tomato, which is resistant to C. reflexa We discovered that tomato responds to a small peptide factor occurring in Cuscuta spp. with immune responses typically activated after perception of microbe-associated molecular patterns. We identified the cell surface receptor-like protein CUSCUTA RECEPTOR 1 (CuRe1) as essential for the perception of this parasite-associated molecular pattern. CuRe1 is sufficient to confer responsiveness to the Cuscuta factor and increased resistance to parasitic C. reflexa when heterologously expressed in otherwise susceptible host plants. Our findings reveal that plants recognize parasitic plants in a manner similar to perception of microbial pathogens. Copyright © 2016, American Association for the Advancement of Science.

International Journal of Molecular Science 2017 Best Paper Award.

PubMed

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 [...].

Metal oxide nanosensors using polymeric membranes, enzymes and antibody receptors as ion and molecular recognition elements.

PubMed

Willander, Magnus; Khun, Kimleang; Ibupoto, Zafar Hussain

2014-05-16

The concept of recognition and biofunctionality has attracted increasing interest in the fields of chemistry and material sciences. Advances in the field of nanotechnology for the synthesis of desired metal oxide nanostructures have provided a solid platform for the integration of nanoelectronic devices. These nanoelectronics-based devices have the ability to recognize molecular species of living organisms, and they have created the possibility for advanced chemical sensing functionalities with low limits of detection in the nanomolar range. In this review, various metal oxides, such as ZnO-, CuO-, and NiO-based nanosensors, are described using different methods (receptors) of functionalization for molecular and ion recognition. These functionalized metal oxide surfaces with a specific receptor involve either a complex formation between the receptor and the analyte or an electrostatic interaction during the chemical sensing of analytes. Metal oxide nanostructures are considered revolutionary nanomaterials that have a specific surface for the immobilization of biomolecules with much needed orientation, good conformation and enhanced biological activity which further improve the sensing properties of nanosensors. Metal oxide nanostructures are associated with certain unique optical, electrical and molecular characteristics in addition to unique functionalities and surface charge features which shows attractive platforms for interfacing biorecognition elements with effective transducing properties for signal amplification. There is a great opportunity in the near future for metal oxide nanostructure-based miniaturization and the development of engineering sensor devices.

The Dye Sensitized Photoelectrosynthesis Cell (DSPEC) for Solar Water Splitting and CO2 Reduction

NASA Astrophysics Data System (ADS)

Meyer, Thomas; Alibabaei, Leila; Sherman, Benjamin; Sheridan, Matthew; Ashford, Dennis; Lapides, Alex; Brennaman, Kyle; Nayak, Animesh; Roy, Subhangi; Wee, Kyung-Ryang; Gish, Melissa; Meyer, Jerry; Papanikolas, John

The dye-sensitized photoelectrosynthesis cell (DSPEC) integrates molecular level light absorption and catalysis with the bandgap properties of stable oxide materials such as TiO2 and NiO. Excitation of surface-bound chromophores leads to excited state formation and rapid electron or hole injection into the conduction or valence bands of n or p-type oxides. Addition of thin layers of TiO2 or NiO on the surfaces of mesoscopic, nanoparticle films of semiconductor or transparent conducting oxides to give core/shell structures provides a basis for accumulating multiple redox equivalents at catalysts for water oxidation or CO2 reduction. UNC EFRC Center for Solar Fuels, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001011.

Walking peptide on Au(110) surface: Origin and nature of interfacial process

NASA Astrophysics Data System (ADS)

Humblot, V.; Tejeda, A.; Landoulsi, J.; Vallée, A.; Naitabdi, A.; Taleb, A.; Pradier, C.-M.

2014-10-01

IGF tri-peptide adsorption on Au(110)-(1 × 2) under Ultra High Vacuum (UHV) conditions has been investigated using surface science techniques such as synchrotron based Angle Resolved X-ray Photoemission Spectroscopy (AR-PES or AR-XPS), Low Energy Electron Diffraction (LEED) and Scanning Tunnelling Microscopy (STM). The behaviour of IGF molecules has been revealed to be coverage dependent; at low coverage, there is formation of islands presenting a chiral self-organised molecular network with a (4 2, - 3 2) symmetry as shown by Low Energy Electron Diffraction (LEED) and Scanning Tunnelling Microscopy (STM) on the unaltered Au(110)-(1 × 2) reconstruction, suggesting significant intermolecular interactions. When the coverage is increased, the islands grow bigger, and one can observe the disappearance of the self-organised network, along with a remarkable destruction of the (1 × 2) substrate reconstruction, as shown by STM. The effect of IGF on the surface gold atoms has been further confirmed by angle-resolved photoemission measurements which suggest a modification of the electronic states with the (1 × 2) symmetry. The resulting molecular organisation, and overall the gold surface disorganisation, prove a strong surface-molecule interaction, which may be probably be explained by a covalent bonding.

Molecular carbon nitride ion beams for enhanced corrosion resistance of stainless steel

NASA Astrophysics Data System (ADS)

Markwitz, A.; Kennedy, J.

2017-10-01

A novel approach is presented for molecular carbon nitride beams to coat stainless surfaces steel using conventional safe feeder gases and electrically conductive sputter targets for surface engineering with ion implantation technology. GNS Science's Penning type ion sources take advantage of the breaking up of ion species in the plasma to assemble novel combinations of ion species. To test this phenomenon for carbon nitride, mixtures of gases and sputter targets were used to probe for CN+ ions for simultaneous implantation into stainless steel. Results from mass analysed ion beams show that CN+ and a variety of other ion species such as CNH+ can be produced successfully. Preliminary measurements show that the corrosion resistance of stainless steel surfaces increased sharply when implanting CN+ at 30 keV compared to reference samples, which is interesting from an application point of view in which improved corrosion resistance, surface engineering and short processing time of stainless steel is required. The results are also interesting for novel research in carbon-based mesoporous materials for energy storage applications and as electrode materials for electrochemical capacitors, because of their high surface area, electrical conductivity, chemical stability and low cost.

Molecular science for drug development and biomedicine.

PubMed

Zhong, Wei-Zhu; Zhou, Shu-Feng

2014-11-04

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

Niobium pentoxide: a promising surface-enhanced Raman scattering active semiconductor substrate

NASA Astrophysics Data System (ADS)

Shan, Yufeng; Zheng, Zhihui; Liu, Jianjun; Yang, Yong; Li, Zhiyuan; Huang, Zhengren; Jiang, Dongliang

2017-03-01

Surface-enhanced Raman scattering technique, as a powerful tool to identify the molecular species, has been severely restricted to the noble metals. The surface-enhanced Raman scattering substrates based on semiconductors would overcome the shortcomings of metal substrates and promote development of surface-enhanced Raman scattering technique in surface science, spectroscopy, and biomedicine studies. However, the detection sensitivity and enhancement effects of semiconductor substrates are suffering from their weak activities. In this work, a semiconductor based on Nb2O5 is reported as a new candidate for highly sensitive surface-enhanced Raman scattering detection of dye molecules. The largest enhancement factor value greater than 107 was observed with the laser excitation at 633 and 780 nm for methylene blue detection. As far as literature review shows, this is in the rank of the highest sensitivity among semiconductor materials; even comparable to the metal nanostructure substrates with "hot spots". The impressive surface-enhanced Raman scattering activities can be attributed to the chemical enhancement dominated by the photo-induced charge transfer, as well as the electromagnetic enhancement, which have been supported by the density-functional-theory and finite element method calculation results. The chemisorption of dye on Nb2O5 creates a new highest occupied molecular orbital and lowest unoccupied molecular orbital contributed by both fragments in the molecule-Nb2O5 system, which makes the charge transfer more feasible with longer excitation wavelength. In addition, the electromagnetic enhancement mechanism also accounts for two orders of magnitude enhancement in the overall enhancement factor value. This work has revealed Nb2O5 nanoparticles as a new semiconductor surface-enhanced Raman scattering substrate that is able to replace noble metals and shows great potentials applied in the fields of biology related.

Switchable host-guest systems on surfaces.

PubMed

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, such as light, pH variations, competitive binding, and enzyme. Rotaxanes have also been assembled onto the surfaces of gold nanodisks and microcantilevers to realize active molecular plasmonics and synthetic molecular actuators for device fabrication and function. Pillararenes have been successfully used to control and aid the synthesis of gold nanoparticles, semiconducting quantum dots, and magnetic nanoparticles. The resulting organic-inorganic hydrid nanomaterials have been successfully used for controlled self-assembly, herbicide sensing and detection, pesticide removal, and so forth, taking advantage of the selective binding of pillarenes toward target molecules. Cyclodextrins have also been successfully functionalized onto the surface of gold nanoparticles to serve as recycling extractors for C60. Many interesting prototypes of nanodevices based on synthetic macrocycles and their host-guest chemistry have been constructed and served for different potential applications. This Account will be a summary of the efforts made mainly by us, and others, on the host-guest chemistry of synthetic macrocyclic compounds on the surfaces of different solid supports.

Nanoscale surface modifications of medically relevant metals: state-of-the art and perspectives.

PubMed

Variola, Fabio; Brunski, John B; Orsini, Giovanna; Tambasco de Oliveira, Paulo; Wazen, Rima; Nanci, Antonio

2011-02-01

Evidence that nanoscale surface properties stimulate and guide various molecular and biological processes at the implant/tissue interface is fostering a new trend in designing implantable metals. Cutting-edge expertise and techniques drawn from widely separated fields, such as nanotechnology, materials engineering and biology, have been advantageously exploited to nanoengineer surfaces in ways that control and direct these processes in predictable manners. In this review, we present and discuss the state-of-the-art of nanotechnology-based approaches currently adopted to modify the surface of metals used for orthopedic and dental applications, and also briefly consider their use in the cardiovascular field. The effects of nanoengineered surfaces on various in vitro molecular and cellular events are firstly discussed. This review also provides an overview of in vivo and clinical studies with nanostructured metallic implants, and addresses the potential influence of nanotopography on biomechanical events at interfaces. Ultimately, the objective of this work is to give the readership a comprehensive picture of the current advances, future developments and challenges in the application of the infinitesimally small to biomedical surface science. We believe that an integrated understanding of the in vitro and particularly of the in vivo behavior is mandatory for the proper exploitation of nanostructured implantable metals and, indeed, of all biomaterials.

Cysteine and cystine adsorption on FeS2(100)

NASA Astrophysics Data System (ADS)

Suzuki, Teppei; Yano, Taka-aki; Hara, Masahiko; Ebisuzaki, Toshikazu

2018-08-01

Iron pyrite (FeS2) is the most abundant metal sulfide on Earth. Owing to its reactivity and catalytic activity, pyrite has been studied in various research fields such as surface science, geochemistry, and prebiotic chemistry. Importantly, native iron-sulfur clusters are typically coordinated by cysteinyl ligands of iron-sulfur proteins. In the present paper, we study the adsorption of L-cysteine and its oxidized dimer, L-cystine, on the FeS2 surface, using electronic structure calculations based density functional theory and Raman spectroscopy measurements. Our calculations suggest that sulfur-deficient surfaces play an important role in the adsorption of cysteine and cystine. In the thiol headgroup adsorption on the sulfur-vacancy site, dissociative adsorption is found to be energetically favorable compared with molecular adsorption. In addition, the calculations indicate that, in the cystine adsorption on the defective surface under vacuum conditions, the formation of the S-Fe bond is energetically favorable compared with molecular adsorption. Raman spectroscopic measurements suggest the formation of cystine molecules through the S-S bond on the pyrite surface in aqueous solution. Our results might have implications for chemical evolution at mineral surfaces on the early Earth and the origin of iron-sulfur proteins, which are believed to be one of the most ancient families of proteins.

Nanoscale surface modifications of medically-relevant metals: state-of-the art and perspectives

PubMed Central

Variola, Fabio; Brunski, John; Orsini, Giovanna; de Oliveira, Paulo Tambasco; Wazen, Rima; Nanci, Antonio

2011-01-01

Evidence that nanoscale surface properties stimulate and guide various molecular and biological processes at the implant/tissue interface is fostering a new trend in designing implantable metals. Cutting-edge expertise and techniques drawn from widely separated fields, such as nanotechnology, materials engineering and biology, have been advantageously exploited to nanoengineer surfaces in ways that control and direct these processes in predictable manners. In this review, we present and discuss the state-of-the-art of nanotechnology-based approaches currently used to modify the surface of metals used for orthopedic and dental applications, and also briefly consider their use in the cardiovascular field. The effects of nanoengineered surfaces on various in vitro molecular and cellular events are firstly discussed. Importantly, this review also provides an overview of in vivo and clinical studies with nanostructured metallic implants, and addresses the potential influence of nanotopography on biomechanical events at interfaces. Ultimately the objective of this work is to give the readership a comprehensive picture of the current advances, future developments and challenges in the application of the infinitesimally small to biomedical surface science. We believe that an integrated understanding of the in vitro and particularly of the in vivo behavior is mandatory for the proper exploitation of nanostructured implantable metals and, as a matter of fact, all biomaterials. PMID:20976359

Direct observation of triplet energy transfer from semiconductor nanocrystals.

PubMed

Mongin, Cédric; Garakyaraghi, Sofia; Razgoniaeva, Natalia; Zamkov, Mikhail; Castellano, Felix N

2016-01-22

Triplet excitons are pervasive in both organic and inorganic semiconductors but generally remain confined to the material in which they originate. We demonstrated by transient absorption spectroscopy that cadmium selenide semiconductor nanoparticles, selectively excited by green light, engage in interfacial Dexter-like triplet-triplet energy transfer with surface-anchored polyaromatic carboxylic acid acceptors, extending the excited-state lifetime by six orders of magnitude. Net triplet energy transfer also occurs from surface acceptors to freely diffusing molecular solutes, further extending the lifetime while sensitizing singlet oxygen in an aerated solution. The successful translation of triplet excitons from semiconductor nanoparticles to the bulk solution implies that such materials are generally effective surrogates for molecular triplets. The nanoparticles could thereby potentially sensitize a range of chemical transformations that are relevant for fields as diverse as optoelectronics, solar energy conversion, and photobiology. Copyright © 2016, American Association for the Advancement of Science.

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

PubMed

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 catalysis science: Perspective on unifying the fields of catalysis

PubMed Central

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

2016-01-01

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. PMID:27114536

The Millimeter Wave Observatory antenna now at INAOE-Mexico

NASA Astrophysics Data System (ADS)

Luna, A.

2017-07-01

The antenna of 5 meters in diameter of the legendary "Millimeter Wave Observatory" is now installed in the INAOE-Mexico. This historic antenna was reinstalled and was equipped with a control system and basic primary focus receivers that enabled it in teaching activities. We work on the characterization of its surface and on the development of receivers and spectrometers to allow it to do research Solar and astronomical masers. The historical contributions of this antenna to science and technology in radio astronomy, serve as the guiding force and the inspiration of the students and technicians of our postgrade in Astrophysics. It is enough to remember that it was with this antenna, that the first molecular outflow was discovered, several lines of molecular emission were discovered and it was the first antenna whose surface was characterized by holography; among many other technological and scientific contributions.

Supramolecular clusters and chains of 2,6-dimethylpyridine on Cu(110): Observation of dynamic configuration change with real-space surface science techniques and DFT calculations

DOE PAGES

Lee, Junseok; Sorescu, Dan C.; Lee, Jae -Gook; ...

2016-02-02

Here, the adsorption of 2,6-dimethylpyridine (2,6-DMP) on Cu(110) has been studied using low temperature scanning tunneling microscopy (LT-STM), time-of-flight electron stimulated desorption ion angular distribution (TOF-ESDIAD), and density functional theory (DFT) calculations. At low temperatures (T < ~ 150 K), the 2,6-DMP adsorbs in a flat configuration on Cu(110) producing clusters and extended domains via weak hydrogen bonding (C—H···N) with the molecular symmetry axis aligned along the < 001 > surface direction.

Black hole mass measurement using molecular gas kinematics: what ALMA can do

NASA Astrophysics Data System (ADS)

Yoon, Ilsang

2017-04-01

We study the limits of the spatial and velocity resolution of radio interferometry to infer the mass of supermassive black holes (SMBHs) in galactic centres using the kinematics of circum-nuclear molecular gas, by considering the shapes of the galaxy surface brightness profile, signal-to-noise ratios (S/Ns) of the position-velocity diagram (PVD) and systematic errors due to the spatial and velocity structure of the molecular gas. We argue that for fixed galaxy stellar mass and SMBH mass, the spatial and velocity scales that need to be resolved increase and decrease, respectively, with decreasing Sérsic index of the galaxy surface brightness profile. We validate our arguments using simulated PVDs for varying beam size and velocity channel width. Furthermore, we consider the systematic effects on the inference of the SMBH mass by simulating PVDs including the spatial and velocity structure of the molecular gas, which demonstrates that their impacts are not significant for a PVD with good S/N unless the spatial and velocity scale associated with the systematic effects are comparable to or larger than the angular resolution and velocity channel width of the PVD from pure circular motion. Also, we caution that a bias in a galaxy surface brightness profile owing to the poor resolution of a galaxy photometric image can largely bias the SMBH mass by an order of magnitude. This study shows the promise and the limits of ALMA observations for measuring SMBH mass using molecular gas kinematics and provides a useful technical justification for an ALMA proposal with the science goal of measuring SMBH mass.

Physics through the 1990s: Atomic, molecular and optical physics

NASA Technical Reports Server (NTRS)

1986-01-01

The volume presents a program of research initiatives in atomic, molecular, and optical physics. The current state of atomic, molecular, and optical physics in the US is examined with respect to demographics, education patterns, applications, and the US economy. Recommendations are made for each field, with discussions of their histories and the relevance of the research to government agencies. The section on atomic physics includes atomic theory, structure, and dynamics; accelerator-based atomic physics; and large facilities. The section on molecular physics includes spectroscopy, scattering theory and experiment, and the dynamics of chemical reactions. The section on optical physics discusses lasers, laser spectroscopy, and quantum optics and coherence. A section elucidates interfaces between the three fields and astrophysics, condensed matter physics, surface science, plasma physics, atmospheric physics, and nuclear physics. Another section shows applications of the three fields in ultra-precise measurements, fusion, national security, materials, medicine, and other topics.

Stern Layer Structure and Energetics at Mica-Water Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bourg, Ian C.; Lee, Sang Soo; Fenter, Paul

2017-04-11

The screening of surface charge by dissolved ions at solid liquid interfaces in the region of interfacial fluid known as the electrical double layer (EDL)-plays a recurrent role in surface science, from ion adsorption to colloidal mechanics to the transport properties of nanoporous media. A persistent unknown in theories of EDL-related phenomena is the structure of the Stern layer, the near-surface portion of the EDL where water molecules and adsorbed ions form specific short-range interactions with surface atoms. Here, we describe a set of synchrotron X-ray reflectivity (XRR) experiments and molecular dynamics (MD) simulations carried out under identical conditions formore » a range of 0.1 M alkali chloride (Li-, Na-, K-, Rb-, or CsCl) solutions on the basal surface of muscovite mica, a mineral isostructural to phyllosilicate clay minerals and one of the most widely studied reference surfaces in interfacial science. Our XRR and MD simulation results provide a remarkably consistent view of the structure and energetics of the Stern layer, with some discrepancy on the fraction of the minor outer-sphere component of Rb and on the adsorption energetics of Li. The results of both techniques, along with surface complexation model calculations, provide insight into the sensitivity of water structure and ion adsorption to surface topography and the type of adsorbed counterion.« less

Nanoscale heterogeneity at the aqueous electrolyte-electrode interface

NASA Astrophysics Data System (ADS)

Limmer, David T.; Willard, Adam P.

2015-01-01

Using molecular dynamics simulations, we reveal emergent properties of hydrated electrode interfaces that while molecular in origin are integral to the behavior of the system across long times scales and large length scales. Specifically, we describe the impact of a disordered and slowly evolving adsorbed layer of water on the molecular structure and dynamics of the electrolyte solution adjacent to it. Generically, we find that densities and mobilities of both water and dissolved ions are spatially heterogeneous in the plane parallel to the electrode over nanosecond timescales. These and other recent results are analyzed in the context of available experimental literature from surface science and electrochemistry. We speculate on the implications of this emerging microscopic picture on the catalytic proficiency of hydrated electrodes, offering a new direction for study in heterogeneous catalysis at the nanoscale.

Surface tension and contact angles: Molecular origins and associated microstructure

NASA Technical Reports Server (NTRS)

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.

Molecular recognition of 7-(2-octadecyloxycarbonylethyl)guanine to cytidine at the air/water interface and LB film studied by Fourier transform infrared spectroscopy.

PubMed

Miao, Wangen; Luo, Xuzhong; Liang, Yingqiu

2003-03-15

Monolayer behavior of a nucleolipid amphiphile, 7-(2-octadecyloxycarbonylethyl)guanine (ODCG), on aqueous cytidine solution was investigated by means of surface-molecular area (pi-A) isotherms. It indicates that molecular recognition by hydrogen bonding is present between ODCG monolayer and the cytidine in subphase. The Fourier transform infrared (FTIR) transmission spectroscopic result indicates that the cytidine molecules in the subphase can be transferred onto solid substrates by Langmuir-Blodgett (LB) technique as a result of the formation of Watson-Crick base-pairing at the air/water interface. Investigation by rotating polarized FTIR transmission also suggests that the headgroup recognition of this amphiphile to the dissolved cytidine influence the orientation of the tailchains. Copyright 2002 Elsevier Science B.V.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willow, Soohaeng Yoo; Xantheas, Sotiris S.

The effect of the Hofmeister anion series on the structure and stability of proteins is often discussed using simple systems such as a water-vapor interface with the assumption that the vapor region mimics the hydrophobic surface. Microscopic theories suggest that the Hofmeister anion series is highly correlated with the different contributions of the various ions to the surface tension of such a water-vapor interface. Proteins, however, have both hydrophobic and hydrophilic regions rather than just a pure hydrophobic one. Using a solvated parallel β -sheet layer consisting of both hydrophobic and positively charged hydrophilic surfaces as a more realistic modelmore » to represent a protein surface, we investigated the interaction of such a system with hydrophilic-like (SO42-) and hydrophobic-like (ClO4-) anions via Born-Oppenheimer Molecular Dynamics (BOMD) simulations. We found that both the SO42- and ClO4- anions prefer to reside on the hydrophilic rather than on the hydrophobic surface of the parallel β -sheet layer. In addition, our simulations suggest that the ClO4- ions not only penetrate towards the peptide groups through the hydrophilic residues, but also allow water molecules to penetrate as well to form water-peptide hydrogen bonds, while the SO42- ions stabilize the interface of the water-hydrophilic surface. Our results render a plausible explanation of why hydrophobic-like Hofmeister anions act as protein denaturants. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

Post-Self-Assembly Cross-Linking to Integrate Molecular Nanofibers with Copolymers in Oscillatory Hydrogels

DTIC Science & Technology

2013-05-09

The BZ reaction provides a model system to mimic a variety of complex processes, such as biological morphogenesis, in monodisperse microemulsions .15...surfaces, ion-exchange resins, membranes, and microemulsions . For example, in addition to minimizing the hydrodynamic effects and formation of bubbles...Reaction-Diffusion Microemulsions Reveals Three-Dimensional Tu- ring Patterns. Science (Washington, DC, U.S.) 2011, 331, 1309−1312. (16) Agladze, K. I

Opto-Electronically Efficient Conjugated Polymers by Stress-Induced Molecular Constraints

DTIC Science & Technology

2012-07-15

TEM, JEOL JEM-2010) and checked by weight losses obtained from the thermogravimetric scans (TGA, Perkin-Elmer).[49-55] Scheme 1. Grafting P3HT...further analysis of the conduction pathways, e.g., the linear resistance networks,[40] but even without it, the jump frequency is predicted to...Nanocomposites: CNT Surface grafting, p-p interactions, and Gold Nanoparticles adsorption effect, Mater Thesis, Department of Materials Science and Engineering

Mechanisms and Dynamics of Abiotic and Biotic Interactions at Environmental Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roso, Kevin M.

The Stanford EMSI (SEMSI) was established in 2004 through joint funding by the National Science Foundation and the OBER-ERSD. It encompasses a number of universities and national laboratories. The PNNL component of the SEMSI is funded by ERSD and is the focus of this report. This component has the objective of providing theory support to the SEMSI by bringing computational capabilities and expertise to bear on important electron transfer problems at mineral/water and mineral/microbe interfaces. PNNL staff member Dr. Kevin Rosso, who is also ''matrixed'' into the Environmental Molecular Sciences Laboratory (EMSL) at PNNL, is a co-PI on the SEMSImore » project and the PNNL lead. The EMSL computational facilities being applied to the SEMSI project include the 11.8 teraflop massively-parallel supercomputer. Science goals of this EMSL/SEMSI partnership include advancing our understanding of: (1) The kinetics of U(VI) and Cr(VI) reduction by aqueous and solid-phase Fe(II), (2) The structure of mineral surfaces in equilibrium with solution, and (3) Mechanisms of bacterial electron transfer to iron oxide surfaces via outer-membrane cytochromes.« less

Metal Oxide Nanosensors Using Polymeric Membranes, Enzymes and Antibody Receptors as Ion and Molecular Recognition Elements

PubMed Central

Willander, Magnus; Khun, Kimleang; Ibupoto, Zafar Hussain

2014-01-01

The concept of recognition and biofunctionality has attracted increasing interest in the fields of chemistry and material sciences. Advances in the field of nanotechnology for the synthesis of desired metal oxide nanostructures have provided a solid platform for the integration of nanoelectronic devices. These nanoelectronics-based devices have the ability to recognize molecular species of living organisms, and they have created the possibility for advanced chemical sensing functionalities with low limits of detection in the nanomolar range. In this review, various metal oxides, such as ZnO-, CuO-, and NiO-based nanosensors, are described using different methods (receptors) of functionalization for molecular and ion recognition. These functionalized metal oxide surfaces with a specific receptor involve either a complex formation between the receptor and the analyte or an electrostatic interaction during the chemical sensing of analytes. Metal oxide nanostructures are considered revolutionary nanomaterials that have a specific surface for the immobilization of biomolecules with much needed orientation, good conformation and enhanced biological activity which further improve the sensing properties of nanosensors. Metal oxide nanostructures are associated with certain unique optical, electrical and molecular characteristics in addition to unique functionalities and surface charge features which shows attractive platforms for interfacing biorecognition elements with effective transducing properties for signal amplification. There is a great opportunity in the near future for metal oxide nanostructure-based miniaturization and the development of engineering sensor devices. PMID:24841244

Adsorption of Potassium on the MoS2(100) Surface: A First-Principles Investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Amity; Kathmann, Shawn M.; Lilga, Michael A.

2011-04-15

Periodic density functional theory calculations were performed to investigate the interaction that potassium with the Mo and S edges of the MoS2(100) surface. Both neutral and cationic (+1) charged potassium-promoted systems at different sulfur coverages were considered. Our calculations indicate that the potassium atom readily donates its single 4s valence electron to the MoS2 structure for the neutral potassium-promoted system, and the neutral and cationic potassium-promoted systems demonstrate a similar adsorption behavior. Moreover, potassium changes the magnetic properties known to occur at the metallic edge surface, which have implications for electron spin dependent surface characterization methods (i.e., electron spin/paramagnetic spectroscopy).more » Potassium in both the neutral and cationic systems tends to maximize its interactions with the available sulfur atoms at the edge surface, preferring sites over four-fold S hollows on fully sulfided Mo and S edges and over the interstitial gap where two to four edge surface S atoms are available for coordination. As the potassium coverage increases, the adsorption energy per potassium atom, surface work function, and transfer of the K 4s electron to the MoS2(100) surface decreases, which is in line with an increased metallization of the potassium adlayer. The potassium adlayer tends to form chains along the interstitial with K-K distances ~1 Å, which is notably less than those of bulk bcc K metal (4.61 Å). Density of states for the potassium-saturated surface suggests enhanced involvement of broad K 3d states beginning just above the Fermi level. Potassium-promotion of MoS2(100) has implications for alcohol catalysis: increasing the surface basicity by increasing the electron charge of the surface, providing hydrogenation-promoting CO site, blocking edge surface that dissociate CO and lead to methanation, and limiting H2 dissociative adsorption to the edge surface and possibly inhibiting the H2 dissociative adsorption via s character electron repulsion. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, a U.S. Department of Energy (DOE) national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.« less

Probing the (110)-Oriented plane of rutile ZnF2: A DFT investigation

NASA Astrophysics Data System (ADS)

Tamijani, Ali Abbaspour; Ebrahimiaqda, Elham

2017-12-01

For many years, rutile-like crystals have given rise to pronounced enthusiasm amongst mineralogists. In this context, rutile-type ZnF2 has found numerous applications across a variety of disciplines, ranging from material sciences to optoelectronics. Surprisingly, very limited literature is concerned with the molecular adsorption on ZnF2 surfaces and related energetics. Additionally, surface probing with small particles is a well-entrenched technique to analyze the interfacial properties. In this regard, small organic species are valuable picks. In the present work, we have employed electronic structure calculations to simulate the adsorption of methane, chloroform, pyrrole, benzene, naphthalene, anthracene, tetracene and pentacene at the (110) plane of rutile ZnF2. Dispersion-corrected DFT method was chosen to predict the binding energies and structures of molecule-adsorbed surfaces. Interestingly, a linear proportionality relationship was found between the binding energies of aromatic adsorbates and their respective molecular lengths. By applying this relationship, we were able to predict the adsorption energy of pentacene on ZnF2 to within 2% of our DFT-based result.

Computational design of protein interactions: designing proteins that neutralize influenza by inhibiting its hemagglutinin surface protein

NASA Astrophysics Data System (ADS)

Fleishman, Sarel

2012-02-01

Molecular recognition underlies all life processes. Design of interactions not seen in nature is a test of our understanding of molecular recognition and could unlock the vast potential of subtle control over molecular interaction networks, allowing the design of novel diagnostics and therapeutics for basic and applied research. We developed the first general method for designing protein interactions. The method starts by computing a region of high affinity interactions between dismembered amino acid residues and the target surface and then identifying proteins that can harbor these residues. Designs are tested experimentally for binding the target surface and successful ones are affinity matured using yeast cell surface display. Applied to the conserved stem region of influenza hemagglutinin we designed two unrelated proteins that, following affinity maturation, bound hemagglutinin at subnanomolar dissociation constants. Co-crystal structures of hemagglutinin bound to the two designed binders were within 1Angstrom RMSd of their models, validating the accuracy of the design strategy. One of the designed proteins inhibits the conformational changes that underlie hemagglutinin's cell-invasion functions and blocks virus infectivity in cell culture, suggesting that such proteins may in future serve as diagnostics and antivirals against a wide range of pathogenic influenza strains. We have used this method to obtain experimentally validated binders of several other target proteins, demonstrating the generality of the approach. We discuss the combination of modeling and high-throughput characterization of design variants which has been key to the success of this approach, as well as how we have used the data obtained in this project to enhance our understanding of molecular recognition. References: Science 332:816 JMB, in press Protein Sci 20:753

Instability of Hydrogenated TiO2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nandasiri, Manjula I.; Shutthanandan, V.; Manandhar, Sandeep

2015-11-06

Hydrogenated TiO2 (H-TiO2) is toted as a viable visible light photocatalyst. We report a systematic study on the thermal stability of H-implanted TiO2 using X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), Rutherford backscattering spectrometry (RBS) and nuclear reaction analysis (NRA). Protons (40 keV) implanted at a ~2 atom % level within a ~120 nm wide profile of rutile TiO2(110) were situated ~300 nm below the surface. NRA revealed that this H-profile broadened preferentially toward the surface after annealing at 373 K, dissipated out of the crystal into vacuum at 473 K, and was absent within the beam sampling depthmore » (~800 nm) at 523 K. Photoemission showed that the surface was reduced in concert with these changes. Similar anneals had no effect on pristine TiO2(110). The facile bulk diffusivity of H in rutile, as well as its activity toward interfacial reduction, significantly limits the utilization of H-TiO2 as a photocatalyst. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The research was performed using the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Recent science and its exploration: the case of molecular biology.

PubMed

Rheinberger, Hans-Jörg

2009-03-01

This paper is about the interaction and the intertwinement between history of science as a historical process and history of science as the historiography of this process, taking molecular biology as an example. In the first part, two historical shifts are briefly characterized that appear to have punctuated the emergence of molecular biology between the 1930s and the 1980s, one connected to a new generation of analytical apparatus, the other to properly molecular tools. The second part concentrates on the historiography of this development. Basically, it distinguishes three phases. The first phase was largely dominated by accounts of the actors themselves. The second coincided with the general 'practical turn' in history of science at large, and today's historical appropriations of the molecularization of the life sciences appear to be marked by the changing disciplinary status of the science under review. In a closing remark, an argument is made for differentiating between long-range, middle-range and short-range perspectives in dealing with the history of the sciences.

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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 Iori, K Sakamoto, H Narita, A Kimura, M Taniguchi, S Qiao, K Hasegawa, K Shimada, H Namatame and S Blügel Activated associative desorption of C + O → CO from Ru(001) induced by femtosecond laser pulses S Wagner, H Öström, A Kaebe, M Krenz, M Wolf, A C Luntz and C Frischkorn Surface structure of Sn-doped In2O3 (111) thin films by STM Erie H Morales, Yunbin He, Mykola Vinnichenko, Bernard Delley and Ulrike Diebold Coulomb oscillations in three-layer graphene nanostructures J Güttinger, C Stampfer, F Molitor, D Graf, T Ihn and K Ensslin Adsorption processes of hydrogen molecules on SiC(001), Si(001) and C(001) surfaces Xiangyang Peng, Peter Krüger and Johannes Pollmann Fermi surface nesting in several transition metal dichalcogenides D S Inosov, V B Zabolotnyy, D V Evtushinsky, A A Kordyuk, B Büchner, R Follath, H Berger and S V Borisenko Probing molecule-surface interactions through ultra-fast adsorbate dynamics: propane/Pt(111) A P Jardine, H Hedgeland, D Ward, Y Xiaoqing, W Allison, J Ellis and G Alexandrowicz A novel method achieving ultra-high geometrical resolution in scanning tunnelling microscopy R Temirov, S Soubatch, O Neucheva, A C Lassise and F S Tautz

Davisson-Germer Prize in Atomic or Surface Physics Talk: Soft X-Ray Studies of Surfaces, Interfaces and Thin Films: From Spectroscopy to Ultrafast Nanoscale Movies

NASA Astrophysics Data System (ADS)

Stöhr, Joachim

2011-03-01

My talk will review the development of soft x-ray spectroscopy and microscopy and its impact on our understanding of chemical bonding, magnetism and dynamics at surfaces and interfaces. I will first outline important soft x-ray spectroscopy and microscopy techniques that have been developed over the last 30 years and their key strengths such as elemental and chemical specificity, sensitivity to small atomic concentrations, separation of charge and spin properties, spatial resolution down to the nanometer scale, and temporal resolution down to the intrinsic femtosecond timescale of atomic and electronic motions. I will then present scientific breakthroughs based on soft x-ray studies in three selected areas: the nature of molecular bonding and reactivity on metal surfaces, the molecular origin of liquid crystal alignment on surfaces, and the microscopic origin of interface-mediated spin alignments in modern magnetic devices. My talk will also cover the use of soft x-rays for revealing the temporal evolution of electronic structure, addressing the key problem of ``function,'' down to the intrinsic femtosecond time scale of charge and spin configuration changes. As examples I will present the formation and breaking of chemical bonds in surface complexes and the motion of the magnetization in magnetic devices. Work supported by the Office of Basic Energy Science of the US Department of Energy.

Ice formation on kaolinite: Insights from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

2016-12-01

The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.

Molecular environmental geochemistry

NASA Astrophysics Data System (ADS)

O'Day, Peggy A.

1999-05-01

The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at 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.

Characterization of oxygen and titanium diffusion at the anatase TiO2(001) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herman, Gregory S.; Zehr, Robert T.; Henderson, Michael A.

2013-06-01

The diffusion of intrinsic defects in a single crystal anatase TiO2(001) film was explored by isotopic labeling and static secondary ion mass spectrometry. Using both 46Ti and 18O as isotopic labels, we show that the anatase surface responds to redox imbalances by diffusion of both Ti and O into the bulk under vacuum reduction and (at least) Ti from the bulk to the surface during oxidation. The diffusion of Ti between the bulk and surface in anatase TiO2(001) closely resembles what was observed in the literature for the rutile TiO2(110) surface, however the latter is not known to have oxygenmore » diffusion between the bulk and surface under typical ultrahigh vacuum conditions. We speculate that the open lattice of the anatase bulk structure may facilitate independent diffusion of both point defects (Ti interstitials and O vacancies) or concerted diffusion of "TiO" subunits. The authors gratefully acknowledge S.A. Chambers of Pacific Northwest National Laboratory (PNNL) for providing the anatase samples. This research was supported by the U.S. Department of Energy (DOE) Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division, the Office of Naval Research Contract Number 200CAR262, and the Oregon Nanoscience and Microtechnologies Institute. PNNL is operated for the U.S. DOE by Battelle under Contract Number DE05-AC76RL0 1830. The research was performed in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility funded by the U.S. DOE Office of Biological and Environmental Research.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 ofmore » 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.« less

PREFACE: The International Conference on Science of Friction

NASA Astrophysics Data System (ADS)

Miura, Kouji; Matsukawa, Hiroshi

2007-07-01

The first international conference on the science of friction in Japan was held at Irago, Aichi on 9-13 September 2007. The conference focused on the elementary process of friction phenomena from the atomic and molecular scale view. Topics covered in the conference are shown below.:

Hummingbird Comet Nucleus Analysis Mission

NASA Technical Reports Server (NTRS)

Kojiro, Daniel; Carle, Glenn C.; Lasher, Larry E.

2000-01-01

Hummingbird is a highly focused scientific mission, proposed to NASA s Discovery Program, designed to address the highest priority questions in cometary science-that of the chemical composition of the cometary nucleus. After rendezvous with the comet, Hummingbird would first methodically image and map the comet, then collect and analyze dust, ice and gases from the cometary atmosphere to enrich characterization of the comet and support landing site selection. Then, like its namesake, Hummingbird would carefully descend to a pre-selected surface site obtaining a high-resolution image, gather a surface material sample, acquire surface temperature and then immediately return to orbit for detailed chemical and elemental analyses followed by a high resolution post-sampling image of the site. Hummingbird s analytical laboratory contains instrumentation for a comprehensive molecular and elemental analysis of the cometary nucleus as well as an innovative surface sample acquisition device.

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry.

PubMed

Caron, Etienne; Kowalewski, Daniel J; Chiek Koh, Ching; Sturm, Theo; Schuster, Heiko; Aebersold, Ruedi

2015-12-01

The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Kennicutt-Schmidt Law in the Central Region of NGC 4321 as Seen by ALMA

PubMed Central

Azeez, Jazeel H.; Hwang, C.-Y.; Abidin, Zamri Z.; Ibrahim, Zainol A.

2016-01-01

We present the Atacama Large Millimeter/Sub-millimeter Array (ALMA) cycle-0 science verification data of the CO(1–0) line emission in the central region of NGC 4321 (also known as M100) at the distance of 17.1 Mpc and VLA, L-band data of HI of the same galaxy. We have drawn the center area of M100 in the 12CO(J = 1–0) line with the resolution of (3.87″ × 2.53″) as viewed by ALMA, along with HI and Spitzer 8 and 3.6 μm data. The relationship between the surface density of molecular gas mass ∑H2 and that of star formation rate ∑SFR has been investigated, in addition to the relationship between the surface density of the neutral atomic hydrogen mass and that of ∑SFR (Kennicutt–Schmidt law) in this galaxy with a high spatial resolution. The results indicate that a significant correlation exists between the SFR surface density and the molecular gas mass density in the ~2 kpc region. The power-law index has been determined for three regions: center, upper and lower arms. The value of this index in the center region is 1.13, which follows the traditional (K-S) law and indicates that the molecular gas is affected by star formation. PMID:27247251

JPRS Report, Science & Technology, Japan, Government and Private Sector Joint R&D Projects

DTIC Science & Technology

1988-08-16

is that if this system uses exogenous genes represented by the DNA that codes for hepatitis B surface antigen, polyvaccines can be produced easily...that can express in large quantities molecular clones of genetic products is awaited. Vectors using cells of higher mammals including man have been...functions of IVM and MMD using cultured spinal nerve cells with a great advantage that the same sample can be used for both electrophysiological and

Introducing Molecular Life Science Students to Model Building Using Computer Simulations

ERIC Educational Resources Information Center

Aegerter-Wilmsen, Tinri; Kettenis, Dik; Sessink, Olivier; Hartog, Rob; Bisseling, Ton; Janssen, Fred

2006-01-01

Computer simulations can facilitate the building of models of natural phenomena in research, such as in the molecular life sciences. In order to introduce molecular life science students to the use of computer simulations for model building, a digital case was developed in which students build a model of a pattern formation process in…

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

PubMed Central

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. PMID:20194805

Fundamental approaches in molecular biology for communication sciences and disorders.

PubMed

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

2012-08-01

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. Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has increased at a remarkable pace. Most of this progress can be attributed to concomitant advances in basic molecular biology and, specifically, the development of an ever-expanding armamentarium of technologies for analysis of DNA, RNA, and protein structure and function. Details of these methodologies, their limitations, and examples from the communication sciences and disorders literature are presented. Results/Conclusions The use of molecular biology techniques in the fields of speech, language, and hearing sciences is increasing, facilitating the need for an understanding of molecular biology fundamentals and common experimental assays.

Low-temperature, ultrahigh-vacuum tip-enhanced Raman spectroscopy combined with molecular beam epitaxy for in situ two-dimensional materials' studies

NASA Astrophysics Data System (ADS)

Sheng, Shaoxiang; Li, Wenbin; Gou, Jian; Cheng, Peng; Chen, Lan; Wu, Kehui

2018-05-01

Tip-enhanced Raman spectroscopy (TERS), which combines scanning probe microscopy with the Raman spectroscopy, is capable to access the local structure and chemical information simultaneously. However, the application of ambient TERS is limited by the unstable and poorly controllable experimental conditions. Here, we designed a high performance TERS system based on a low-temperature ultrahigh-vacuum scanning tunneling microscope (LT-UHV-STM) and combined with a molecular beam epitaxy (MBE) system. It can be used for growing two-dimensional (2D) materials and for in situ STM and TERS characterization. Using a 2D silicene sheet on the Ag(111) surface as a model system, we achieved an unprecedented 109 Raman single enhancement factor in combination with a TERS spatial resolution down to 0.5 nm. The results show that TERS combined with a MBE system can be a powerful tool to study low dimensional materials and surface science.

Tracking Site-specific C-C Coupling of Formaldehyde Molecules on Rutile TiO2(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Ke; Xia, Yaobiao; Tang, Miru

2015-06-25

Direct imaging of site-specific reactions of individual mole-cules as a function of temperature is a long-sought goal in molecular science. Here, we report the direct visualization of molecular coupling of formaldehyde on reduced rutile TiO2(110) surfaces as we track the same set of molecules when the temperature is increased from 75 to 170 K using scanning tunneling microscope (STM). Our recent study showed that formaldehyde preferably adsorbs on bridging-bonded oxygen (Ob) vacancy (VO) defect site. Herein, images from the same area as the temperature is increased show that VO-bound formaldehyde couples with Ti-bound formaldehyde forming a diolate intermediate. Exposure ofmore » formaldehyde at room temperature leads to diolate as the majority species on the surface and no VO-bound formaldehyde is observed. The diolate species are the key reaction intermediates in the formation of ethylene reported in previous ensemble-averaged studies.« less

Molecular catalysis science: Perspective on unifying the fields of catalysis

DOE PAGES

Ye, Rong; Hurlburt, Tyler J.; Sabyrov, Kairat; ...

2016-04-25

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 sumfrequency 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. Itmore » was also found that catalytic performance can be tuned by carefully designing and fabricating catalysts from the bottom up. Homogeneous and h eterogeneous catalysts, and likely enzymes, behave similarly at the molecular level. Finally, unifying the fields of catalysis is the key to achieving the goal of 100% selectivity in catalysis.« less

Molecularly Imprinted Nanomaterials for Sensor Applications

PubMed Central

Irshad, Muhammad; Iqbal, Naseer; Mujahid, Adnan; Afzal, Adeel; Hussain, Tajamal; Sharif, Ahsan; Ahmad, Ejaz; Athar, Muhammad Makshoof

2013-01-01

Molecular imprinting is a well-established technology to mimic antibody-antigen interaction in a synthetic platform. Molecularly imprinted polymers and nanomaterials usually possess outstanding recognition capabilities. Imprinted nanostructured materials are characterized by their small sizes, large reactive surface area and, most importantly, with rapid and specific analysis of analytes due to the formation of template driven recognition cavities within the matrix. The excellent recognition and selectivity offered by this class of materials towards a target analyte have found applications in many areas, such as separation science, analysis of organic pollutants in water, environmental analysis of trace gases, chemical or biological sensors, biochemical assays, fabricating artificial receptors, nanotechnology, etc. We present here a concise overview and recent developments in nanostructured imprinted materials with respect to various sensor systems, e.g., electrochemical, optical and mass sensitive, etc. Finally, in light of recent studies, we conclude the article with future perspectives and foreseen applications of imprinted nanomaterials in chemical sensors. PMID:28348356

Application of the Molecular Adsorber Coating Technology on the Ionospheric Connection Explorer Program

NASA Technical Reports Server (NTRS)

Abraham, Nithin S.; Hasegawa, Mark M.; Secunda, Mark S.

2016-01-01

The Molecular Adsorber Coating (MAC) is a zeolite based highly porous coating technology that was developed by NASA Goddard Space Flight Center (GSFC) to capture outgassed contaminants, such as plastics, adhesives, lubricants, silicones, epoxies, potting compounds, and other similar materials. This paper describes the use of the MAC technology to address molecular contamination concerns on NASAs Ionospheric Connection Explorer (ICON) program led by the University of California (UC) Berkeleys Space Sciences Laboratory. The sprayable paint technology was applied onto plates that were installed within the instrument cavity of ICONs Far Ultraviolet Imaging Spectrograph (FUV). However, due to the instruments particulate sensitivity, the coating surface was vibrationally cleaned through simulated acoustics to reduce the risk of particle fall-out contamination. This paper summarizes the coating application efforts on the FUV adsorber plates, the simulated laboratory acoustic level cleaning test methods, particulation characteristics, and future plans for the MAC technology.

Application of the Molecular Adsorber Coating technology on the Ionospheric Connection Explorer program

NASA Astrophysics Data System (ADS)

Abraham, Nithin S.; Hasegawa, Mark M.; Secunda, Mark S.

2016-09-01

The Molecular Adsorber Coating (MAC) is a zeolite based highly porous coating technology that was developed by NASA Goddard Space Flight Center (GSFC) to capture outgassed contaminants, such as plastics, adhesives, lubricants, silicones, epoxies, potting compounds, and other similar materials. This paper describes the use of the MAC technology to address molecular contamination concerns on NASA's Ionospheric Connection Explorer (ICON) program led by the University of California (UC) Berkeley's Space Sciences Laboratory. The sprayable paint technology was applied onto plates that were installed within the instrument cavity of ICON's Far Ultraviolet Imaging Spectrograph (FUV). However, due to the instrument's particulate sensitivity, the coating surface was vibrationally cleaned through simulated acoustics to reduce the risk of particle fall-out contamination. This paper summarizes the coating application efforts on the FUV adsorber plates, the simulated laboratory acoustic level cleaning test methods, particulation characteristics, and future plans for the MAC technology.

Porphyrins at interfaces

NASA Astrophysics Data System (ADS)

Auwärter, Willi; Écija, David; Klappenberger, Florian; Barth, Johannes V.

2015-02-01

Porphyrins and other tetrapyrrole macrocycles possess an impressive variety of functional properties that have been exploited in natural and artificial systems. Different metal centres incorporated within the tetradentate ligand are key for achieving and regulating vital processes, including reversible axial ligation of adducts, electron transfer, light-harvesting and catalytic transformations. Tailored substituents optimize their performance, dictating their arrangement in specific environments and mediating the assembly of molecular nanoarchitectures. Here we review the current understanding of these species at well-defined interfaces, disclosing exquisite insights into their structural and chemical properties, and also discussing methods by which to manipulate their intramolecular and organizational features. The distinct characteristics arising from the interfacial confinement offer intriguing prospects for molecular science and advanced materials. We assess the role of surface interactions with respect to electronic and physicochemical characteristics, and describe in situ metallation pathways, molecular magnetism, rotation and switching. The engineering of nanostructures, organized layers, interfacial hybrid and bio-inspired systems is also addressed.

Flow in porous media, phase and ultralow interfacial tensions: Mechanisms of enhanced petroleum recovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, H.T.; Scriven, L.E.

1991-07-01

A major program of university research, longer-ranged and more fundamental in approach than industrial research, into basic mechanisms of enhancing petroleum recovery and into underlying physics, chemistry, geology, applied mathematics, computation, and engineering science has been built at Minnesota. The original focus was surfactant-based chemical flooding, but the approach taken was sufficiently fundamental that the research, longer-ranged than industrial efforts, has become quite multidirectional. Topics discussed are volume controlled porosimetry; fluid distribution and transport in porous media at low wetting phase saturation; molecular dynamics of fluids in ultranarrow pores; molecular dynamics and molecular theory of wetting and adsorption; new numericalmore » methods to handle initial and boundary conditions in immiscible displacement; electron microscopy of surfactant fluid microstructure; low cost system for animating liquid crystallites viewed with polarized light; surfaces of constant mean curvature with prescribed contact angle.« less

Conceptual Considerations in Molecular Science

ERIC Educational Resources Information Center

Sawyer, Donald T.

2005-01-01

There are significant misconceptions within the chemical community and molecular science, particularly in the undergraduate curriculum and the associated textbooks. Some of the misconceptions are described, which give poor basis to understand molecular bonding and structure, and reaction mechanisms.

The Interaction of Water with Solid Surfaces: Fundamental Aspects Revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, Michael A.

2002-05-01

Water is perhaps the most important and most pervasive chemical on our planet. The influence of water permeates virtually all areas of biochemical, chemical and physical importance, and is especially evident in phenomena occurring at the interfaces of solid surfaces. Since 1987, when Thiel and Madey (TM) published their review titled "The Interaction of Water with Solid Surfaces: Fundamental Aspects" in Surface Science Reports, there has been considerable progress made in further understanding the fundamental interactions of water with solid surfaces. In the decade and a half, the increased capability of surface scientists to probe at the molecular-level has resultedmore » in more detailed information of the properties of water on progressively more complicated materials and under more stringent conditions. This progress in understanding the properties of water on solid surfaces is evident both in areas for which surface science methodology has traditionally been strong (catalysis and electronic materials) and also in new areas not traditionally studied by surface scientists, such as electrochemistry, photoconversion, mineralogy, adhesion, sensors, atmospheric chemistry, and tribology. Researchers in all these fields grapple with very basic questions regarding the interactions of water with solid surfaces, such as how is water adsorbed, what are the chemical and electrostatic forces that constitute the adsorbed layer, how is water thermally or non-thermally activated, and how do coadsorbates influence these properties of water. The attention paid to these and other fundamental questions in the past decade and a half has been immense. In this review, experimental studies published since the TM review are assimilated with those covered by TM to provide a current picture of the fundamental interactions of water with solid surfaces.« less

Free energy calculation of permeant-membrane interactions using molecular dynamics simulations.

PubMed

Elvati, Paolo; Violi, Angela

2012-01-01

Nanotoxicology, the science concerned with the safe use of nanotechnology and nanostructure design for biological applications, is a field of research that has recently received great attention, as a result of the rapid growth in nanotechnology. Many nanostructures are of a scale and chemical composition similar to many biomolecular environments, and recent papers have reported evident toxicity of selected nanoparticles. Molecular simulations can help develop a mechanistic understanding of how structural properties affect bioactivity. In this chapter, we describe how to compute the free energy of interactions between cellular membranes and benzene, the main constituent of some toxic carbonaceous particles, with well-tempered metadynamics. This algorithm reconstructs the free energy surface and accelerates rare events in a coarse-grained representation of the system.

Properties of liquid Ti alloys from electrostatic levitation experiments and simulation

NASA Astrophysics Data System (ADS)

Novak, Brian; Raush, Jonathan; Zhang, Xiaoman; Moldovan, Dorel; Meng, Wenjin; Guo, Shengmin

Accurate thermophysical property data for liquid metals and alloys are important for the development of realistic simulations of laser-based 3D printing processes. We are using the container-less electrostatic levitation (ESL) method, molecular simulation, and CALPHAD calculations to obtain such data for Ti alloys. We performed vacuum ESL measurements of viscosity and surface tension with an oscillating drop technique at NASA MSFC on molten elemental Ti, Ti-xAl binaries (x = 0-10 wt%), Ti-6Al-4V, and Ti-6Al-4V-10Mo which showed improved mechanical properties compared with traditional β Ti alloys. We also used classical molecular simulations to obtain viscosities and surface tensions for Ti-xAl. Pair distribution functions, diffusivities, and vapor pressures were also obtained from simulations. The simulated viscosities and surface tensions for pure Ti agree well with the ESL data while the Ti-xAl viscosities have the same trends as the ESL data, but not quantitative agreement. Chemical activity and Gibbs free energy of Ti-10Al were generated using the CALPHAD technique and compared to experimental values. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

Micropatterned Surfaces for Atmospheric Water Condensation via Controlled Radical Polymerization and Thin Film Dewetting.

PubMed

Wong, Ian; Teo, Guo Hui; Neto, Chiara; Thickett, Stuart C

2015-09-30

Inspired by an example found in nature, the design of patterned surfaces with chemical and topographical contrast for the collection of water from the atmosphere has been of intense interest in recent years. Herein we report the synthesis of such materials via a combination of macromolecular design and polymer thin film dewetting to yield surfaces consisting of raised hydrophilic bumps on a hydrophobic background. RAFT polymerization was used to synthesize poly(2-hydroxypropyl methacrylate) (PHPMA) of targeted molecular weight and low dispersity; spin-coating of PHPMA onto polystyrene films produced stable polymer bilayers under appropriate conditions. Thermal annealing of these bilayers above the glass transition temperature of the PHPMA layer led to complete dewetting of the top layer and the formation of isolated PHPMA domains atop the PS film. Due to the vastly different rates of water nucleation on the two phases, preferential dropwise nucleation of water occurred on the PHPMA domains, as demonstrated by optical microscopy. The simplicity of the preparation method and ability to target polymers of specific molecular weight demonstrate the value of these materials with respect to large-scale water collection devices or other materials science applications where patterning is required.

Controllable growth of GeSi nanostructures by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Ma, Yingjie; Zhou, Tong; Zhong, Zhenyang; Jiang, Zuimin

2018-06-01

We present an overview on the recent progress achieved on the controllable growth of diverse GeSi alloy nanostructures by molecular beam epitaxy. Prevailing theories for controlled growth of Ge nanostructures on patterned as well as inclined Si surfaces are outlined firstly, followed by reviews on the preferential growth of Ge nanoislands on patterned Si substrates, Ge nanowires and high density nanoislands grown on inclined Si surfaces, and the readily tunable Ge nanostructures on Si nanopillars. Ge nanostructures with controlled geometries, spatial distributions and densities, including two-dimensional ordered nanoislands, three-dimensional ordered quantum dot crystals, ordered nanorings, coupled quantum dot molecules, ordered nanowires and nanopillar alloys, are discussed in detail. A single Ge quantum dot-photonic crystal microcavity coupled optical emission device demonstration fabricated by using the preferentially grown Ge nanoisland technique is also introduced. Finally, we summarize the current technology status with a look at the future development trends and application challenges for controllable growth of Ge nanostructures. Project supports by the Natural Science Foundation of China (Nos. 61605232, 61674039) and the Open Research Project of State Key Laboratory of Surface Physics from Fudan University (Nos. KF2016_15s, KF2017_05).

Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

NASA Astrophysics Data System (ADS)

Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

International Symposium on Molecular Spectroscopy (70th)

DTIC Science & Technology

2015-06-22

N DAY June 22 8:30 AM TU ESDAY June 23 8:30 AM W EDN ESDAY June 24 8:30 AM THU RSDAY June 25 8:30 AM FRIDAY June 26 8:30 AM Foellinger Auditorium M A...energy surfaces Room 100 N oyes Laboratory TB M ini-sym posium : Accelerator-Based Spectroscopy RB M ini-sym posium : Accelerator-Based...Conform ers, isom ers, chirality, stereochem istry RD Astronom y FD Atm ospheric science Room 217 N oyes Laboratory TE Instrum

Biofilms 2015: Multidisciplinary Approaches Shed Light into Microbial Life on Surfaces

PubMed Central

Yildiz, Fitnat

2016-01-01

The 7th ASM Conference on Biofilms was held in Chicago, Illinois, from 24 to 29 October 2015. The conference provided an international forum for biofilm researchers across academic and industry platforms, and from different scientific disciplines, to present and discuss new findings and ideas. The meeting covered a wide range of topics, spanning environmental sciences, applied biology, evolution, ecology, physiology, and molecular biology of the biofilm lifestyle. This report summarizes the presentations with regard to emerging biofilm-related themes. PMID:26977109

Coulomb blockade and charge ordering in a few layers of TTF-TCNQ investigated by low-temperature STM/STS

NASA Astrophysics Data System (ADS)

Jeon, Seokmin; Maksymovych, Petro

In contrast to the vast effort on bulk crystal phases of the prototypical organic charge-transfer complex, TTF-TCNQ, study of low-dimensional phases has been limited to monolayer phases on substrates. In this state, however, none of the physics of the bulk phase is observed owing to the overwhelming effect of the substrate. We investigate the molecular structure and electronic properties of a few layers of TTF-TCNQ grown on Au(111) and Ag(111) using STM/STS at 4.3 K. By decoupling the molecular electronic state from the metal surface, we have made the first observation of the effect of confinement on the electronic properties of TTF-TCNQ. STS reveals a plethora of sharp features due to molecular orbitals, each influenced by charge-transfer between the molecules. We hypothesize the existence of a Mott-insulator state in 3-layer islands, with a Coulomb gap of ~1 eV. In contrast, the corresponding bulk phase is a Peierls insulator with a gap of ~20 meV. The root cause of the nanoscale phase is traced to simultaneous electron confinement and structural frustration, which dramatically modify the energy balance of self-ionization allowing for integer charge transfer. These studies open broad opportunities to explore correlated electron physics in molecular systems. This research was conducted at the Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility.

Molecular imprinted polymers for separation science: a review of reviews.

PubMed

Cheong, Won Jo; Yang, Song Hee; Ali, Faiz

2013-02-01

Molecular imprinted polymer is an artificial receptor made by imprinting molecules of a template in a polymer matrix followed by removing the template molecules via thorough washing to give the permanent template grooves. They show favored affinity to the template molecule compared to other molecules, and this property is the basic driving force for such diverse application of this techniques. Such techniques have been increasingly employed in a wide scope of applications such as chromatography, sample pretreatment, purification, catalysts, sensors, and drug delivery, etc., mostly in bioanalytical areas. A major part of them is related to development of new stationary phases and their application in chromatography and sample pretreatment. Embodiments of molecular imprinted polymer materials have been carried out in a variety of forms such as irregularly ground particles, regular spherical particles, nanoparticles, monoliths in a stainless steel or capillary column, open tubular layers in capillaries, surface attached thin layers, membranes, and composites, etc. There have been numerous review articles on molecular imprinted polymer issues. In this special review, the reviews in recent ca. 10 years will be categorized into several subgroups according to specified topics in separation science, and each review in each subgroup will be introduced in the order of date with brief summaries and comments on new developments and different scopes of prospects. Brief summaries of each categories and conclusive future perspectives are also given. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discovery of an Unexplored Protein Structural Scaffold of Serine Protease from Big Blue Octopus (Octopus cyanea): A New Prospective Lead Molecule.

PubMed

Panda, Subhamay; Kumari, Leena

2017-01-01

Serine proteases are a group of enzymes that hydrolyses the peptide bonds in proteins. In mammals, these enzymes help in the regulation of several major physiological functions such as digestion, blood clotting, responses of immune system, reproductive functions and the complement system. Serine proteases obtained from the venom of Octopodidae family is a relatively unexplored area of research. In the present work, we tried to effectively utilize comparative composite molecular modeling technique. Our key aim was to propose the first molecular model structure of unexplored serine protease 5 derived from big blue octopus. The other objective of this study was to analyze the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the aid of different bioinformatic tools. In the present study, molecular model has been generated with the help of I-TASSER suite. Afterwards the refined structural model was validated with standard methods. For functional annotation of protein molecule we used Protein Information Resource (PIR) database. Serine protease 5 of big blue octopus was analyzed with different bioinformatical algorithms for the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) were determined using the COACH program. The molecular model data in cooperation to other pertinent post model analysis data put forward molecular insight to proteolytic activity of serine protease 5, which helps in the clear understanding of procoagulant and anticoagulant characteristics of this natural lead molecule. Our approach was to investigate the octopus venom protein as a whole or a part of their structure that may result in the development of new lead molecule. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Developing the Cleanliness Requirements for an Organic-detection Instrument MOMA-MS

NASA Technical Reports Server (NTRS)

Perry, Radford; Canham, John; Lalime, Erin

2015-01-01

The cleanliness requirements for an organic-detection instrument, like the Mars Organic Molecule Analyzer Mass Spectrometer (MOMA-MS), on a Planetary Protection Class IVb mission can be extremely stringent. These include surface molecular and particulate, outgassing, and bioburden. The prime contractor for the European Space Agencys ExoMars 2018 project, Thales Alenia Space Italy, provided requirements based on a standard, conservative approach of defining limits which yielded levels that are unverifiable by standard cleanliness verification methods. Additionally, the conservative method for determining contamination surface area uses underestimation while conservative bioburden surface area relies on overestimation, which results in inconsistencies for the normalized reporting. This presentation will provide a survey of the challenge to define requirements that can be reasonably verified and still remain appropriate to the core science of the ExoMars mission.

Marine molecular biology: an emerging field of biological sciences.

PubMed

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.

Studies of lithiumization and boronization of ATJ graphite PFCs for NSTX-U

NASA Astrophysics Data System (ADS)

Dominguez, Javier; Bedoya, Felipe; Krstic, Predrag; Allain, Jean Paul; Neff, Anton; Luitjohan, Kara

2016-10-01

We examine and compare the effects of boron and lithium conditioning on ATJ graphite surfaces bombarded by low-energy deuterium atoms on deuterium retention and chemical sputtering. We use atomistic simulations and compare them with experimental in-situ ex-tempore studies with X-ray photoelectron spectroscopy (XPS), to understand the effects of deuterium exposure on the chemistry in lithiated, boronized and oxidized amorphous carbon surfaces. Our results are validated qualitatively by comparison with experiments and with classical-quantum molecular dynamic simulations. We explain the important role of oxygen in D retention for lithiated surfaces and the suppression of the oxygen role by boron in boronized surfaces. The calculated increase of the oxygen role in deuterium uptake after D accumulation in a B-C-O surface configuration is discussed. The sputtering yield per low-energy D impact is significantly smaller in boronized surfaces than in lithiated surfaces. This work was supported by the USDOE Grants DE-SC0013752 (PSK), DE-SC0010717 (JPA and FB) and DE-SC0010719 (AN) and by National council for Science and Technology of Mexico (CONACyT) through postdoctoral fellowship # 267898 (JD).

Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

ERIC Educational Resources Information Center

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…

Advanced Heat/Mass Exchanger Technology for Geothermal and Solar Renewable Energy Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greiner, Miles; Childress, Amy; Hiibel, Sage

2014-12-16

Northern Nevada has abundant geothermal and solar energy resources, and these renewable energy sources provide an ample opportunity to produce economically viable power. Heat/mass exchangers are essential components to any energy conversion system. Improvements in the heat/mass exchange process will lead to smaller, less costly (more efficient) systems. There is an emerging heat transfer technology, based on micro/nano/molecular-scale surface science that can be applied to heat/mass exchanger design. The objective is to develop and characterize unique coating materials, surface configurations and membranes capable of accommodating a 10-fold increase in heat/mass exchanger performance via phase change processes (boiling, condensation, etc.) andmore » single phase convective heat/mass transfer.« less

Atomistic simulation of frictional anisotropy on quasicrystal approximant surfaces

DOE PAGES

Ye, Zhijiang; Martini, Ashlie; Thiel, Patricia; ...

2016-06-23

J. Y. Park et al. [Science 309, 1354 (2005)] have reported eight times greater atomic-scale friction in the periodic than in the quasiperiodic direction on the twofold face of a decagonal Al-Ni-Co quasicrystal. Here we present results of molecular-dynamics simulations intended to elucidate mechanisms behind this giant frictional anisotropy. Simulations of a bare atomic-force-microscope tip on several model substrates and under a variety of conditions failed to reproduce experimental results. On the other hand, including the experimental passivation of the tip with chains of hexadecane thiol, we reproduce qualitatively the experimental anisotropy in friction, finding evidence for entrainment of themore » organic chains in surface furrows parallel to the periodic direction.« less

In-situ spectro-microscopy on organic films: Mn-Phthalocyanine on Ag(100)

NASA Astrophysics Data System (ADS)

Al-Mahboob, Abdullah; Sadowski, Jerzy T.; Vescovo, Elio

2013-03-01

Metal phthalocyanines are attracting significant attention, owing to their potential for applications in chemical sensors, solar cells and organic magnets. As the electronic properties of molecular films are determined by their crystallinity and molecular packing, the optimization of film quality is important for improving the performance of organic devices. Here, we present the results of in situ low-energy electron microscopy / photoemission electron microscopy (LEEM/PEEM) studies of incorporation-limited growth of manganese-phthalocyanine (MnPc) on Ag(100) surfaces. MnPc thin films were grown on both, bulk Ag(100) surface and thin Ag(100)/Fe(100) films, where substrate spin-polarized electronic states can be modified through tuning the thickness of the Ag film. We also discuss the electronic structure and magnetic ordering in MnPc thin films, investigated by angle- and spin-resolved photoemission spectroscopy. Research carried out at the Center for Functional Nanomaterials and National Synchrotron Light Source, Brookhaven National Laboratory, which are supported by the U.S. Dept. of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

The Development of a Post-Baccalaureate Certificate Program in Molecular Diagnostics

PubMed Central

Williams, Gail S.; Brown, Judith D.; Keagle, Martha B.

2000-01-01

A post-baccalaureate certificate program in diagnostic molecular sciences was created in 1995 by the Diagnostic Genetic Sciences Program in the School of Allied Health at the University of Connecticut. The required on-campus lecture and laboratory courses include basic laboratory techniques, health care issues, cell biology, immunology, human genetics, research, management, and molecular diagnostic techniques and laboratory in molecular diagnostics. These courses precede a 6-month, full-time practicum at an affiliated full-service molecular laboratory. The practicum includes amplification and blotting methods, a research project, and a choice of specialized electives including DNA sequencing, mutagenesis, in situ hybridization methods, or molecular diagnostic applications in microbiology. Graduates of the program are immediately eligible to sit for the National Credentialing Agency examination in molecular biology to obtain the credential Clinical Laboratory Specialist in Molecular Biology (CLSp(MB). This description of the University of Connecticut program may assist other laboratory science programs in creating similar curricula. PMID:11232107

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

Background Discerning the similarity between molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeting exploration of molecular structural space, query-retrieval in molecular databases, and structure-activity modelling. Determining molecular similarity is related to the choice of molecular representation. Currently, representations with high descriptive power and physical relevance like 3D surface-based descriptors are available. Information from such representations is both surface-based and volumetric. However, most techniques for determining molecular similarity tend to focus on idealized 2D graph-based descriptors due to the complexity that accompanies reasoning with more elaborate representations. Results This paper addresses the problem of determining similarity when molecules are described using complex surface-based representations. It proposes an intrinsic, spherical representation that systematically maps points on a molecular surface to points on a standard coordinate system (a sphere). Molecular surface properties such as shape, field strengths, and effects due to field super-positioningcan then be captured as distributions on the surface of the sphere. Surface-based molecular similarity is subsequently determined by computing the similarity of the surface-property distributions using a novel formulation of histogram-intersection. The similarity formulation is not only sensitive to the 3D distribution of the surface properties, but is also highly efficient to compute. Conclusion The proposed method obviates the computationally expensive step of molecular pose-optimisation, can incorporate conformational variations, and facilitates highly efficient determination of similarity by directly comparing molecular surfaces and surface-based properties. Retrieval performance, applications in structure-activity modeling of complex biological properties, and comparisons with existing research and commercial methods demonstrate the validity and effectiveness of the approach. PMID:17634096

Use of Laboratory Data to Model Interstellar Chemistry

NASA Technical Reports Server (NTRS)

Vidali, Gianfranco; Roser, J. E.; Manico, G.; Pirronello, V.

2006-01-01

Our laboratory research program is about the formation of molecules on dust grains analogues in conditions mimicking interstellar medium environments. Using surface science techniques, in the last ten years we have investigated the formation of molecular hydrogen and other molecules on different types of dust grain analogues. We analyzed the results to extract quantitative information on the processes of molecule formation on and ejection from dust grain analogues. The usefulness of these data lies in the fact that these results have been employed by theoreticians in models of the chemical evolution of ISM environments.

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

PubMed

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.

Imaging molecular interaction of NO on Cu(110) with a scanning tunneling microscope.

PubMed

Okuyama, Hiroshi

2014-10-01

Molecular interaction on metal surfaces is one of the central issues of surface science for the microscopic understanding of heterogeneous catalysis. In this Personal Account, I review the recent studies on NO/Cu(110) employing a scanning tunneling microscope (STM) to probe and control the molecule-molecule interaction on the surface. An individual NO molecule was observed as a characteristic dumbbell-shaped protrusion, visualizing the 2π* orbital. By manipulating the intermolecular distance with the STM, the overlap of the 2π* orbital between two NO molecules was controlled. The interaction causes the formation of the bonding and antibonding orbitals below and above the Fermi level, respectively, as a function of the intermolecular distance. The 2π* orbital also plays a role in the reaction of NO with water molecules. A water molecule donates a H-bond to NO, giving rise to the down-shift of the 2π* level below the Fermi level. This causes electron transfer from the substrate to NO, weakening, and eventually rupturing, the N-O bond. The facile bond cleavage by water molecules has implications for the catalytic reduction of NO under ambient conditions. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

When biomolecules meet graphene: from molecular level interactions to material design and applications.

PubMed

Li, Dapeng; Zhang, Wensi; Yu, Xiaoqing; Wang, Zhenping; Su, Zhiqiang; Wei, Gang

2016-12-01

Graphene-based materials have attracted increasing attention due to their atomically-thick two-dimensional structures, high conductivity, excellent mechanical properties, and large specific surface areas. The combination of biomolecules with graphene-based materials offers a promising method to fabricate novel graphene-biomolecule hybrid nanomaterials with unique functions in biology, medicine, nanotechnology, and materials science. In this review, we focus on a summarization of the recent studies in functionalizing graphene-based materials using different biomolecules, such as DNA, peptides, proteins, enzymes, carbohydrates, and viruses. The different interactions between graphene and biomolecules at the molecular level are demonstrated and discussed in detail. In addition, the potential applications of the created graphene-biomolecule nanohybrids in drug delivery, cancer treatment, tissue engineering, biosensors, bioimaging, energy materials, and other nanotechnological applications are presented. This review will be helpful to know the modification of graphene with biomolecules, understand the interactions between graphene and biomolecules at the molecular level, and design functional graphene-based nanomaterials with unique properties for various applications.

Recent Advances of Activatable Molecular Probes Based on Semiconducting Polymer Nanoparticles in Sensing and Imaging

PubMed Central

Lyu, Yan

2017-01-01

Molecular probes that change their signals in response to the target of interest have a critical role in fundamental biology and medicine. Semiconducting polymer nanoparticles (SPNs) have recently emerged as a new generation of purely organic photonic nanoagents with desirable properties for biological applications. In particular, tunable optical properties of SPNs allow them to be developed into photoluminescence, chemiluminescence, and photoacoustic probes, wherein SPNs usually serve as the energy donor and internal reference for luminescence and photoacoustic probes, respectively. Moreover, facile surface modification and intraparticle engineering provide the versatility to make them responsive to various biologically and pathologically important substances and indexes including small‐molecule mediators, proteins, pH and temperature. This article focuses on recent advances in the development of SPN‐based activatable molecular probes for sensing and imaging. The designs and applications of these probes are discussed in details, and the present challenges to further advance them into life science are also analyzed. PMID:28638783

Imaging-based molecular barcoding with pixelated dielectric metasurfaces.

PubMed

Tittl, Andreas; Leitis, Aleksandrs; Liu, Mingkai; Yesilkoy, Filiz; Choi, Duk-Yong; Neshev, Dragomir N; Kivshar, Yuri S; Altug, Hatice

2018-06-08

Metasurfaces provide opportunities for wavefront control, flat optics, and subwavelength light focusing. We developed an imaging-based nanophotonic method for detecting mid-infrared molecular fingerprints and implemented it for the chemical identification and compositional analysis of surface-bound analytes. Our technique features a two-dimensional pixelated dielectric metasurface with a range of ultrasharp resonances, each tuned to a discrete frequency; this enables molecular absorption signatures to be read out at multiple spectral points, and the resulting information is then translated into a barcode-like spatial absorption map for imaging. The signatures of biological, polymer, and pesticide molecules can be detected with high sensitivity, covering applications such as biosensing and environmental monitoring. Our chemically specific technique can resolve absorption fingerprints without the need for spectrometry, frequency scanning, or moving mechanical parts, thereby paving the way toward sensitive and versatile miniaturized mid-infrared spectroscopy devices. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Organotypic vasculature: From descriptive heterogeneity to functional pathophysiology.

PubMed

Augustin, Hellmut G; Koh, Gou Young

2017-08-25

Blood vessels form one of the body's largest surfaces, serving as a critical interface between the circulation and the different organ environments. They thereby exert gatekeeper functions on tissue homeostasis and adaptation to pathologic challenge. Vascular control of the tissue microenvironment is indispensable in development, hemostasis, inflammation, and metabolism, as well as in cancer and metastasis. This multitude of vascular functions is mediated by organ-specifically differentiated endothelial cells (ECs), whose cellular and molecular heterogeneity has long been recognized. Yet distinct organotypic functional attributes and the molecular mechanisms controlling EC differentiation and vascular bed-specific functions have only become known in recent years. Considering the involvement of vascular dysfunction in numerous chronic and life-threatening diseases, a better molecular understanding of organotypic vasculatures may pave the way toward novel angiotargeted treatments to cure hitherto intractable diseases. This Review summarizes recent progress in the understanding of organotypic vascular differentiation and function. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Water condensation: a multiscale phenomenon.

PubMed

Jensen, Kasper Risgaard; Fojan, Peter; Jensen, Rasmus Lund; Gurevich, Leonid

2014-02-01

The condensation of water is a phenomenon occurring in multiple situations in everyday life, e.g., when fog is formed or when dew forms on the grass or on windows. This means that this phenomenon plays an important role within the different fields of science including meteorology, building physics, and chemistry. In this review we address condensation models and simulations with the main focus on heterogeneous condensation of water. The condensation process is, at first, described from a thermodynamic viewpoint where the nucleation step is described by the classical nucleation theory. Further, we address the shortcomings of the thermodynamic theory in describing the nucleation and emphasize the importance of nanoscale effects. This leads to the description of condensation from a molecular viewpoint. Also presented is how the nucleation can be simulated by use of molecular models, and how the condensation process is simulated on the macroscale using computational fluid dynamics. Finally, examples of hybrid models combining molecular and macroscale models for the simulation of condensation on a surface are presented.

Dehydration of 1-octadecanol over H-BEA: A combined experimental and computational study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Wenji; Liu, Yuanshuai; Barath, Eszter

Liquid phase dehydration of 1-octdecanol, which is intermediately formed during the hydrodeoxygenation of microalgae oil, has been explored in a combined experimental and computational study. The alkyl chain of C18 alcohol interacts with acid sites during diffusion inside the zeolite pores, resulting in an inefficient utilization of the Brønsted acid sites for samples with high acid site concentrations. The parallel intra- and inter- molecular dehydration pathways having different activation energies pass through alternative reaction intermediates. Formation of surface-bound alkoxide species is the rate-limiting step during intramolecular dehydration, whereas intermolecular dehydration proceeds via a bulky dimer intermediate. Octadecene is the primarymore » dehydration product over H-BEA at 533 K. Despite of the main contribution of Brønsted acid sites towards both dehydration pathways, Lewis acid sites are also active in the formation of dioctadecyl ether. The intramolecular dehydration to octadecene and cleavage of the intermediately formed ether, however, require strong BAS. L. Wang, D. Mei and J. A. Lercher, acknowledge the partial support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Molecular Simulations of Carbon Dioxide and Water: Cation Solvation and Wettability

NASA Astrophysics Data System (ADS)

Criscenti, L. J.; Bracco, J.; Cygan, R. T.

2010-12-01

Proposed carbon dioxide sequestration scenarios in sedimentary basins require investigation into the interaction between supercritical carbon dioxide, brines, and the mineral phases found in the basin and overlying caprock. Classical molecular dynamics (MD) simulations can be used to investigate some of these interactions such as the partitioning of metal cations between aqueous solutions and supercritical carbon dioxide, and the relative wettability of basin and caprock minerals with different fluid phases including water, carbon dioxide, and oil. Initial research has lead to the development of a new flexible carbon dioxide force field that successfully reproduces the vibrational properties of carbon dioxide, and a methodology for extracting contact angle information from large-scale MD simulations. Molecular simulations were performed to compare the solvation of alkali and alkaline metal cations in water and liquid carbon dioxide at 300K, using a flexible simple point charge (SPC) model for water and the new carbon dioxide force field. Solvation energies for Na+, Cs+, Mg2+, and Ba2+ are larger in water than in carbon dioxide, suggesting that these cations will partition preferentially into water. In both solutions, the solvation energy for the cations decreases with ion size and increases with ion charge. However, changes in solvation energy with increasing ionic radii are smaller in carbon dioxide than in water. Therefore, the overall partitioning of cations into carbon dioxide is predicted to increase with ion size. Molecular dynamics simulations are also useful to examine the relative wettability of minerals with different fluid phases. Large-scale MD simulations involving between 100,000 and 200,000 atoms have been conducted to establish a dynamic equilibrium between a drop of liquid water, water vapor, and kaolinite surfaces. The water drops consisted of at least 1700 molecules. Simulations were performed for five nanoseconds. The contact angle calculated for the siloxane surface of kaolinite is approximately 110°, and compares well with calculated contact angles for silica reported in the literature. The contact angle determined for the gibbsite surface of kaolinite is approximately 13° and compares favorably to reported experimental results. As expected, the siloxane surface is calculated to be hydrophobic and the gibbsite surface hydrophilic. This technique should prove useful to investigate the relative wettability of different minerals with subsurface fluids including supercritical CO2. This material is based upon work partially supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

Interactions of polymer surfaces and thin films

NASA Astrophysics Data System (ADS)

Zeng, Hongbo

2007-12-01

Characterization of the adhesion, tribological properties and dynamics of polymer surfaces has been of great interest for many years since polymers are commonly used as adhesive and lubricant coatings to produce both high and low adhesion or friction. Improving our fundamental understanding of the interactions of polymer surfaces at the molecular level is needed to develop further techniques in materials science and chemical engineering. The objectives of my research were to correlate the nano- and micro-scale properties of various polymer thin film and surface phenomena: adhesion, adhesion hysteresis, friction, lubrication, surface deformations, coalescence, spreading, and wear, and identify the fundamental physical forces and mechanisms at the molecular and micro-scales. I studied the adhesion of polymer films at temperatures ranging from below to above the glass transition temperature, Tg. The adhesion hysteresis was found to peak somewhere around Tg, but to also depend on the load, contact time and detachment rate. The results revealed some new scaling relations for the dynamic (rate-dependent) adhesion forces and effective surface energies of polymers. I studied the way polymer surfaces deform during adhesion (coalescence), spreading (wetting) and separation (detachment, rupture, fracture and failure) processes, and characterized the differences (and transition) between liquid-like and solid-like behavior during these processes, e.g., the transition from liquid-to-viscoelastic-to-ductile-to-brittle behavior. Complex and novel transient (dynamic) surface shape changes were found to occur during transitions that involved highly-ordered or disordered fingers, ripples, waves or cracks. A full picture has emerged for the transition from viscous liquid-like to brittle solid-like behavior of adhering and detaching interfaces. Finally, I developed a new experiment technique whereby an electric field can be applied across the two surfaces in a Surface Force Apparatus for the first time, and two types of experiments were performed to measure the normal and/or lateral forces between two surfaces under an E-field.

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

PubMed

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.

Effect of Molecular Architecture on Polymer Melt Surface Dynamics

NASA Astrophysics Data System (ADS)

Foster, Mark

The dynamics of the thermally stimulated surface height fluctuations in a polymer melt dictate wetting, adhesion, and tribology at that surface. These surface fluctuations can be profoundly altered by tethering of the chains. One type of tethering is the tethering of one part of a molecule to another part of the same molecule. This tethering is found in both long chain branched polymers and in macrocycles. We have studied the surface fluctuations with X-ray Photon Correlation Spectroscopy for melts of well-defined, anionically polymerized polystyrenes of various architectures, including linear, 6 arm star, pom-pom, comb and cyclic architectures. For linear chains, the variation of surface relaxation time with in-plane scattering vector can be fit using a hydrodynamic continuum theory (HCT) of thermally stimulated capillary waves that knows nothing of the chain architecture. Assuming the theory is applicable, apparent viscosities of the films may then be inferred from the XPCS data. For unentangled linear chains, the viscosity inferred from XPCS data in this manner is the same as that measured by conventional bulk rheometry. The HCT does a reasonable job of describing the variation of relaxation time with scattering vector for long branched chains also, but only if a viscosity much larger than that of the bulk is assumed. The discrepancy between the viscosity inferred from surface relaxation times using the HCT and that derived from conventional rheometry grows larger as the bulk Tg is approached and is different for each long chain branched architecture. However, for densely branched combs and cyclic chains different behaviors are found. Acknowledgement: Thanks to NSF (CBET 0730692) and the Advanced Photon Source, supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Science, under Contract No. W-31-109-ENG-38.

Modeling Shear Induced Von Willebrand Factor Binding to Collagen

NASA Astrophysics Data System (ADS)

Dong, Chuqiao; Wei, Wei; Morabito, Michael; Webb, Edmund; Oztekin, Alparslan; Zhang, Xiaohui; Cheng, Xuanhong

2017-11-01

Von Willebrand factor (vWF) is a blood glycoprotein that binds with platelets and collagen on injured vessel surfaces to form clots. VWF bioactivity is shear flow induced: at low shear, binding between VWF and other biological entities is suppressed; for high shear rate conditions - as are found near arterial injury sites - VWF elongates, activating its binding with platelets and collagen. Based on parameters derived from single molecule force spectroscopy experiments, we developed a coarse-grain molecular model to simulate bond formation probability as a function of shear rate. By introducing a binding criterion that depends on the conformation of a sub-monomer molecular feature of our model, the model predicts shear-induced binding, even for conditions where binding is highly energetically favorable. We further investigate the influence of various model parameters on the ability to predict shear-induced binding (vWF length, collagen site density and distribution, binding energy landscape, and slip/catch bond length) and demonstrate parameter ranges where the model provides good agreement with existing experimental data. Our results may be important for understanding vWF activity and also for achieving targeted drug therapy via biomimetic synthetic molecules. National Science Foundation (NSF),Division of Mathematical Sciences (DMS).

Molecular Imprinting Applications in Forensic Science

PubMed Central

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

2017-01-01

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. PMID:28350333

Molecular Imprinting Applications in Forensic Science.

PubMed

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.

Molecular Foundry Workshop draws overflow crowd to BerkeleyLab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, Art

2002-11-27

Nanoscale science and technology is now one of the top research priorities in the United States. With this background, it is no surprise that an overflow crowd or more than 350 registrants filled two auditoriums to hear about and contribute ideas for the new Molecular Foundry during a two-day workshop at the Lawrence Berkeley National Laboratory (Berkeley Lab). Scheduled to open for business at Berkeley Labin early 2006, the Molecular Foundry is one of three Nanoscale Science Research Centers (NSRCs) put forward for funding by the DOE's Office of Basic Energy Sciences (BES).

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

NASA Astrophysics Data System (ADS)

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.

Classic versus millennial medical lab anatomy.

PubMed

Benninger, Brion; Matsler, Nik; Delamarter, Taylor

2014-10-01

This study investigated the integration, implementation, and use of cadaver dissection, hospital radiology modalities, surgical tools, and AV technology during a 12-week contemporary anatomy course suggesting a millennial laboratory. The teaching of anatomy has undergone the greatest fluctuation of any of the basic sciences during the past 100 years in order to make room for the meteoric rise in molecular sciences. Classically, anatomy consisted of a 2-year methodical, horizontal, anatomy course; anatomy has now morphed into a 12-week accelerated course in a vertical curriculum, at most institutions. Surface and radiological anatomy is the language for all clinicians regardless of specialty. The objective of this study was to investigate whether integration of full-body dissection anatomy and modern hospital technology, during the anatomy laboratory, could be accomplished in a 12-week anatomy course. Literature search was conducted on anatomy text, journals, and websites regarding contemporary hospital technology integrating multiple image mediums of 37 embalmed cadavers, surgical suite tools and technology, and audio/visual technology. Surgical and radiology professionals were contracted to teach during the anatomy laboratory. Literature search revealed no contemporary studies integrating full-body dissection with hospital technology and behavior. About 37 cadavers were successfully imaged with roentograms, CT, and MRI scans. Students were in favor of the dynamic laboratory consisting of multiple activity sessions occurring simultaneously. Objectively, examination scores proved to be a positive outcome and, subjectively, feedback from students was overwhelmingly positive. Despite the surging molecular based sciences consuming much of the curricula, full-body dissection anatomy is irreplaceable regarding both surface and architectural, radiological anatomy. Radiology should not be a small adjunct to understand full-body dissection, but rather, full-body dissection aids the understanding of radiology mediums. The millennial anatomy dissection laboratory should consist of, at least, 50% radiology integration during full-body dissection. This pilot study is an example of the most comprehensive integration of full-body dissection, radiology, and hospital technology. © 2014 Wiley Periodicals, Inc.

Interaction of acidic trace gases with ice from a surface science perspective

NASA Astrophysics Data System (ADS)

Waldner, A.; Kong, X.; Ammann, M.; Orlando, F.; Birrer, M.; Artiglia, L.; Bartels-Rausch, T.

2016-12-01

Acidic trace gases, such as HCOOH, HCl and HONO, play important roles in atmospheric chemistry. The presence of ice is known to have the capability to modify this chemistry (Neu et al. 2012). The molecular level processes of the interaction of acidic trace gases with ice are still a matter of debate and a quantification of the uptake is difficult (Dash et al. 2006, Bartels-Rausch et al. 2014, Huthwelker et al. 2006). This hampers a proper inclusion of ice as a substrate in models of various scales as for example in global chemistry climate models that would among others allow predicting large-scale effects of ice clouds. So far, direct observations of the ice surface and of the interaction with trace gases at temperatures and concentrations relevant to the environment are very limited. In this study, we take advantage of the surface and analytical sensitivity as well as the chemical selectivity of photoemission and absorption spectroscopy performed at ambient pressure using the near ambient pressure photoemission endstation (NAPP) at Swiss Light Source to overcome this limitation in environmental science (Orlando et al. 2016). Specifically, ambient pressure X-ray Photoelectron Spectroscopy (XPS) allows us to get information about chemical state and concentration depth profiles of dopants. The combination of XPS with auger electron yield Near-Edge X-ray Absorption Fine Structure (NEXAFS) enables us to locate the dopant and analyse wheather the interaction leads to enhanced surface disorder and to what extent different disorders influences the uptake of the trace gas. For the first time, this study looks directly at the interaction of HCOOH, the strongest organic acid, with ice at 2 different temperatures (233 and 253 K) relevant for environmental science by means of electron spectroscopy. XPS depth profiles indicate that the HCOOH basically remains within the topmost ice layers and O K-edge NEXAFS analysis show that the interaction ice-HCOOH does not lead to enhanced surface disorder at environmentally relevant conditions.

The Physical Character of the Au (001) Surface Reconstruction in the Presence of CO and O2

NASA Astrophysics Data System (ADS)

Loheac, Andrew; Pierce, Michael S.; Barbour, Andi; Komanicky, Vladimir; Zhu, Chenhui; You, Hoydoo

2014-03-01

The interaction of carbon monoxide and oxygen on Au (001) single crystal facets has been investigated using synchrotron based surface x-ray diffraction and scattering techniques. Preliminary experiments confirm the quasi-hexagonal surface reconstruction can be influenced by exposure to CO and O, and indicate that oxidation may be present. Subsequent surface x-ray scattering experiments included a residual gas analyzer (RGA) with isotopic CO to tag the chemical species. Both CO (by itself) and O (dissociated from molecular O2 by the x-rays) are capable of lifting the hexagonal surface reconstruction resulting in a disordered bulk truncated surface. A wide range of pressures (1 mTorr - 10 Torr) and temperatures (300 K - 900 K) have been explored. We have also adapted a system of coupled partial differential equations to model the absorption kinetics and surface reconstructions. This work and use of the Advanced Photon Source were supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. The work at Safarik University was supported by Slovak grant VEGA 1/0782/12.

Surface structural reconstruction of SrVO3 thin films on SrTiO3 (001)

NASA Astrophysics Data System (ADS)

Wang, Gaomin; Saghayezhian, Mohammad; Chen, Lina; Guo, Hangwen; Zhang, Jiandi

Paramagnetic metallic oxide SrVO3>(SVO) is an itinerant system known to undergo thickness-induced metal-insulator-transition (MIT) in ultrathin film form, which makes it a prototype system for the study of the mechanism behind metal-insulator-transition like structure distortion, electron correlations and disorder-induced localization. We have grown SrVO3 thin film with atomically flat surface through the layer-by-layer deposition by laser Molecular Beam Epitaxy (laser-MBE) on SrTiO3 (001) surface. Low Energy Electron Diffraction (LEED) measurements reveal that there is a (√2X √2) R45°surface reconstruction independent of film thickness. By using LEED-I(V) structure refinement, we determine the surface structure. In combination with X-ray Photoelectron Spectroscopy (XPS) and Scanning Tunneling Microscopy (STM), we discuss the implication on the MIT in ultrathin films below 2-3 unit cell thickness. This work is supported by the National Science Foundation under the NSF EPSCoR Cooperative Agreement No. EPS-1003897 with additional support from the Louisiana Board of Regents.

Specific material recognition by small peptides mediated by the interfacial solvent structure.

PubMed

Schneider, Julian; Ciacchi, Lucio Colombi

2012-02-01

We present evidence that specific material recognition by small peptides is governed by local solvent density variations at solid/liquid interfaces, sensed by the side-chain residues with atomic-scale precision. In particular, we unveil the origin of the selectivity of the binding motif RKLPDA for Ti over Si using a combination of metadynamics and steered molecular dynamics simulations, obtaining adsorption free energies and adhesion forces in quantitative agreement with corresponding experiments. For an accurate description, we employ realistic models of the natively oxidized surfaces which go beyond the commonly used perfect crystal surfaces. These results have profound implications for nanotechnology and materials science applications, offering a previously missing structure-function relationship for the rational design of materials-selective peptide sequences. © 2011 American Chemical Society

Improving Ion Mobility Spectrometry Detection Methods for Trace Forensics and Military Field Applications

DTIC Science & Technology

2016-10-11

UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES F. EDWARD HEBERT SCHOOL OF MEDICINE 4301 JONES BRIDGE ROAD BETHESDA, MARYLAND 20814-4799...ofPublic Health (Dr.P.H.) Master ofScience Degrees Departmental -Clinical Psychology -Environmental Health Sciences -Medical Psychology -Medical...Zoology -Pathology Interdisciplinary -Emerging Infectious Diseases -Molecular & Cell Biology -Neuroscience -Molecular & Cell Biology -Public Health Masters

Tribology. LC Science Tracer Bullet.

ERIC Educational Resources Information Center

Havas, George D., Comp.

Tribology is the science and technology of interacting surfaces in relative motion. It incorporates a number of scientific fields, including friction, wear, lubrication, materials science, and various branches of surface physics and surface chemistry. Tribology forms a vital part of engineering science. The interacting surfaces may be on machinery…

The Electrode as Organolithium Reagent: Catalyst-Free Covalent Attachment of Electrochemically Active Species to an Azide-Terminated Glassy Carbon Electrode Surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Atanu K.; Engelhard, Mark H.; Liu, Fei

2013-12-02

Glassy carbon electrodes have been activated for modification with azide groups and subsequent coupling with ferrocenyl reagents by a catalyst-free route using lithium acetylide-ethylenediamine complex, and also by the more common Cu(I)-catalyzed alkyne-azide coupling (CuAAC) route, both affording high surface coverages. Electrodes were preconditioned at ambient temperature under nitrogen, and ferrocenyl surface coverages obtained by CuAAC were comparable to those reported with preconditioning at 1000 °C under hydrogen/nitrogen. The reaction of lithium acetylide-ethylenediamine with the azide-terminated electrode affords a 1,2,3-triazolyllithium-terminated surface that is active toward covalent C-C coupling reactions including displacement at an aliphatic halide and nucleophilic addition at anmore » aldehyde. For example, surface ferrocenyl groups were introduced by reaction with (6-iodohexyl)ferrocene; the voltammetry shows narrow, symmetric peaks indicating uniform attachment. Coverages are competitive with those obtained by the CuAAC route. X-ray photoelectron spectroscopic data, presented for each synthetic step, are consistent with the proposed reactions. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

PubMed

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.

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

PubMed

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.

Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

PubMed Central

Da Silva, Franck; Empereur-mot, Charly; Chavent, Matthieu; Baaden, Marc

2013-01-01

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/. PMID:23483961

Game on, science - how video game technology may help biologists tackle visualization challenges.

PubMed

Lv, Zhihan; Tek, Alex; Da Silva, Franck; Empereur-mot, Charly; Chavent, Matthieu; Baaden, Marc

2013-01-01

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/.

76 FR 370 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-04

... . Name of Committee: Genes, Genomes, and Genetics Integrated Review Group; Molecular Genetics B Study... Committee: Cardiovascular and Respiratory Sciences Integrated Review Group; Lung Cellular, Molecular, and... Committee: Population Sciences and Epidemiology Integrated Review Group; Behavioral Genetics and...

Committee on Atomic, Molecular and Optical Sciences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lancaster, James

The Committee on Atomic, Molecular, and Optical Sciences (CAMOS) is a standing activity of the National Research Council (NRC) that operates under the auspices of the Board on Physics and Astronomy. CAMOS is one of five standing committees of the BPA that are charged with assisting it in achieving its goals—monitoring the health of physics and astronomy, identifying important new developments at the scientific forefronts, fostering interactions with other fields, strengthening connections to technology, facilitating effective service to the nation, and enhancing education in physics. CAMOS provides these capabilities for the atomic, molecular and optical (AMO) sciences.

[Molecular imaging; current status and future prospects in USA].

PubMed

Kobayashi, Hisataka

2007-02-01

The goal of this review is to introduce the definition, current status, and future prospects of the molecular imaging, which has recently been a hot topic in medicine and the biological science in USA. In vivo imaging methods to visualize the molecular events and functions in organs or animals/humans are overviewed and discussed especially in combinations of imaging modalities (machines) and contrast agents(chemicals) used in the molecular imaging. Next, the close relationship between the molecular imaging and the nanotechnology, an important part of nanomedicine, is stressed from the aspect of united multidisciplinary sciences such as physics, chemistry, biology, and medicine.

Preface

NASA Astrophysics Data System (ADS)

Kövér, László

2014-10-01

This Special Issue of the journal Applied Surface Science contains full papers from a selection of contributions presented in the Applied Surface Science sessions of the 19th International Vacuum Congress (IVC-19) held in the Palais des Congrès, Paris, between September 9 and 13, 2013. The triennial IVC conferences represent major meetings in the field of the vacuum related sciences and are the largest scientific events of the International Union for Vacuum Science, Technique and Applications (IUVSTA). The IVC-19 and partner conferences had altogether 2555 participants. Supported by the Applied Surface Science Division of IUVSTA, the Applied Surface Science part was one of the most attended among the sub-conferences of the IVC-19. This Special Issue - without trying to achieve completeness - intends to provide a cross section of the topics of the Applied Surface Science and joint sessions of the IVC-19, covering important fields such as Surface Analysis, Surface Modifications, Surface Chemistry and Catalysis, Quantitative Surface and Interface Analysis, Coatings, Tribology, Adhesion, Characterization of Nanomaterials, Energy and Sustainable Development, Self Assembly, Nano-instrumentation, SPM and Novel Probe Techniques, New Approaches and Novel Applications of Surface/Interface Analytical Methods.

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

NASA Astrophysics Data System (ADS)

Bartels, Ludwig; Ernst, Karl-Heinz

2012-09-01

This issue is dedicated to Karl-Heinz Rieder on the occasion of his 70th birthday. It contains contributions written by his former students and colleagues from all over the world. Experimental techniques based on free electrons, such as photoelectron spectroscopy, electron microscopy and low energy electron diffraction (LEED), were foundational to surface science. While the first revealed the band structures of materials, the second provided nanometer scale imagery and the latter elucidated the atomic scale periodicity of surfaces. All required an (ultra-)high vacuum, and LEED illustrated impressively that adsorbates, such as carbon monoxide, hydrogen or oxygen, can markedly and periodically restructure surfaces from their bulk termination, even at pressures ten orders of magnitude or more below atmospheric. Yet these techniques were not generally able to reveal atomic scale surface defects, nor could they faithfully show adsorption of light atoms such as hydrogen. Although a complete atom, helium can also be regarded as a wave with a de Broglie wavelength that allows the study of surface atomic periodicities at a delicateness and sensitivity exceeding that of electrons-based techniques. In combination, these and other techniques generated insight into the periodicity of surfaces and their vibrational properties, yet were limited to simple and periodic surface setups. All that changed with the advent of scanning tunneling microscopy (STM) roughly 30 years ago, allowing real space access to surface defects and individual adsorbates. Applied at low temperatures, not only can STM establish a height profile of surfaces, but can also perform spectroscopy and serve as an actuator capable of rearranging individual species at atomic scale resolution. The direct and intuitive manner in which STM provided access as a spectator and as an actor to the atomic scale was foundational to today's surface science and to the development of the concepts of nanoscience in general. The cover image of this issue honors this achievement. It shows 27 chiral heptahelicene molecules arranged by one of the guest editors (KHE) with the very same STM at IBM Almaden Research Center, San José that was used for moving xenon atoms more than 20 years ago. Karl-Heinz Rieder's career, as briefly outlined in the biography by G Benedek in this issue, reflected this paradigm shift in surface science from reciprocal to real space investigations: initially focusing on helium scattering as a superior technique for the investigation of delicate surfaces, his group at the Freie University in Berlin became the second in the world to rearrange atoms and molecules at surfaces in a controlled way and they generated much of the foundational work of low temperature STM investigations. Besides his saxophone skills and many other hobbies, Karl-Heinz is a real poet and loves composing funny limericks and spoonerisms. He wrote the following poem (passed on to us by W-D Schneider) at the International School of Solid State Physics in 1998 in Erice, Italy. It is a real masterpiece, beautifully summarizing us all, the 'Surface Science Society'. The top atom sheetSome become real slaves is important and neat.looking at standing waves. Therefore there is a strong raceThe producers of coatings in the science of surface.get really good quotings. To clean it you needStill others use new ways ions and heat.with electrons and x-rays. Then the atoms arrangeAnd all has to be in some ways that are strange,in good UHV—except theory, they relax, reconstructwhich thinks on extensions as a matter of fact.to still lower dimensions, And reacting with gasesand with lots of computing they form quite new phasestries to get solid footing. with large unit cellsSo everybody with joy as diffraction tells.plays his own special toy. Some people use lightAnd all think they are better from a synchrotron brightshould get published a letter. and claim it is bestBut before there's more cluster to do this in 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 and Hans-Joachim Freund Mapping the first electronic resonances of a Cu phthalocyanine STM tunnel junctionW-H Soe, C Manzano, H S Wong and C Joachim Epitaxial Bi allotropes on quasicrystal surfaces as templates for adsorption of pentacene and fullereneH R Sharma, J A Smerdon, K M Young and R McGrath Island formation and manipulation of prochiral azobenzene derivatives on Au(111)Sofia Selvanathan, Maike V Peters, Stefan Hecht and Leonhard Grill

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

PubMed

Long, Run; Prezhdo, Oleg V

2011-11-30

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

Early Earth Science Activities in the Sanford Underground Science and Engineering Laboratory at Homestake

NASA Astrophysics Data System (ADS)

Wang, J. S.; Glaser, S. D.; Moore, J. R.; Hart, K.; King, G.; Regan, T.; Bang, S. S.; Sani, R. K.; Roggenthen, W. M.

2007-12-01

On July 10, 2007, the former Homestake Mine, Lead, South Dakota, was selected as the development site for the Deep Underground Science and Engineering Laboratory, to become the Sanford Underground Science and Engineering Laboratory at Homestake. Work on refurbishment and certification of the Ross Shaft began in August 2007 to effect pumping of water that had reached the 5000 level in late July. Completion of this work will allow a physics and geosciences laboratory to be constructed on the 4,850 ft level (1,478 m from the surface). Concurrent with reentry operations, several earth science research activities have been initiated. These early activities are as follows: (1) Seismic monitoring system: Accelerometers will be installed in surface boreholes and underground drifts as they become available as a result of the reentry work. (2) Evaluation of the 300 level (91 m), which has multiple locations for horizontal access, is ongoing. This near- surface level, with varying overburden thicknesses, offers excellent opportunities to investigate the "critical zone" in terms of hydrology, ecology, and geochemistry, yielding measurements of both moisture and carbon fluxes to evaluate fluid exchanges with the atmosphere. (3) Water and soil samples were collected in the Ross Shaft as part of the first reentry work. Molecular survey of microbial diversity showed the presence of mesophilic and thermophilic cellulose-degrading microorganisms. (4) Supercritical carbon dioxide injection experiments are being planned that will take advantage of three pairs of existing, nearly vertical, open 8-inch (0.2 m) boreholes that are easily accessible from the Ross Shaft. The candidate holes are located between the 1550 and the 2900 levels and are between 90 to 180 m in length (5) Monitoring of the response of the water during the dewatering operations will be facilitated by the use of existing boreholes. Ultimately, the dewatering operation provide access to the 8000 level (depth of 2,438 m), the deepest level. These five examples of ongoing research activities should provide a basis for many other earth science and engineering investigations at this multilevel facility, which already has extensive underground workings. These examples address different aspects of three main themes identified as important by deep underground research communities: restless earth for geo-science, ground truth for geo-engineering, and dark life for geo-microbiology.

Manipulating, Reacting, and Constructing Single Molecules with a Scanning Tunneling Microscope Tip

NASA Astrophysics Data System (ADS)

Hla, S.-W.

The fascinating advances in atom and molecule manipulation with the scanning tunneling microscope (STM) tip allow scientists to fabricate artificial atomic scale structures, to study local quantum phenomena, or to probe physical and chemical properties of single atoms and molecules on surfaces. Recent achievements in individual synthesis of single molecules with the STM tip further open up an entirely new opportunities in nanoscience and technology. The STM manipulation techniques usef ul in the molecular construction are reviewed and prospects for future opportunities of single molecule chemical engineering and their possible implications to nano-scale science and technology are discussed.

EDITORIAL: Molecular Imaging Technology

NASA Astrophysics Data System (ADS)

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.

Mobile modeling in the molecular sciences

EPA Science Inventory

The art of modeling in the molecular sciences is highly dependent on both the available computational technology, underlying data, and ability to collaborate. With the ever increasing market share of mobile devices, it is assumed by many that tablets will overtake laptops as the...

Monitoring the degrafting of polyelectrolyte brushes by using surface gradients

NASA Astrophysics Data System (ADS)

Ko, Yeongun; Genzer, Jan

Polymer brushes comprise densely grafted polymer chains on surfaces, which possess high stability and high concentration of reactive centers per unit area compared to physisorbed polymer film. Polymer brushes are employed in many applications, including anti-fouling surfaces, cell adhesive surfaces, responsive surfaces, low-friction surfaces, etc. Recently, researchers reported that charged (or chargeable) polymer brushes can be degrafted from substrate while incubated in buffer solutions. Based on previous experiments conducted in our group and by others, we assume that chain degrafting results from the hydrolysis of Si-O groups in head-group of the initiator and/or the ester groups in main body of the initiator. The kinetic of hydrolysis is affected by mechanical forces acting on the initiator. Those forces depend on the molecular weight and the grafting density of the brush, and the concentration and distribution of charges along the macromolecule (tuned by pH - for weak electrolytes - and concentration of external salt). In this work, we study the stability of poly(2-dimethylaminoethyl methacrylate) (PDMAEMA) brushes in two solvents (ethanol and water) at various pH values in water and under different levels of external salt concentration. National Science Foundation.

A review of nanostructured surfaces and materials for dental implants: surface coating, patterning and functionalization for improved performance.

PubMed

Rasouli, Rahimeh; Barhoum, Ahmed; Uludag, Hasan

2018-05-10

The emerging field of nanostructured implants has enormous scope in the areas of medical science and dental implants. Surface nanofeatures provide significant potential solutions to medical problems by the introduction of better biomaterials, improved implant design, and surface engineering techniques such as coating, patterning, functionalization and molecular grafting at the nanoscale. This review is of an interdisciplinary nature, addressing the history and development of dental implants and the emerging area of nanotechnology in dental implants. After a brief introduction to nanotechnology in dental implants and the main classes of dental implants, an overview of different types of nanomaterials (i.e. metals, metal oxides, ceramics, polymers and hydrides) used in dental implant together with their unique properties, the influence of elemental compositions, and surface morphologies and possible applications are presented from a chemical point of view. In the core of this review, the dental implant materials, physical and chemical fabrication techniques and the role of nanotechnology in achieving ideal dental implants have been discussed. Finally, the critical parameters in dental implant design and available data on the current dental implant surfaces that use nanotopography in clinical dentistry have been discussed.

Corrosion chemistry closing comments: opportunities in corrosion science facilitated by operando experimental characterization combined with multi-scale computational modelling.

PubMed

Scully, John R

2015-01-01

Recent advances in characterization tools, computational capabilities, and theories have created opportunities for advancement in understanding of solid-fluid interfaces at the nanoscale in corroding metallic systems. The Faraday Discussion on Corrosion Chemistry in 2015 highlighted some of the current needs, gaps and opportunities in corrosion science. Themes were organized into several hierarchical categories that provide an organizational framework for corrosion. Opportunities to develop fundamental physical and chemical data which will enable further progress in thermodynamic and kinetic modelling of corrosion were discussed. These will enable new and better understanding of unit processes that govern corrosion at the nanoscale. Additional topics discussed included scales, films and oxides, fluid-surface and molecular-surface interactions, selected topics in corrosion science and engineering as well as corrosion control. Corrosion science and engineering topics included complex alloy dissolution, local corrosion, and modelling of specific corrosion processes that are made up of collections of temporally and spatially varying unit processes such as oxidation, ion transport, and competitive adsorption. Corrosion control and mitigation topics covered some new insights on coatings and inhibitors. Further advances in operando or in situ experimental characterization strategies at the nanoscale combined with computational modelling will enhance progress in the field, especially if coupling across length and time scales can be achieved incorporating the various phenomena encountered in corrosion. Readers are encouraged to not only to use this ad hoc organizational scheme to guide their immersion into the current opportunities in corrosion chemistry, but also to find value in the information presented in their own ways.

Nanocrystalline Anatase Titania Supported Vanadia Catalysts: Facet-dependent Structure of Vanadia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wei-Zhen; Gao, Feng; Li, Yan

2015-07-09

Titania supported vanadia, a classic heterogeneous catalyst for redox reactions, typically has nonhomogeneous vanadia species on various titania facets, making it challenging not only to determine and quantify each species but also to decouple their catalytic contributions. We prepared truncated tetragonal bipyramidal (TiO2-TTB) and rod-like (TiO2-Rod) anatase titania with only {101} and {001} facets at ratios of about 80:20 and 93:7, respectively, and used them as supports of sub-monolayer vanadia. The structure and redox properties of supported vanadia were determined by XRD, TEM, XPS, EPR, Raman, FTIR and TPR, etc. It was found that vanadia preferentially occupy TiO2 {001} facetsmore » and form isolated O=V4+(O-Ti)2 species, and with further increase in vanadia surface coverage, isolated O=V5+(O-Ti)3 and oligomerized O=V5+(O-M)3 (M = Ti or V) species form on TiO2 {101} facets. The discovery on support facet-dependent structure of vanadia on anatase titania is expected to enable the elucidation of structure-function correlations on high surface area TiO2 supported vanadia catalysts. This work was supported by U. S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Biosciences and Geosciences. The research was performed in the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE Office of Biological and Environmental Research, and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for DOE by Battelle.« less

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Surface diffusion of Si, Ge and C adatoms on Si (001) substrate studied by the molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Chen, Zhi-Hui; Yu, Zhong-Yuan; Lu, Peng-Fei; Liu, Yu-Min

2009-10-01

Depositions of Si, Ge and C atoms onto a preliminary Si (001) substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on the flat terraces between steps is suggested. Diffusion and arrangement patterns of adatoms at different temperatures are observed. At 900 K, the deposited atoms are more likely to form dimers in the perpendicular [110] direction due to the more favourable movement along the perpendicular [110] direction. C adatoms are more likely to break or reconstruct the dimers on the substrate surface and have larger diffusion distances than Ge and Si adatoms. Exchange between C adatoms and substrate atoms are obvious and the epitaxial thickness is small. Total potential energies of adatoms and substrate atoms involved in the simulation cell are computed. When a newly arrived adatom reaches the stable position, the potential energy of the system will decrease and the curves turns into a ladder-like shape. It is found that C adatoms can lead to more reduction of the system energy and the potential energy of the system will increase as temperature increases.

Parallel, stochastic measurement of molecular surface area.

PubMed

Juba, Derek; Varshney, Amitabh

2008-08-01

Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering. We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy.

Molecular biomimetics: utilizing nature's molecular ways in practical engineering.

PubMed

Tamerler, Candan; Sarikaya, Mehmet

2007-05-01

In nature, proteins are the machinery that accomplish many functions through their specific recognition and interactions in biological systems from single-celled to multicellular organisms. Biomolecule-material interaction is accomplished via molecular specificity, leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, molecular recognition and, consequently, functions developed through successive cycles of mutation and selection. Using biology as a guide, we can now understand, engineer and control peptide-material interactions and exploit these to tailor novel materials and systems for practical applications. We adapted combinatorial biology protocols to display peptide libraries, either on the cell surface or on phages, to select short peptides specific to a variety of practical materials systems. Following the selection step, we determined the kinetics and stability of peptide binding experimentally to understand the bound peptide structure via modeling and its assembly via atomic force microscopy. The peptides were further engineered to have multiple repeats or their amino acid sequences varied to tailor their function. Both nanoparticles and flat inorganic substrates containing multimaterials patterned at the nano- and microscales were used for self-directed immobilization of molecular constructs. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems with wide ranging applications, from tissue engineering, drug delivery and biosensors, to nanotechnology and bioremediation. Here we give examples of protein-mediated functional materials in biology, peptide selection and engineering with affinity to inorganics, demonstrate potential utilizations in materials science, engineering and medicine, and describe future prospects.

Molecular pathology curriculum for medical laboratory scientists: A report of the association for molecular pathology training and education committee.

PubMed

Taylor, Sara; Bennett, Katie M; Deignan, Joshua L; Hendrix, Ericka C; Orton, Susan M; Verma, Shalini; Schutzbank, Ted E

2014-05-01

Molecular diagnostics is a rapidly growing specialty in the clinical laboratory assessment of pathology. Educational programs in medical laboratory science and specialized programs in molecular diagnostics must address the training of clinical scientists in molecular diagnostics, but the educational curriculum for this field is not well defined. Moreover, our understanding of underlying genetic contributions to specific diseases and the technologies used in molecular diagnostics laboratories change rapidly, challenging providers of training programs in molecular diagnostics to keep their curriculum current and relevant. In this article, we provide curriculum recommendations to molecular diagnostics training providers at both the baccalaureate and master's level of education. We base our recommendations on several factors. First, we considered National Accrediting Agency for Clinical Laboratory Sciences guidelines for accreditation of molecular diagnostics programs, because educational programs in clinical laboratory science should obtain its accreditation. Second, the guidelines of several of the best known certifying agencies for clinical laboratory scientists were incorporated into our recommendations. Finally, we relied on feedback from current employers of molecular diagnostics scientists, regarding the skills and knowledge that they believe are essential for clinical scientists who will be performing molecular testing in their laboratories. We have compiled these data into recommendations for a molecular diagnostics curriculum at both the baccalaureate and master's level of education. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Quantitative SIMS Imaging of Agar-Based Microbial Communities.

PubMed

Dunham, Sage J B; Ellis, Joseph F; Baig, Nameera F; Morales-Soto, Nydia; Cao, Tianyuan; Shrout, Joshua D; Bohn, Paul W; Sweedler, Jonathan V

2018-05-01

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review

PubMed Central

Dong, Yonghui; Li, Bin; Malitsky, Sergey; Rogachev, Ilana; Aharoni, Asaph; Kaftan, Filip; Svatoš, Aleš; Franceschi, Pietro

2016-01-01

Mass spectrometry imaging (MSI) is a mass spectrometry based molecular ion imaging technique. It provides the means for ascertaining the spatial distribution of a large variety of analytes directly on tissue sample surfaces without any labeling or staining agents. These advantages make it an attractive molecular histology tool in medical, pharmaceutical, and biological research. Likewise, MSI has started gaining popularity in plant sciences; yet, information regarding sample preparation methods for plant tissues is still limited. Sample preparation is a crucial step that is directly associated with the quality and authenticity of the imaging results, it therefore demands in-depth studies based on the characteristics of plant samples. In this review, a sample preparation pipeline is discussed in detail and illustrated through selected practical examples. In particular, special concerns regarding sample preparation for plant imaging are critically evaluated. Finally, the applications of MSI techniques in plants are reviewed according to different classes of plant metabolites. PMID:26904042

Adsorption of Poly(methyl methacrylate) on Concave Al2O3 Surfaces in Nanoporous Membranes

PubMed Central

Nunnery, Grady; Hershkovits, Eli; Tannenbaum, Allen; Tannenbaum, Rina

2009-01-01

The objective of this study was to determine the influence of polymer molecular weight and surface curvature on the adsorption of polymers onto concave surfaces. Poly(methyl methacrylate) (PMMA) of various molecular weights was adsorbed onto porous aluminum oxide membranes having various pore sizes, ranging from 32 to 220 nm. The surface coverage, expressed as repeat units per unit surface area, was observed to vary linearly with molecular weight for molecular weights below ~120 000 g/mol. The coverage was independent of molecular weight above this critical molar mass, as was previously reported for the adsorption of PMMA on convex surfaces. Furthermore, the coverage varied linearly with pore size. A theoretical model was developed to describe curvature-dependent adsorption by considering the density gradient that exists between the surface and the edge of the adsorption layer. According to this model, the density gradient of the adsorbed polymer segments scales inversely with particle size, while the total coverage scales linearly with particle size, in good agreement with experiment. These results show that the details of the adsorption of polymers onto concave surfaces with cylindrical geometries can be used to calculate molecular weight (below a critical molecular weight) if pore size is known. Conversely, pore size can also be determined with similar adsorption experiments. Most significantly, for polymers above a critical molecular weight, the precise molecular weight need not be known in order to determine pore size. Moreover, the adsorption developed and validated in this work can be used to predict coverage also onto surfaces with different geometries. PMID:19415910

Designing an educative curriculum unit for teaching molecular geometry in high school chemistry

NASA Astrophysics Data System (ADS)

Makarious, Nader N.

Chemistry is a highly abstract discipline that is taught and learned with the aid of various models. Among the most challenging, yet a fundamental topic in general chemistry at the high school level, is molecular geometry. This study focused on developing exemplary educative curriculum materials pertaining to the topic of molecular geometry. The methodology used in this study consisted of several steps. First, a diverse set of models were analyzed to determine to what extent each model serves its purpose in teaching molecular geometry. Second, a number of high school teachers and college chemistry professors were asked to share their experiences on using models in teaching molecular geometry through an online questionnaire. Third, findings from the comparative analysis of models, teachers’ experiences, literature review on models and students’ misconceptions, the curriculum expectations of the Next Generation Science Standards and their emphasis on three-dimensional learning and nature of science (NOS) contributed to the development of the molecular geometry unit. Fourth, the developed unit was reviewed by fellow teachers and doctoral-level science education experts and was revised to further improve its coherence and clarity in support of teaching and learning of the molecular geometry concepts. The produced educative curriculum materials focus on the scientific practice of developing and using models as promoted in the Next Generations Science Standards (NGSS) while also addressing nature of science (NOS) goals. The educative features of the newly developed unit support teachers’ pedagogical knowledge (PK) and pedagogical content knowledge (PCK). The unit includes an overview, teacher’s guide, and eight detailed lesson plans with inquiry oriented modeling activities replete with models and suggestions for teachers, as well as formative and summative assessment tasks. The unit design process serves as a model for redesigning other instructional units in science disciplines in general and chemistry courses in particular.

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

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

PubMed

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

2014-04-01

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

Molecular genetics at the Fort Collins Science Center

USGS Publications Warehouse

Oyler-McCance, S.J.; Stevens, P.D.

2011-01-01

The Fort Collins Science Center operates a molecular genetic and systematics research facility (FORT Molecular Ecology Laboratory) that uses molecular genetic tools to provide genetic information needed to inform natural resource management decisions. For many wildlife species, the data generated have become increasingly important in the development of their long-term management strategies, leading to a better understanding of species diversity, population dynamics and ecology, and future conservation and management needs. The Molecular Ecology Lab serves Federal research and resource management agencies by developing scientifically rigorous research programs using nuclear, mitochondrial and chloroplast DNA to help address many of today's conservation biology and natural resource management issues.

Development of a Linear Ion Trap Mass Spectrometer (LITMS) Investigation for Future Planetary Surface Missions

NASA Technical Reports Server (NTRS)

Brinckerhoff, W.; Danell, R.; Van Ameron, F.; Pinnick, V.; Li, X.; Arevalo, R.; Glavin, D.; Getty, S.; Mahaffy, P.; Chu, P.;

Defense Against Pathogens: Structural Insights into the Mechanism of Chitin Induced Activation of Innate Immunity.

PubMed

Squeglia, Flavia; Berisio, Rita; Shibuya, Naoto; Kaku, Hanae

2017-11-24

Pattern recognition receptors on the plant cell surface mediate the recognition of microbe-associated molecular patterns, in a process which activates downstream immune signaling. These receptors are plasma membrane-localized kinases which need to be autophosphorylated to activate downstream responses. Perception of attacks from fungi occurs through recognition of chitin, a polymer of an N-acetylglucosamine which is a characteristic component of the cell walls of fungi. This process is regulated in Arabidopsis by chitin elicitor receptor kinase CERK1. A more complex process characterizes rice, in which regulation of chitin perception is operated by a complex composed of OsCERK1, a homolog of CERK1, and the chitin elicitor binding protein OsCEBiP. Recent literature has provided a mechanistic description of the complex regulation of activation of innate immunity in rice and an advance in the structural description of molecular players involved in this process. This review describes the current status of the understanding of molecular events involved in innate immunity activation in rice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Molecular-dynamics study on characteristics of energy and tangential momentum accommodation coefficients

NASA Astrophysics Data System (ADS)

Yamaguchi, Hiroki; Matsuda, Yu; Niimi, Tomohide

2017-07-01

Gas-surface interaction is studied by the molecular dynamics method to investigate qualitatively characteristics of accommodation coefficients. A large number of trajectories of gas molecules colliding to and scattering from a surface are statistically analyzed to calculate the energy (thermal) accommodation coefficient (EAC) and the tangential momentum accommodation coefficient (TMAC). Considering experimental measurements of the accommodation coefficients, the incident velocities are stochastically sampled to represent a bulk condition. The accommodation coefficients for noble gases show qualitative coincidence with experimental values. To investigate characteristics of these accommodation coefficients in detail, the gas-surface interaction is parametrically studied by varying the molecular mass of gas, the gas-surface interaction strength, and the molecular size of gas, one by one. EAC increases with increasing every parameter, while TMAC increases with increasing the interaction strength, but decreases with increasing the molecular mass and the molecular size. Thus, contradictory results in experimentally measured TMAC for noble gases could result from the difference between the surface conditions employed in the measurements in the balance among the effective parameters of molecular mass, interaction strength, and molecular size, due to surface roughness and/or adsorbed molecules. The accommodation coefficients for a thermo-fluid dynamics field with a temperature difference between gas and surface and a bulk flow at the same time are also investigated.

Supramolecular assembly/reassembly processes: molecular motors and dynamers operating at surfaces.

PubMed

Ciesielski, Artur; Samorì, Paolo

2011-04-01

Among the many significant advances within the field of supramolecular chemistry over the past decades, the development of the so-called "dynamers" features a direct relevance to materials science. Defined as "combinatorial dynamic polymers", dynamers are constitutional dynamic systems and materials resulting from the application of the principles of supramolecular chemistry to polymer science. Like supramolecular materials in general, dynamers are reversible dynamic multifunctional architectures, capable of modifying their constitution by exchanging, recombining, incorporating components. They may exhibit a variety of novel properties and behave as adaptive materials. In this review we focus on the design of responsive switchable monolayers, i.e. monolayers capable to undergo significant changes in their physical or chemical properties as a result of external stimuli. Scanning tunneling microscopy studies provide direct evidence with a sub-nanometre resolution, on the formation and dynamic response of these self-assembled systems featuring controlled geometries and properties.

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

PubMed Central

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, can capture processes that are otherwise obscured to the amino acid-based formalism. PMID:25462574

Molecular Evolution in Historical Perspective.

PubMed

Suárez-Díaz, Edna

2016-12-01

In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms. These developments sparked important debates between defendants of the molecular and organismic approaches. The most vocal confrontations focused on the relation between primates and humans, and the neutral theory of molecular evolution. By the 1980s and 1990s, the construction of large protein and DNA sequences databases, and the development of computer-based statistical tools, facilitated the coming together of molecular and evolutionary biology. Although in its contemporary form the field of molecular evolution can be traced back to the last five decades, the field has deep roots in twentieth century experimental life sciences. For historians of science, the origins and consolidation of molecular evolution provide a privileged field for the study of scientific debates, the relation between technological advances and scientific knowledge, and the connection between science and broader social concerns.

Molecular effective coverage surface area of optical clearing agents for predicting optical clearing potential

NASA Astrophysics Data System (ADS)

Feng, Wei; Ma, Ning; Zhu, Dan

2015-03-01

The improvement of methods for optical clearing agent prediction exerts an important impact on tissue optical clearing technique. The molecular dynamic simulation is one of the most convincing and simplest approaches to predict the optical clearing potential of agents by analyzing the hydrogen bonds, hydrogen bridges and hydrogen bridges type forming between agents and collagen. However, the above analysis methods still suffer from some problem such as analysis of cyclic molecule by reason of molecular conformation. In this study, a molecular effective coverage surface area based on the molecular dynamic simulation was proposed to predict the potential of optical clearing agents. Several typical cyclic molecules, fructose, glucose and chain molecules, sorbitol, xylitol were analyzed by calculating their molecular effective coverage surface area, hydrogen bonds, hydrogen bridges and hydrogen bridges type, respectively. In order to verify this analysis methods, in vitro skin samples optical clearing efficacy were measured after 25 min immersing in the solutions, fructose, glucose, sorbitol and xylitol at concentration of 3.5 M using 1951 USAF resolution test target. The experimental results show accordance with prediction of molecular effective coverage surface area. Further to compare molecular effective coverage surface area with other parameters, it can show that molecular effective coverage surface area has a better performance in predicting OCP of agents.

Metal oxide nanoparticle mediated enhanced Raman scattering and its use in direct monitoring of interfacial chemical reactions.

PubMed

Li, Li; Hutter, Tanya; Finnemore, Alexander S; Huang, Fu Min; Baumberg, Jeremy J; Elliott, Stephen R; Steiner, Ullrich; Mahajan, Sumeet

2012-08-08

Metal oxide nanoparticles (MONPs) have widespread usage across many disciplines, but monitoring molecular processes at their surfaces in situ has not been possible. Here we demonstrate that MONPs give highly enhanced (×10(4)) Raman scattering signals from molecules at the interface permitting direct monitoring of their reactions, when placed on top of flat metallic surfaces. Experiments with different metal oxide materials and molecules indicate that the enhancement is generic and operates at the single nanoparticle level. Simulations confirm that the amplification is principally electromagnetic and is a result of optical modulation of the underlying plasmonic metallic surface by MONPs, which act as scattering antennae and couple light into the confined region sandwiched by the underlying surface. Because of additional functionalities of metal oxides as magnetic, photoelectrochemical and catalytic materials, enhanced Raman scattering mediated by MONPs opens up significant opportunities in fundamental science, allowing direct tracking and understanding of application-specific transformations at such interfaces. We show a first example by monitoring the MONP-assisted photocatalytic decomposition reaction of an organic dye by individual nanoparticles.

Effects of incident energy and angle on carbon cluster ions implantation on silicon substrate: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Wei, Ye; Sang, Shengbo; Zhou, Bing; Deng, Xiao; Chai, Jing; Ji, Jianlong; Ge, Yang; Huo, Yuanliang; Zhang, Wendong

2017-09-01

Carbon cluster ion implantation is an important technique in fabricating functional devices at micro/nanoscale. In this work, a numerical model is constructed for implantation and implemented with a cutting-edge molecular dynamics method. A series of simulations with varying incident energies and incident angles is performed for incidence on silicon substrate and correlated effects are compared in detail. Meanwhile, the behavior of the cluster during implantation is also examined under elevated temperatures. By mapping the nanoscopic morphology with variable parameters, numerical formalism is proposed to explain the different impacts on phrase transition and surface pattern formation. Particularly, implantation efficiency (IE) is computed and further used to evaluate the performance of the overall process. The calculated results could be properly adopted as the theoretical basis for designing nano-structures and adjusting devices’ properties. Project supported by the National Natural Science Foundation of China (Nos. 51622507, 61471255, 61474079, 61403273, 51502193, 51205273), the Natural Science Foundation of Shanxi (Nos. 201601D021057, 201603D421035), the Youth Foundation Project of Shanxi Province (Nos. 2015021097), the Doctoral Fund of MOE of China (No. 20131402110013), the National High Technology Research and Development Program of China (No. 2015AA042601), and the Specialized Project in Public Welfare from The Ministry of Water Resources of China (Nos. 1261530110110).

Developing nanotechnology for biofuel and plant science applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valenstein, Justin

2012-01-01

This dissertation presents the research on the development of mesoporous silica based nanotechnology for applications in biofuels and plant science. Mesoporous silica nanoparticles (MSNs) have been the subject of great interest in the last two decades due to their unique properties of high surface area, tunable pore size and particle morphology. The robust nature of the silica framework is easily functionalized to make the MSNs a promising option for selective separations. Also, the independent channels that form the pores of MSN have been exploited in the use of particles as platforms for molecular delivery. Pore size and organic functionality aremore » varied to identify the ideal adsorbent material for free fatty acids (FFAs). The resulting material is able to sequester FFAs with a high degree of selectivity from a simulated solution and microalgal oil. The recyclability and industrial implications are also explored. A continuation of the previous material, further tuning of MSN pore size was investigated. Particles with a smaller diameter selectively sequester polyunsaturated free fatty acids (PUFAs) over monounsaturated FFAs and saturated FFAs. The experimental results were verified with molecular modeling. Mesoporous silica nanoparticle materials with a pore diameter of 10 nm (MSN-10) were decorated with small gold nanoparticles. The resulting materials were shown to deliver proteins and DNA into plant cells using the biolistic method.« less

Origin of change in molecular-weight dependence for polymer surface tension.

PubMed

Thompson, R B; Macdonald, J R; Chen, P

2008-09-01

Self-consistent-field theory is used to reproduce the behavior of polymer surface tension with molecular-weight for both lower and higher molecular-weight polymers. The change in behavior of the surface tension between these two regimes is shown to be due to the almost total exclusion of polymer from the nonpolymer bulk phase. The predicted two regime surface tension behavior with molecular-weight and the exclusion explanation are shown to be valid for a range of different polymer compressibilities.

Mapping hydration dynamics and coupled water-protein fluctuations around a protein surface

NASA Astrophysics Data System (ADS)

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2009-03-01

Elucidation of the molecular mechanism of water-protein interactions is critical to understanding many fundamental aspects of protein science, such as protein folding and misfolding and enzyme catalysis. We recently carried out a global mapping of protein-surface hydration dynamics around a globular α-helical protein apomyoglobin. The intrinsic optical probe tryptophan was employed to scan the protein surface one at a time by site-specific mutagenesis. With femtosecond resolution, we mapped out the dynamics of water-protein interactions with more than 20 mutants and for two states, native and molten globular. A robust bimodal distribution of time scales was observed, representing two types of water motions: local relaxation and protein-coupled fluctuations. The time scales show a strong correlation with the local protein structural rigidity and chemical identity. We also resolved two distinct contributions to the overall Stokes-shifts from the two time scales. These results are significant to understanding the role of hydration water on protein structural stability, dynamics and function.

Chemical Structure and Surface Modification of Dendritic Nanomaterials Tailored for Therapeutic and Diagnostic Applications.

PubMed

Myung, Ja Hye; Hsu, Hao-Jui; Bugno, Jason; Tam, Kevin A; Hong, Seungpyo

2017-01-01

Dendritic nanomaterials have attracted a great deal of scientific interest due to their high capacity for multifunctionalization and potential in various biomedical applications, such as drug/gene delivery and diagnostic systems. Depending on the molecular structure and starting monomers, several different types of dendrimers have been developed, including poly(amidoamine) (PAMAM), poly(propylenimine) (PPI), and poly(L-lysine) (PLL) dendrimers, in addition to modified dendritic nanomaterials, such as Janus dendrimers and dendritic block copolymers. The chemical structure and surface modification of dendritic nanomaterials have been found to play a critical role in governing their biological behaviors. In this review, we present a comprehensive overview focusing on the synthesis and chemical structures of dendrimers and modified dendritic nanomaterials that are currently being investigated for drug delivery, gene delivery, and diagnostic applications. In addition, the impact of chemical surface modification and functionalization to the dendritic nanomaterials on their therapeutic and diagnostic applications are highlighted. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Comprehensive investigation of HgCdTe metalorganic chemical vapor deposition

NASA Technical Reports Server (NTRS)

Raupp, Gregory B.

1993-01-01

The principal objective of this experimental and theoretical research program was to explore the possibility of depositing high quality epitaxial CdTe and HgCdTe at very low pressures through metalorganic chemical vapor deposition (MOCVD). We explored two important aspects of this potential process: (1) the interaction of molecular flow transport and deposition in an MOCVD reactor with a commercial configuration, and (2) the kinetics of metal alkyl source gas adsorption, decomposition and desorption from the growing film surface using ultra high vacuum surface science reaction techniques. To explore the transport-reaction issue, we have developed a reaction engineering analysis of a multiple wafer-in-tube ultrahigh vacuum chemical vapor deposition (UHV/CVD) reactor which allows an estimate of wafer or substrate throughput for a reactor of fixed geometry and a given deposition chemistry with specified film thickness uniformity constraints. The model employs a description of ballistic transport and reaction based on the pseudo-steady approximation to the Boltzmann equation in the limit of pure molecular flow. The model representation takes the form of an integral equation for the flux of each reactant or intermediate species to the wafer surfaces. Expressions for the reactive sticking coefficients (RSC) for each species must be incorporated in the term which represents reemission from a wafer surface. The interactions of MOCVD precursors with Si and CdTe were investigated using temperature programmed desorption (TPD) in ultra high vacuum combined with Auger electron spectroscopy (AES). These studies revealed that diethyltellurium (DETe) and dimethylcadmium (DMCd) adsorb weakly on clean Si(100) and desorb upon heating without decomposing. These precursors adsorb both weakly and strongly on CdTe(111)A, with DMCd exhibiting the stronger interaction with the surface than DETe.

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

PubMed

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.

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

PubMed

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.

Quantitative biological surface science: challenges and recent advances.

PubMed

Höök, Fredrik; Kasemo, Bengt; Grunze, Michael; Zauscher, Stefan

2008-12-23

Biological surface science is a broad, interdisciplinary subfield of surface science, where properties and processes at biological and synthetic surfaces and interfaces are investigated, and where biofunctional surfaces are fabricated. The need to study and to understand biological surfaces and interfaces in liquid environments provides sizable challenges as well as fascinating opportunities. Here, we report on recent progress in biological surface science that was described within the program assembled by the Biomaterial Interface Division of the Science and Technology of Materials, Interfaces and Processes (www.avs.org) during their 55th International Symposium and Exhibition held in Boston, October 19-24, 2008. The selected examples show that the rapid progress in nanoscience and nanotechnology, hand-in-hand with theory and simulation, provides increasingly sophisticated methods and tools to unravel the mechanisms and details of complex processes at biological surfaces and in-depth understanding of biomolecular surface interactions.

Rock Formation and Cosmic Radiation Exposure Ages in Gale Crater Mudstones from the Mars Science Laboratory

NASA Astrophysics Data System (ADS)

Mahaffy, Paul; Farley, Ken; Malespin, Charles; Gellert, Ralph; Grotzinger, John

2014-05-01

The quadrupole mass spectrometer (QMS) in the Sample Analysis at Mars (SAM) suite of the Mars Science Laboratory (MSL) has been utilized to secure abundances of 3He, 21Ne, 36Ar, and 40Ar thermally evolved from the mudstone in the stratified Yellowknife Bay formation in Gale Crater. As reported by Farley et al. [1] these measurements of cosmogenic and radiogenic noble gases together with Cl and K abundances measured by MSL's alpha particle X-ray spectrometer enable a K-Ar rock formation age of 4.21+0.35 Ga to be established as well as a surface exposure age to cosmic radiation of 78+30 Ma. Understanding surface exposures to cosmic radiation is relevant to the MSL search for organic compounds since even the limited set of studies carried out, to date, indicate that even 10's to 100's of millions of years of near surface (1-3 meter) exposure may transform a significant fraction of the organic compounds exposed to this radiation [2,3,4]. Transformation of potential biosignatures and even loss of molecular structural information in compounds that could point to exogenous or endogenous sources suggests a new paradigm in the search for near surface organics that incorporates a search for the most recently exposed outcrops through erosional processes. The K-Ar rock formation age determination shows promise for more precise in situ measurements that may help calibrate the martian cratering record that currently relies on extrapolation from the lunar record with its ground truth chronology with returned samples. We will discuss the protocol for the in situ noble gas measurements secured with SAM and ongoing studies to optimize these measurements using the SAM testbed. References: [1] Farley, K.A.M Science Magazine, 342, (2013). [2] G. Kminek et al., Earth Planet Sc Lett 245, 1 (2006). [3] Dartnell, L.R., Biogeosciences 4, 545 (2007). [4] Pavlov, A. A., et al. Geophys Res Lett 39, 13202 (2012).

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

PubMed

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.

Molecular surface mesh generation by filtering electron density map.

PubMed

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 switches and motors on surfaces.

PubMed

Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

2013-01-01

Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

Adsorption of TCDD with 1-butyl-3-methylimidazolium dicyanamide ionic liquid: a combined molecular dynamics simulation and quantum chemistry study.

PubMed

Pan, Wenxiao; Qi, Yuanyuan; Wang, Ruoxi; Han, Zhe; Zhang, Dongju; Zhan, Jinhua

2013-04-01

The effective abatement of flue gas emissions, especially polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs), is one of the challenging issues in the field of environmental science currently. Imidazolium-based dicyanamide ionic liquids (ILs) were proposed to have potential in controlling the emissions of PCDD/Fs. However, the relevant mechanism at the molecular level still remains unclear. To address this subject, we here present a combined molecular dynamics (MD) simulation and quantum chemical (QM) study on the adsorption of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the most toxic congener among PCDD/F family, by 1-butyl-3-methylimidazolium dicyanamide IL, a representative imidazolium dicyanoamide ILs, which were demonstrated to possess high capture capability for PCDD/Fs. The MD simulation results show that TCDD molecules can be effectively adsorbed on the IL surface to form a dense layer, but cannot enter the interior of the IL. The results of QM calculations show that the adsorption of TCDDs on the IL surface occurs via intra-molecular hydrogen bond interactions. The calculated interaction energy of the anion with TCDD molecule is two times more than that of the cation, implying that the IL anion dominates the interaction with TCDD molecules, while the cation plays a secondary role. Based on the calculated results, we propose that imidazolium dicyanamide IL films/membranes may be better materials than the corresponding bulk for capturing TCDD. The present theoretical results may be helpful to designing the functional ILs which effectively capture and concentrate PCDD/F compounds. Copyright © 2013 Elsevier Ltd. All rights reserved.

Safe Science: Be Protected!

ERIC Educational Resources Information Center

Roy, Ken

2006-01-01

Science education is a changing landscape. Changes over the past ten years alone have been both evolutionary and revolutionary--Science Education Standards, new required assessments, science teacher certification issues, science teacher shortages and retirements, molecular approach to Biology, etc. These changes and issues range from…

Laboratory Directed Research and Development Annual Report for 2009

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, Pamela J.

This report documents progress made on all LDRD-funded projects during fiscal year 2009. As a US Department of Energy (DOE) Office of Science (SC) national laboratory, Pacific Northwest National Laboratory (PNNL) has an enduring mission to bring molecular and environmental sciences and engineering strengths to bear on DOE missions and national needs. Their vision is to be recognized worldwide and valued nationally for leadership in accelerating the discovery and deployment of solutions to challenges in energy, national security, and the environment. To achieve this mission and vision, they provide distinctive, world-leading science and technology in: (1) the design and scalablemore » synthesis of materials and chemicals; (2) climate change science and emissions management; (3) efficient and secure electricity management from generation to end use; and (4) signature discovery and exploitation for threat detection and reduction. PNNL leadership also extends to operating EMSL: the Environmental Molecular Sciences Laboratory, a national scientific user facility dedicated to providing itnegrated experimental and computational resources for discovery and technological innovation in the environmental molecular sciences.« less

Reprogrammable Assembly of Molecular Motor on Solid Surfaces via Dynamic Bonds.

PubMed

Yu, Li; Sun, Jian; Wang, Qian; Guan, Yan; Zhou, Le; Zhang, Jingxuan; Zhang, Lanying; Yang, Huai

2017-06-01

Controllable assembly of molecular motors on solid surfaces is a fundamental issue for providing them to perform physical tasks. However, it can hardly be achieved by most previous methods due to their inherent limitations. Here, a general strategy is designed for the reprogrammable assembly of molecular motors on solid surfaces based on dynamic bonds. In this method, molecular motors with disulfide bonds can be remotely, reversibly, and precisely attached to solid surfaces with disulfide bonds, regardless of their chemical composition and microstructure. More importantly, it not only allows encoding geometric information referring to a pattern of molecular motors, but also enables erasing and re-encoding of geometric information via hemolytic photocleavage and recombination of disulfide bonds. Thus, solid surfaces can be regarded as "computer hardware", where molecular motors can be reformatted and reprogramed as geometric information. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective scanning tunnelling microscope electron-induced reactions of single biphenyl molecules on a Si(100) surface.

PubMed

Riedel, Damien; Bocquet, Marie-Laure; Lesnard, Hervé; Lastapis, Mathieu; Lorente, Nicolas; Sonnet, Philippe; Dujardin, Gérald

2009-06-03

Selective electron-induced reactions of individual biphenyl molecules adsorbed in their weakly chemisorbed configuration on a Si(100) surface are investigated by using the tip of a low-temperature (5 K) scanning tunnelling microscope (STM) as an atomic size source of electrons. Selected types of molecular reactions are produced, depending on the polarity of the surface voltage during STM excitation. At negative surface voltages, the biphenyl molecule diffuses across the surface in its weakly chemisorbed configuration. At positive surface voltages, different types of molecular reactions are activated, which involve the change of adsorption configuration from the weakly chemisorbed to the strongly chemisorbed bistable and quadristable configurations. Calculated reaction pathways of the molecular reactions on the silicon surface, using the nudge elastic band method, provide evidence that the observed selectivity as a function of the surface voltage polarity cannot be ascribed to different activation energies. These results, together with the measured threshold surface voltages and the calculated molecular electronic structures via density functional theory, suggest that the electron-induced molecular reactions are driven by selective electron detachment (oxidation) or attachment (reduction) processes.

Monod and the spirit of molecular biology.

PubMed

Morange, Michel

2015-06-01

The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly, Monod anticipated some recent evolutions of this discipline. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Supersonic molecular beam experiments on surface chemical reactions.

PubMed

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.

The EDGE-CALIFA Survey: Interferometric Observations of 126 Galaxies with CARMA

NASA Astrophysics Data System (ADS)

Bolatto, Alberto D.; Wong, Tony; Utomo, Dyas; Blitz, Leo; Vogel, Stuart N.; Sánchez, Sebastián F.; Barrera-Ballesteros, Jorge; Cao, Yixian; Colombo, Dario; Dannerbauer, Helmut; García-Benito, Rubén; Herrera-Camus, Rodrigo; Husemann, Bernd; Kalinova, Veselina; Leroy, Adam K.; Leung, Gigi; Levy, Rebecca C.; Mast, Damián; Ostriker, Eve; Rosolowsky, Erik; Sandstrom, Karin M.; Teuben, Peter; van de Ven, Glenn; Walter, Fabian

2017-09-01

We present interferometric CO observations, made with the Combined Array for Millimeter-wave Astronomy (CARMA) interferometer, of galaxies from the Extragalactic Database for Galaxy Evolution survey (EDGE). These galaxies are selected from the Calar Alto Legacy Integral Field Area (CALIFA) sample, mapped with optical integral field spectroscopy. EDGE provides good-quality CO data (3σ sensitivity {{{Σ }}}{mol}˜ 11 {M}⊙ {{pc}}-2 before inclination correction, resolution ˜1.4 kpc) for 126 galaxies, constituting the largest interferometric CO survey of galaxies in the nearby universe. We describe the survey and data characteristics and products, then present initial science results. We find that the exponential scale lengths of the molecular, stellar, and star-forming disks are approximately equal, and galaxies that are more compact in molecular gas than in stars tend to show signs of interaction. We characterize the molecular-to-stellar ratio as a function of Hubble type and stellar mass and present preliminary results on the resolved relations between the molecular gas, stars, and star-formation rate. We then discuss the dependence of the resolved molecular depletion time on stellar surface density, nebular extinction, and gas metallicity. EDGE provides a key data set to address outstanding topics regarding gas and its role in star formation and galaxy evolution, which will be publicly available on completion of the quality assessment.

Surface Immobilization of Molecular Electrocatalysts for Energy Conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bullock, R. Morris; Das, Atanu K.; Appel, Aaron M.

2017-03-22

Electrocatalysts are critically important for a secure energy future, as they facilitate the conversion between electrical energy and chemical energy. Molecular catalysts offer precise control of their structure, and the ability to modify the substituents to understand structure-reactivity relationships that are more difficult to achieve with heterogeneous catalysts. Molecular electrocatalysts can be immobilized on surfaces by covalent bonds or through non-covalent interactions. Advantages of surface immobilization include the need for less catalyst, avoidance of bimolecular decomposition pathways, and easier determination of catalyst lifetime. Copper-catalyzed click reactions are often used to form covalent bonds to surfaces, and pi-pi stacking of pyrenemore » substituents appended to the ligand of a molecular complex is a frequently used method to achieve non-covalent surface immobilization. This mini-review highlights surface confinement of molecular electrocatalysts for reduction of O2, oxidation of H2O, production of H2, and reduction of CO2.« less

Liquid Metals as Plasma-facing Materials for Fusion Energy Systems: From Atoms to Tokamaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stone, Howard A.; Koel, Bruce E.; Bernasek, Steven L.

The objective of our studies was to advance our fundamental understanding of liquid metals as plasma-facing materials for fusion energy systems, with a broad scope: from atoms to tokamaks. The flow of liquid metals offers solutions to significant problems of the plasma-facing materials for fusion energy systems. Candidate metals include lithium, tin, gallium, and their eutectic combinations. However, such liquid metal solutions can only be designed efficiently if a range of scientific and engineering issues are resolved that require advances in fundamental fluid dynamics, materials science and surface science. In our research we investigated a range of significant and timelymore » problems relevant to current and proposed engineering designs for fusion reactors, including high-heat flux configurations that are being considered by leading fusion energy groups world-wide. Using experimental and theoretical tools spanning atomistic to continuum descriptions of liquid metals, and bridging surface chemistry, wetting/dewetting and flow, our research has advanced the science and engineering of fusion energy materials and systems. Specifically, we developed a combined experimental and theoretical program to investigate flows of liquid metals in fusion-relevant geometries, including equilibrium and stability of thin-film flows, e.g. wetting and dewetting, effects of electromagnetic and thermocapillary fields on liquid metal thin-film flows, and how chemical interactions and the properties of the surface are influenced by impurities and in turn affect the surface wetting characteristics, the surface tension, and its gradients. Because high-heat flux configurations produce evaporation and sputtering, which forces rearrangement of the liquid, and any dewetting exposes the substrate to damage from the plasma, our studies addressed such evaporatively driven liquid flows and measured and simulated properties of the different bulk phases and material interfaces. The range of our studies included (i) quantum mechanical calculations that allow inclusion of many thousands of atoms for the characterization of the interface of liquid metals exposed to continuous bombardment by deuterium and tritium as expected in fusion, (ii) molecular dynamics studies of the phase behavior of liquid metals, which (a) utilize thermodynamic properties computed using our quantum mechanical calculations and (b) establish material and wetting properties of the liquid metals, including relevant eutectics, (iii) experimental investigations of the surface science of liquid metals, interacting both with the solid substrate as well as gaseous species, and (iv) fluid dynamical studies that incorporate the material and surface science results of (ii) and (iii) in order to characterize flow in capillary porous materials and the thin-film flow along curved boundaries, both of which are potentially major components of plasma-facing materials. The outcome of these integrated studies was new understanding that enables developing design rules useful for future developments of the plasma-facing components critical to the success of fusion energy systems.« less

Visualization and Interactivity in the Teaching of Chemistry to Science and Non-Science Students

ERIC Educational Resources Information Center

Venkataraman, Bhawani

2009-01-01

A series of interactive, instructional units have been developed that integrate computational molecular modelling and visualization to teach fundamental chemistry concepts and the relationship between the molecular and macro-scales. The units span the scale from atoms, small molecules to macromolecular systems, and introduce many of the concepts…

Matters of Taste: Bridging Molecular Physiology and the Humanities

ERIC Educational Resources Information Center

Rangachari, P. K.; Rangachari, Usha

2015-01-01

Taste perception was the focus of an undergraduate course in the health sciences that bridged the sciences and humanities. A problem-based learning approach was used to study the biological issues, whereas the cultural transmutations of these molecular mechanisms were explored using a variety of resources (novels, cookbooks, and films). Multiple…

Meet the Molecules in Chocolate: Informal Opportunities for Building Thematic Molecular Models with Children

ERIC Educational Resources Information Center

Amey, Jennifer R.; Fletcher, Matthew D.; Fletcher, Rachael V.; Jones, Alison; Roberts, Erica W.; Roberts, Ieuan O.

2008-01-01

We describe the development and use of a molecular model building activity with a chocolate theme, suitable for a public presentation of chemistry through interaction with visitors to science festivals and museums, and as a special classroom activity during science weeks, and so forth. (Contains 3 figures.)

Science Operations on the Lunar Surface - Understanding the Past, Testing in the Present, Considering the Future

NASA Technical Reports Server (NTRS)

Eppler, Dean B.

2013-01-01

The scientific success of any future human lunar exploration mission will be strongly dependent on design of both the systems and operations practices that underpin crew operations on the lunar surface. Inept surface mission preparation and design will either ensure poor science return, or will make achieving quality science operation unacceptably difficult for the crew and the mission operations and science teams. In particular, ensuring a robust system for managing real-time science information flow during surface operations, and ensuring the crews receive extensive field training in geological sciences, are as critical to mission success as reliable spacecraft and a competent operations team.

Discovery and development of microporous metal carboxylates.

PubMed

Mori, Wasuke; Sato, Tomohiko; Kato, Chika Nozaki; Takei, Tohru; Ohmura, Tetsushi

2005-01-01

We have found a form of copper(II) terephthalate that occluded an enormous amount of gases such as N2, Ar, O2, and Xe. Copper(II) terephthalate is the first metal complex found capable of adsorbing gases. This complex has opened a new field of adsorbent chemistry and is recognized as a leader in the construction of microporous metal complexes. In extending the route for the synthesis of microporous complexes, we obtained many new porous materials that are widely recognized as useful materials for applications in areas such as gas storage, molecular sieves, catalysis, inclusion complexes, and surface science. 2005 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

Biological applications of nanobiotechnology.

PubMed

de Morais, Michele Greque; Martins, Vilásia Guimarães; Steffens, Daniela; Pranke, Patricia; da Costa, Jorge Alberto Vieira

2014-01-01

Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices derived from engineering, physics, chemistry, and biology. Nanotechnology has opened up by rapid advances in science and technology, creating new opportunities for advances in the fields of medicine, electronics, foods, and the environment. Nanoscale structures and materials (nanoparticles, nanowires, nanofibers, nanotubes) have been explored in many biological applications (biosensing, biological separation, molecular imaging, anticancer therapy) because their novel properties and functions differ drastically from their bulk counterparts. Their high volume/surface ratio, improved solubility, and multifunctionality open many new possibilities. The objective of this review is to describe the potential benefits and impacts of the nanobiotechnology in different areas.

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1990

1990-01-01

Presented are 27 science activities for secondary school science instruction. Topic areas include microbiology, botany, biochemistry, genetics, safety, earthquakes, problem solving, electricity, heat, solutions, mechanics, quantum mechanics, flame tests, and molecular structure. (CW)

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

PubMed

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.

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

PubMed Central

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.

PubMed

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.

Molecular Research in Aquaculture

USDA-ARS?s Scientific Manuscript database

Molecular research and biotechnology have long been fields of study with applications useful to aquaculture and other animal sciences. Molecular Research in Aquaculture looks to provide an understanding of molecular research and its applications to the aquaculture industry in a format that allows in...

Defining Protein Electrostatic Recognition Processes

DTIC Science & Technology

1989-11-30

of the electrostatic potentiai on the molecular surface of negatively charged Asp-101 in the fifth residue of JH1. the hapten and the V regions of...making and aligning expanded molecular dot surfaces for each molecule and checking these surfaces for interpenetration. The program TURNIP used these...the molecular surfaces are separated by 6 and 12A. All orientations have the exposed heme edge of cytochrome c facing the acidic patch of plastocyanin

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1990

1990-01-01

Presented are 29 science activities for secondary school science instruction. Topic areas include botany, genetics, biochemistry, anatomy, entomology, molecular structure, spreadsheets, chemistry, mechanics, astronomy, relativity, aeronautics, instrumentation, electrostatics, quantum mechanics, and laboratory interfacing. (CW)

Dynamic Cooperation of Hydrogen Binding and π Stacking in ssDNA Adsorption on Graphene Oxide.

PubMed

Xu, Zhen; Lei, Xiaoling; Tu, Yusong; Tan, Zhi-Jie; Song, Bo; Fang, Haiping

2017-09-21

Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on GO surfaces. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and π-π stacking interactions, with preferential binding to the oxidized rather than to the unoxidized region of the GO surface. The adsorption process shows a dynamic cooperation adsorption behavior; the ssDNA segment first captures the oxidized groups of the GO surface by hydrogen bonding interaction, and then the configuration relaxes to maximize the π-π stacking interactions between the aromatic rings of the nucleobases and those of the GO surface. We attributed this behavior to the faster forming hydrogen bonding interaction compared to π-π stacking; the π-π stacking interaction needs more relaxation time to regulate the configuration of the ssDNA segment to fit the aromatic rings on the GO surface. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA

NASA Astrophysics Data System (ADS)

Lin, Chenxiang; Jungmann, Ralf; Leifer, Andrew M.; Li, Chao; Levner, Daniel; Church, George M.; Shih, William M.; Yin, Peng

2012-10-01

The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ˜40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments.

Nanoparticles as biochemical sensors

PubMed Central

El-Ansary, Afaf; Faddah, Layla M

2010-01-01

There is little doubt that nanoparticles offer real and new opportunities in many fields, such as biomedicine and materials science. Such particles are small enough to enter almost all areas of the body, including cells and organelles, potentially leading to new approaches in nanomedicine. Sensors for small molecules of biochemical interest are of critical importance. This review is an attempt to trace the use of nanomaterials in biochemical sensor design. The possibility of using nanoparticles functionalized with antibodies as markers for proteins will be elucidated. Moreover, capabilities and applications for nanoparticles based on gold, silver, magnetic, and semiconductor materials (quantum dots), used in optical (absorbance, luminescence, surface enhanced Raman spectroscopy, surface plasmon resonance), electrochemical, and mass-sensitive sensors will be highlighted. The unique ability of nanosensors to improve the analysis of biochemical fluids is discussed either through considering the use of nanoparticles for in vitro molecular diagnosis, or in the biological/biochemical analysis for in vivo interaction with the human body. PMID:24198472

New insights on molecular regulation of biofilm formation in plant-associated bacteria.

PubMed

Castiblanco, Luisa F; Sundin, George W

2016-04-01

Biofilms are complex bacterial assemblages with a defined three-dimensional architecture, attached to solid surfaces, and surrounded by a self-produced matrix generally composed of exopolysaccharides, proteins, lipids and extracellular DNA. Biofilm formation has evolved as an adaptive strategy of bacteria to cope with harsh environmental conditions as well as to establish antagonistic or beneficial interactions with their host. Plant-associated bacteria attach and form biofilms on different tissues including leaves, stems, vasculature, seeds and roots. In this review, we examine the formation of biofilms from the plant-associated bacterial perspective and detail the recently-described mechanisms of genetic regulation used by these organisms to orchestrate biofilm formation on plant surfaces. In addition, we describe plant host signals that bacterial pathogens recognize to activate the transition from a planktonic lifestyle to multicellular behavior. © 2015 Institute of Botany, Chinese Academy of Sciences.

Studies on metal-dielectric plasmonic structures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chettiar, Uday K.; Liu, Zhengtong; Thoreson, Mark D.

2010-01-01

The interaction of light with nanostructured metal leads to a number of fascinating phenomena, including plasmon oscillations that can be harnessed for a variety of cutting-edge applications. Plasmon oscillation modes are the collective oscillation of free electrons in metals under incident light. Previously, surface plasmon modes have been used for communication, sensing, nonlinear optics and novel physics studies. In this report, we describe the scientific research completed on metal-dielectric plasmonic films accomplished during a multi-year Purdue Excellence in Science and Engineering Graduate Fellowship sponsored by Sandia National Laboratories. A variety of plasmonic structures, from random 2D metal-dielectric films to 3Dmore » composite metal-dielectric films, have been studied in this research for applications such as surface-enhanced Raman sensing, tunable superlenses with resolutions beyond the diffraction limit, enhanced molecular absorption, infrared obscurants, and other real-world applications.« less

Emerging therapies in allergic conjunctivitis and dry eye syndrome.

PubMed

Nye, Michael; Rudner, Shara; Bielory, Leonard

2013-08-01

Inflammatory disorders of the anterior surface of the eye consist of a spectrum of disorders that range from ocular allergy, dry eye syndrome (DES), and various infections. They exhibit similar pathological profiles, but have divergent immune mechanisms with some overlap. A number of novel treatments are currently being studied that capitalize on the growing understanding of underlying immunopathophysiology. The goal of this review is to examine the emerging pipeline for noninfectious inflammatory disorders of the anterior surface of the eye - primarily allergic conjunctivitis (AC) and DES - in light of the recent basic science discoveries that have fueled their development. Novel molecules for the treatment of AC and DES from clinicaltrials.gov as well as recently filed patents for new molecular entities were reviewed from PUBMED and OVID. Significant progress toward targeted treatments for AC and DES has become increasingly reliant on understanding the immunomodulatory and inflammatory mechanisms of the conjunctiva.

Enantioselective recognition at mesoporous chiral metal surfaces.

PubMed

Wattanakit, Chularat; Côme, Yémima Bon Saint; Lapeyre, Veronique; Bopp, Philippe A; Heim, Matthias; Yadnum, Sudarat; Nokbin, Somkiat; Warakulwit, Chompunuch; Limtrakul, Jumras; Kuhn, Alexander

2014-01-01

Chirality is widespread in natural systems, and artificial reproduction of chiral recognition is a major scientific challenge, especially owing to various potential applications ranging from catalysis to sensing and separation science. In this context, molecular imprinting is a well-known approach for generating materials with enantioselective properties, and it has been successfully employed using polymers. However, it is particularly difficult to synthesize chiral metal matrices by this method. Here we report the fabrication of a chirally imprinted mesoporous metal, obtained by the electrochemical reduction of platinum salts in the presence of a liquid crystal phase and chiral template molecules. The porous platinum retains a chiral character after removal of the template molecules. A matrix obtained in this way exhibits a large active surface area due to its mesoporosity, and also shows a significant discrimination between two enantiomers, when they are probed using such materials as electrodes.

Microwave-Assisted Cross-Polarization of Nuclear Spin Ensembles from Optically Pumped Nitrogen-Vacancy Centers in Diamond.

PubMed

Shagieva, F; Zaiser, S; Neumann, P; Dasari, D B R; Stöhr, R; Denisenko, A; Reuter, R; Meriles, C A; Wrachtrup, J

2018-06-13

The ability to optically initialize the electronic spin of the nitrogen-vacancy (NV) center in diamond has long been considered a valuable resource to enhance the polarization of neighboring nuclei, but efficient polarization transfer to spin species outside the diamond crystal has proven challenging. Here we demonstrate variable-magnetic-field, microwave-enabled cross-polarization from the NV electronic spin to protons in a model viscous fluid in contact with the diamond surface. Further, slight changes in the cross-relaxation rate as a function of the wait time between successive repetitions of the transfer protocol suggest slower molecular dynamics near the diamond surface compared to that in bulk. This observation is consistent with present models of the microscopic structure of a fluid and can be exploited to estimate the diffusion coefficient near a solid-liquid interface, of importance in colloid science.

Bio-inspired reversible underwater adhesive.

PubMed

Zhao, Yanhua; Wu, Yang; Wang, Liang; Zhang, Manman; Chen, Xuan; Liu, Minjie; Fan, Jun; Liu, Junqiu; Zhou, Feng; Wang, Zuankai

2017-12-20

The design of smart surfaces with switchable adhesive properties in a wet environment has remained a challenge in adhesion science and materials engineering. Despite intense demands in various industrial applications and exciting progress in mimicking the remarkable wet adhesion through the delicate control of catechol chemistry, polyelectrolyte complex, and supramolecular architectures, the full recapitulation of nature's dynamic function is limited. Here, we show a facile approach to synthesize bioinspired adhesive, which entails the reversible, tunable, and fast regulation of the wet adhesion on diverse surfaces. The smart wet adhesive takes advantage of the host-guest molecular interaction and the adhesive nature of catechol chemistry, as well as the responsive polymer, allowing for screening and activation of the interfacial interaction simply by a local temperature trigger in an on-demand manner. Our work opens up an avenue for the rational design of bioinspired adhesives with performances even beyond nature.

Sub-micrometer Geometrically Encoded Fluorescent Barcodes Self-Assembled from DNA

PubMed Central

Lin, Chenxiang; Jungmann, Ralf; Leifer, Andrew M.; Li, Chao; Levner, Daniel; Church, George M.; Shih, William M.; Yin, Peng

2012-01-01

The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here we use DNA-origami technology to construct sub-micrometer nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be unambiguously decoded using epifluorescence or total internal reflection fluorescence (TIRF) microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ~40 nm. One species of the barcodes was used to tag yeast surface receptors, suggesting their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments. PMID:23000997

Bioinspired interface for nanobiodevices based on phospholipid polymer chemistry

PubMed Central

Ishihara, Kazuhiko; Takai, Madoka

2009-01-01

This review paper describes novel biointerfaces for nanobiodevices. Biocompatible and non-biofouling surfaces are designed largely based on cell membrane structure, and the preparation and functioning of the bioinspired interface are evaluated and compared between living and artificial systems. A molecular assembly of polymers with a phospholipid polar group has been developed as the platform of the interface. At the surface, protein adsorption is effectively reduced and the subsequent bioreactions are suppressed. Through this platform, biomolecules with a high affinity to the specific molecules are introduced under mild conditions. The activity of the biomolecules is retained even after immobilization. This bioinspired interface is adapted to construct bionanodevices, that is, microfluidic chips and nanoparticles for capturing target molecules and cells. The interface functions well and has a very high efficiency for biorecognition. This bioinspired interface is a promising universal platform that integrates various fields of science and has useful applications. PMID:19324688

Identifying Few-Molecule Water Clusters with High Precision on Au(111) Surface.

PubMed

Dong, Anning; Yan, Lei; Sun, Lihuan; Yan, Shichao; Shan, Xinyan; Guo, Yang; Meng, Sheng; Lu, Xinghua

2018-06-01

Revealing the nature of a hydrogen-bond network in water structures is one of the imperative objectives of science. With the use of a low-temperature scanning tunneling microscope, water clusters on a Au(111) surface were directly imaged with molecular resolution by a functionalized tip. The internal structures of the water clusters as well as the geometry variations with the increase of size were identified. In contrast to a buckled water hexamer predicted by previous theoretical calculations, our results present deterministic evidence for a flat configuration of water hexamers on Au(111), corroborated by density functional theory calculations with properly implemented van der Waals corrections. The consistency between the experimental observations and improved theoretical calculations not only renders the internal structures of absorbed water clusters unambiguously, but also directly manifests the crucial role of van der Waals interactions in constructing water-solid interfaces.

Advanced surface chemical analysis of continuously manufactured drug loaded composite pellets.

PubMed

Hossain, Akter; Nandi, Uttom; Fule, Ritesh; Nokhodchi, Ali; Maniruzzaman, Mohammed

2017-04-15

The aim of the present study was to develop and characterise polymeric composite pellets by means of continuous melt extrusion techniques. Powder blends of a steroid hormone (SH) as a model drug and either ethyl cellulose (EC N10 and EC P7 grades) or hydroxypropyl methylcellulose (HPMC AS grade) as polymeric carrier were extruded using a Pharma 11mm twin screw extruder in a continuous mode of operation to manufacture extruded composite pellets of 1mm length. Molecular modelling study using commercial Gaussian 09 software outlined a possible drug-polymer interaction in the molecular level to develop solid dispersions of the drug in the pellets. Solid-state analysis conducted via a differential scanning calorimetry (DSC), hot stage microscopy (HSM) and X-ray powder diffraction (XRPD) analyses revealed the amorphous state of the drug in the polymer matrices. Surface analysis using SEM/energy dispersive X-ray (EDX) of the produced pellets arguably showed a homogenous distribution of the C and O atoms in the pellet matrices. Moreover, advanced chemical surface analysis conducted via atomic force microscopy (AFM) showed a homogenous phase system having the drug molecule dispersed onto the amorphous matrices while Raman mapping confirmed the homogenous single-phase drug distribution in the manufactured composite pellets. Such composite pellets are expected to deliver multidisciplinary applications in drug delivery and medical sciences by e.g. modifying drug solubility/dissolutions or stabilizing the unstable drug (e.g. hormone, protein) in the composite network. Copyright © 2016. Published by Elsevier Inc.

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

ERIC Educational Resources Information Center

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…

Education Catching up with Science: Preparing Students for Three-Dimensional Literacy in Cell Biology

ERIC Educational Resources Information Center

Kramer, IJsbrand M.; Dahmani, Hassen-Reda; Delouche, Pamina; Bidabe, Marissa; Schneeberger, Patricia

2012-01-01

The large number of experimentally determined molecular structures has led to the development of a new semiotic system in the life sciences, with increasing use of accurate molecular representations. To determine how this change impacts students' learning, we incorporated image tests into our introductory cell biology course. Groups of students…

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy.

PubMed

Guo, Jing; You, Sifan; Wang, Zhichang; Peng, Jinbo; Ma, Runze; Jiang, Ying

2018-05-27

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal structure and probing the hydrogen-bond (H-bond) dynamics of the water molecules adsorbed on solid surfaces are fundamental issues of water science, which remains a great challenge owing to the light mass and small size of hydrogen. Scanning tunneling microscopy (STM) is a promising tool for attacking these problems, thanks to its capabilities of sub-Ångström spatial resolution, single-bond vibrational sensitivity, and atomic/molecular manipulation. The designed experimental system consists of a Cl-terminated tip and a sample fabricated by dosing water molecules in situ onto the Au(111)-supported NaCl(001) surfaces. The insulating NaCl films electronically decouple the water from the metal substrates, so the intrinsic frontier orbitals of water molecules are preserved. The Cl-tip facilitates the manipulation of the single water molecules, as well as gating the orbitals of water to the proximity of Fermi level (EF) via tip-water coupling. This paper outlines the detailed methods of submolecular resolution imaging, molecular/atomic manipulation, and single-bond vibrational spectroscopy of interfacial water. These studies open up a new route for investigating the H-bonded systems at the atomic scale.

Modulation of Spatiotemporal Particle Patterning in Evaporating Droplets: Applications to Diagnostics and Materials Science.

PubMed

Guha, Rajarshi; Mohajerani, Farzad; Mukhopadhyay, Ahana; Collins, Matthew D; Sen, Ayusman; Velegol, Darrell

2017-12-13

Spatiotemporal particle patterning in evaporating droplets lacks a common design framework. Here, we demonstrate autonomous control of particle distribution in evaporating droplets through the imposition of a salt-induced self-generated electric field as a generalized patterning strategy. Through modeling, a new dimensionless number, termed "capillary-phoresis" (CP) number, arises, which determines the relative contributions of electrokinetic and convective transport to pattern formation, enabling one to accurately predict the mode of particle assembly by controlling the spontaneous electric field and surface potentials. Modulation of the CP number allows the particles to be focused in a specific region in space or distributed evenly. Moreover, starting with a mixture of two different particle types, their relative placement in the ensuing pattern can be controlled, allowing coassemblies of multiple, distinct particle populations. By this approach, hypermethylated DNA, prevalent in cancerous cells, can be qualitatively distinguished from normal DNA of comparable molecular weights. In other examples, we show uniform dispersion of several particle types (polymeric colloids, multiwalled carbon nanotubes, and molecular dyes) on different substrates (metallic Cu, metal oxide, and flexible polymer), as dictated by the CP number. Depending on the particle, the highly uniform distribution leads to surfaces with a lower sheet resistance, as well as superior dye-printed displays.

Moisture induced polymorphic transition of mannitol and its morphological transformation.

PubMed

Yoshinari, Tomohiro; Forbes, Robert T; York, Peter; Kawashima, Yoshiaki

2002-10-24

The effects of moisture on the polymorphic transition of crystalline mannitol were investigated. Mannitol has three polymorphic forms, and was classified as alpha, beta, and delta form, respectively, by Walter-Lévy (C.R. Acad. Sc. Paris Ser. C (1968) 267, 1779). The water uptake of delta form crystalline was greater than that of the beta form when each crystalline form was stored at 97%RH (25 degrees C). The different powder X-ray diffraction patterns obtained before and after humidification confirmed that a moisture induced polymorphic transition from the delta to beta form had occurred. Morphological changes were also observed with an increase in the specific surface area of the delta sample from 0.4 to 2.3 m(2)/g being found on exposure to humidity. Thus it was suggested that the observed higher hygroscopicity of the newly formed beta form arose from the gradual increase in the surface area with the polymorphic transition from the delta to beta form. When considering the mechanism of this polymorphic transition, the results from molecular modelling, cross-polarisation/magic angle spinning (CP/MAS) solid-state NMR spectra and scanning electron-micrographs suggest that water molecules act as a molecular loosener to facilitate conversion from delta to the beta form as a result of multi-nucleation. Copyright 2002 Elsevier Science B.V.

Bidirectional Reflectance Function Measurement of Molecular Contaminant Scattering in the Vacuum Ultraviolet

NASA Technical Reports Server (NTRS)

Herren, Kenneth A.; Gregory, Don A.

2006-01-01

Bi-directional reflectance distribution function (BRDF) measurements of optical surfaces both before and after molecular contamination were done using UV, VUV and visible light. Molecular contamination of optical surfaces from outgassed material has been shown in many cases to proceed from acclimation centers, and to produce many roughly hemispherical "islands" of contamination on the surface. Vacuum Ultraviolet (VW) wavelengths are used here to measure angularly scattered light from optical surfaces.

First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface

NASA Astrophysics Data System (ADS)

Yang, Yu; Zhang, Ping

2015-05-01

Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the ‘Hot-Atom’ dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces.

Preface - From molecules to molecular materials, biological molecular systems and nanostructures: A collection of contributions presented at the XIIIth International Conference on Molecular Spectroscopy

NASA Astrophysics Data System (ADS)

Ratajczak, Henryk; Drozd, Marek; Fausto, Rui

2016-12-01

This volume contains a series of selected contributions presented at the XIIIth International Conference on Molecular Spectroscopy (ICMS): "From Molecules to Molecular Materials, Biological Molecular Systems and Nanostructures" held in Wrocław, Poland, 9-12 September 2015, under the auspices of the Mayor of Wrocław and the European Academy of Sciences, Arts and Humanities. Wrocław was chosen not accidentally as venue for the conference. With more than a thousand years of history, Wrocław is the location of one of the oldest universities in Central Europe. Being a place where education and science play major roles in the daily life of its inhabitants, Wrocław is also a privileged center for spectroscopy in Poland.

Surface segregation and surface tension of polydisperse polymer melts.

PubMed

Minnikanti, Venkatachala S; Qian, Zhenyu; Archer, Lynden A

2007-04-14

The effect of polydispersity on surface segregation of a lower molecular weight polymer component in a higher molecular weight linear polymer melt host is investigated theoretically. We show that the integrated surface excess zM of a polymer component of molecular weight M satisfies a simple relation zM=2Ue(M/Mw-1)phiM, where Mw is the weight averaged molecular weight, phiM is the polymer volume fraction, and Ue is the attraction of polymer chain ends to the surface. Ue is principally of entropic origin, but also reflects any energetic preference of chain ends to the surface. We further show that the surface tension gammaM of a polydisperse melt of high molar mass components depends on the number average degree of polymerization Mn as, gammaM=gammainfinity+2UerhobRT/Mn. The parameter gammainfinity is the asymptotic surface tension of an infinitely long polymer of the same chemistry, rhob is the bulk density of the polymer, R is the universal gas constant, and T is the temperature. The predicted gammaM compare favorably with surface tension values obtained from self-consistent field theory simulations that include equation of state effects, which account for changes in polymer density with molecular weight. We also compare the predicted surface tension with available experimental data.

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

PubMed

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

2016-09-01

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(-5)M in aqueous NaH2PO4 buffer at pH=7.0 and a maximal adsorption capacity of 1.45μmolg(-1). Upon alternate irradiation at 365 and 440nm, the surface molecularly imprinted polymer on ZnO nanorods can quantitatively uptake and release uric acid. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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.

A molecular model for ice nucleation and growth, attachment 1

NASA Technical Reports Server (NTRS)

Plummer, P. L. M.

1981-01-01

The quantum mechanical technique is used to study ionic, configurational, and impurity defects in the ice surface. In addition to static calculations of the energetics of the water monomer-ice surface interactions, molecular dynamics studies were initiated. The calculations of the monomer-ice surface interaction, molecular dynamics studies were initiated. The calculations of monomer-ice surface interactions indicate that many adsorption sites exist on the ice surfaces and that the barriers between bonding sites are relatively low. Bonding on the prism face of ice is preferentially above lattice sites.

DNA, RNA and the Physical Basis of Life

ERIC Educational Resources Information Center

Fong, Peter

1969-01-01

Presents the application of knowledge in the physical sciences to biological science problems, including those in the behavioral sciences, social sciences, and the humanities. Examples are presented in the areas of molecular psychology and theoretical biology, besides the principal genetic discussion. (RR)

Symmetry-Based Techniques for Qualitative Understanding of Rovibrational Effects in Spherical-Top Molecular Spectra and Dynamics

NASA Astrophysics Data System (ADS)

Mitchell, Justin Chadwick

2011-12-01

Using light to probe the structure of matter is as natural as opening our eyes. Modern physics and chemistry have turned this art into a rich science, measuring the delicate interactions possible at the molecular level. Perhaps the most commonly used tool in computational spectroscopy is that of matrix diagonalization. While this is invaluable for calculating everything from molecular structure and energy levels to dipole moments and dynamics, the process of numerical diagonalization is an opaque one. This work applies symmetry and semi-classical techniques to elucidate numerical spectral analysis for high-symmetry molecules. Semi-classical techniques, such as the Potential Energy Surfaces, have long been used to help understand molecular vibronic and rovibronic spectra and dynamics. This investigation focuses on newer semi-classical techniques that apply Rotational Energy Surfaces (RES) to rotational energy level clustering effects in high-symmetry molecules. Such clusters exist in rigid rotor molecules as well as deformable spherical tops. This study begins by using the simplicity of rigid symmetric top molecules to clarify the classical-quantum correspondence of RES semi-classical analysis and then extends it to a more precise and complete theory of modern high-resolution spectra. RES analysis is extended to molecules having more complex and higher rank tensorial rotational and rovibrational Hamiltonians than were possible to understand before. Such molecules are shown to produce an extraordinary range of rotational level clusters, corresponding to a panoply of symmetries ranging from C4v to C2 and C1 (no symmetry) with a corresponding range of new angular momentum localization and J-tunneling effects. Using RES topography analysis and the commutation duality relations between symmetry group operators in the lab-frame to those in the body-frame, it is shown how to better describe and catalog complex splittings found in rotational level clusters. Symmetry character analysis is generalized to give analytic eigensolutions. An appendix provides vibrational analogies. For the first time, interactions between molecular vibrations (polyads) are described semi-classically by multiple RES. This is done for the nu 3/2nu4 dyad of CF4. The nine-surface RES topology of the U(9)-dyad agrees with both computational and experimental work. A connection between this and a simpler U(2) example is detailed in an Appendix.

Elucidating the Physical and Chemical Structural Changes of Proteins on Clay Mineral Surfaces using Large-scale Molecular Dynamics Simulations in Tandem with NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Washton, N.; Reardon, P.; Chacon, S. S.; Burton, S.; Lipton, A.; Kleber, M.; Qafoku, N. P.

2014-12-01

Carbon cycling among the three major Earth's pools, i.e., atmosphere, terrestrial systems and oceans, has received increased attention because the concentration of CO2 in the atmosphere has increased significantly in recent years reaching concentrations greater than 400 ppm that have never been recorded before, warming the planet and changing the climate. Within the terrestrial system, soil organic matter (SOM) represents an important sub-pool of carbon. The associations of SOM with soil mineral interfaces and particles, creating micro-aggregates, are believed to regulate the bioavailability of the associated organic carbon by protecting it from transformations and mineralization to carbon dioxide. Nevertheless, the molecular scale interactions of different types of SOM with a variety of soil minerals and the controls on the extent and rate of SOM transformation and mineralization are not well documented in the current literature. Given the importance of SOM fate and persistence in soils and the current knowledge gaps, the application of atomistic scale simulations to study SOM/mineral associations in abiotic model systems offers rich territory for original and impactful science. Molecular modeling and simulation of SOM is a burgeoning and challenging avenue for aiding the characterization of these complex compounds and chemical systems and for studying their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types and common in soils, which are thought to contribute to their reactive properties including recalcitrance potential and resistance to mineralization. Here, we will discuss our large-scale molecular dynamics simulation efforts to explore the interaction of proteins with clay minerals (i.e., phyllosilicates such as kaolinite, smectite and micas), including the potential physical and chemical structural changes of proteins, protein adsorption by polar and permanently charged mineral surfaces and variably charged edges, and the potential role of amphiphilic proteins in providing adsorptive layers for SOM-mineral interfaces. Our efforts at characterizing these systems through combined modeling and simulation and NMR will also be discussed.

Nuclear Magnetic Resonance (NMR) Spectroscopic Characterization of Nanomaterials and Biopolymers

NASA Astrophysics Data System (ADS)

Guo, Chengchen

Nanomaterials have attracted considerable attention in recent research due to their wide applications in various fields such as material science, physical science, electrical engineering, and biomedical engineering. Researchers have developed many methods for synthesizing different types of nanostructures and have further applied them in various applications. However, in many cases, a molecular level understanding of nanoparticles and their associated surface chemistry is lacking investigation. Understanding the surface chemistry of nanomaterials is of great significance for obtaining a better understanding of the properties and functions of the nanomaterials. Nuclear magnetic resonance (NMR) spectroscopy can provide a familiar means of looking at the molecular structure of molecules bound to surfaces of nanomaterials as well as a method to determine the size of nanoparticles in solution. Here, a combination of NMR spectroscopic techniques including one- and two-dimensional NMR spectroscopies was used to investigate the surface chemistry and physical properties of some common nanomaterials, including for example, thiol-protected gold nanostructures and biomolecule-capped silica nanoparticles. Silk is a natural protein fiber that features unique properties such as excellent mechanical properties, biocompatibility, and non-linear optical properties. These appealing physical properties originate from the silk structure, and therefore, the structural analysis of silk is of great importance for revealing the mystery of these impressive properties and developing novel silk-based biomaterials as well. Here, solid-state NMR spectroscopy was used to elucidate the secondary structure of silk proteins in N. clavipes spider dragline silk and B. mori silkworm silk. It is found that the Gly-Gly-X (X=Leu, Tyr, Gln) motif in spider dragline silk is not in a beta-sheet or alpha-helix structure and is very likely to be present in a disordered structure with evidence for 31-helix confirmation. In addition, the conformations of the Ala, Ser, and Tyr residues in silk fibroin of B. mori were investigated and it indicates that the Ala, Ser, and Tyr residues are all present in disordered structures in silk I (before spinning), while show different conformations in silk II (after spinning). Specifically, in silk II, the Ala and Tyr residues are present in both disordered structures and beta-sheet structures, and the Ser residues are present primarily in beta-sheet structures.

Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

DOE PAGES

Tringe, J. W.; Ileri, N.; Levie, H. W.; ...

2015-08-01

We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage.more » Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.« less

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

NASA Astrophysics Data System (ADS)

Ramachandra Rao, M. S.; Margaritondo, Giorgio

2011-11-01

Three decades ago, with a tiny tip of platinum, the scientific world saw the real space imaging of single atoms with unprecedented spatial resolution. This signalled the birth of one of the most versatile surface probes, based on the physics of quantum mechanical tunnelling: the scanning tunnelling microscope (STM). Invented in 1981 by Gerd Binnig and Heinrich Rohrer of IBM, Zurich, it led to their award of the 1986 Nobel Prize. Atoms, once speculated to be abstract entities used by theoreticians for mere calculations, can be seen to exist for real with the nano-eye of an STM tip that also gives real-space images of molecules and adsorbed complexes on surfaces. From a very fundamental perspective, the STM changed the course of surface science and engineering. STM also emerged as a powerful tool to study various fundamental phenomena relevant to the properties of surfaces in technological applications such as tribology, medical implants, catalysis, sensors and biology—besides elucidating the importance of local bonding geometries and defects, non-periodic structures and the co-existence of nano-scale phases. Atom-level probing, once considered a dream, has seen the light with the evolution of STM. An important off-shoot of STM was the atomic force microscope (AFM) for surface mapping of insulating samples. Then followed the development of a flurry of techniques under the general name of scanning probe microscopy (SPM). These techniques (STM, AFM, MFM, PFM etc) designed for atomic-scale-resolution imaging and spectroscopy, have led to brand new developments in surface analysis. All of these novel methods enabled researchers in recent years to image and analyse complex surfaces on microscopic and nanoscopic scales. All of them utilize a small probe for sensing the surface. The invention of AFM by Gerd Binnig, Calvin Quate and Christopher Gerber opened up new opportunities for characterization of a variety of materials, and various industrial applications could be 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 scanning probe microscopy, conveying to the readers the full excitement of this forefront domain of physics.

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

PubMed Central

Prigent, Hélène; Maxime, Virginie; Annane, Djillali

2004-01-01

This review describes current knowledge on the mechanisms that underlie glucocorticoid insufficiency in sepsis and the molecular action of glucocorticoids. In patients with severe sepsis, numerous factors predispose to glucocorticoid insufficiency, including drugs, coagulation disorders and inflammatory mediators. These factors may compromise the hypothalamic–pituitary axis (i.e. secondary adrenal insufficiency) or the adrenal glands (i.e. primary adrenal failure), or may impair glucocorticoid access to target cells (i.e. peripheral tissue resistance). Irreversible anatomical damages to the hypothalamus, pituitary, or adrenal glands rarely occur. Conversely, transient functional impairment in hormone synthesis may be a common complication of severe sepsis. Glucocorticoids interact with a specific cytosolic glucocorticoid receptor, which undergoes conformational changes, sheds heat shock proteins and translocates to the nucleus. Glucocorticoids may also interact with membrane binding sites at the surface of the cells. The molecular action of glucocorticoids results in genomic and nongenomic effects. Direct and indirect transcriptional and post-transcriptional effects related to the cytosolic glucocorticoid receptor account for the genomic effects. Nongenomic effects are probably subsequent to cytosolic interaction between the glucocorticoid receptor and proteins, or to interaction between glucocorticoids and specific membrane binding sites. PMID:15312206

A Participant-Oriented, Research-Based Approach for Design of a Biochemistry Workshop for Faculty at Undergraduate Institutions

ERIC Educational Resources Information Center

Owen, Rebecca L.; Breyer, Emelita D.

2005-01-01

The Molecular Genetics and Protein Structure and Function workshop is one of a series of workshops offered by the National Science Foundation-funded Center for Workshops in the Chemical Sciences. The workshop provides a hands-on introduction to current topics and techniques in molecular genetics and protein structure/function as applied to…

Clusters of Concepts in Molecular Genetics: A Study of Swedish Upper Secondary Science Students' Understanding

ERIC Educational Resources Information Center

Gericke, Niklas; Wahlberg, Sara

2013-01-01

To understand genetics, students need to be able to explain and draw connections between a large number of concepts. The purpose of the study reported herein was to explore the way upper secondary science students reason about concepts in molecular genetics in order to understand protein synthesis. Data were collected by group interviews. Concept…

Interdisciplinary Education to Integrate Pathology and Epidemiology: Towards Molecular and Population-Level Health Science

PubMed Central

Ogino, Shuji; King, Emily E.; Beck, Andrew H.; Sherman, Mark E.; Milner, Danny A.; Giovannucci, Edward

2012-01-01

In recent decades, epidemiology, public health, and medical sciences have been increasingly compartmentalized into narrower disciplines. The authors recognize the value of integration of divergent scientific fields in order to create new methods, concepts, paradigms, and knowledge. Herein they describe the recent emergence of molecular pathological epidemiology (MPE), which represents an integration of population and molecular biologic science to gain insights into the etiologies, pathogenesis, evolution, and outcomes of complex multifactorial diseases. Most human diseases, including common cancers (such as breast, lung, prostate, and colorectal cancers, leukemia, and lymphoma) and other chronic diseases (such as diabetes mellitus, cardiovascular diseases, hypertension, autoimmune diseases, psychiatric diseases, and some infectious diseases), are caused by alterations in the genome, epigenome, transcriptome, proteome, metabolome, microbiome, and interactome of all of the above components. In this era of personalized medicine and personalized prevention, we need integrated science (such as MPE) which can decipher diseases at the molecular, genetic, cellular, and population levels simultaneously. The authors believe that convergence and integration of multiple disciplines should be commonplace in research and education. We need to be open-minded and flexible in designing integrated education curricula and training programs for future students, clinicians, practitioners, and investigators. PMID:22935517

The effect of processing on the surface physical stability of amorphous solid dispersions.

PubMed

Yang, Ziyi; Nollenberger, Kathrin; Albers, Jessica; Moffat, Jonathan; Craig, Duncan; Qi, Sheng

2014-11-01

The focus of this study was to investigate the effect of processing on the surface crystallization of amorphous molecular dispersions and gain insight into the mechanisms underpinning this effect. The model systems, amorphous molecular dispersions of felodipine-EUDRAGIT® E PO, were processed both using spin coating (an ultra-fast solvent evaporation based method) and hot melt extrusion (HME) (a melting based method). Amorphous solid dispersions with drug loadings of 10-90% (w/w) were obtained by both processing methods. Samples were stored under 75% RH/room temperatures for up to 10months. Surface crystallization was observed shortly after preparation for the HME samples with high drug loadings (50-90%). Surface crystallization was characterized by powder X-ray diffraction (PXRD), ATR-FTIR spectroscopy and imaging techniques (SEM, AFM and localized thermal analysis). Spin coated molecular dispersions showed significantly higher surface physical stability than hot melt extruded samples. For both systems, the progress of the surface crystal growth followed zero order kinetics on aging. Drug enrichment at the surfaces of HME samples on aging was observed, which may contribute to surface crystallization of amorphous molecular dispersions. In conclusion it was found the amorphous molecular dispersions prepared by spin coating had a significantly higher surface physical stability than the corresponding HME samples, which may be attributed to the increased process-related apparent drug-polymer solubility and reduced molecular mobility due to the quenching effect caused by the rapid solvent evaporation in spin coating. Copyright © 2014 Elsevier B.V. All rights reserved.

A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

ERIC Educational Resources Information Center

Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

2015-01-01

Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

Bridging the PSI Knowledge Gap: A Multi-Scale Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wirth, Brian D.

2015-01-08

Plasma-surface interactions (PSI) pose an immense scientific hurdle in magnetic confinement fusion and our present understanding of PSI in confinement environments is highly inadequate; indeed, a recent Fusion Energy Sciences Advisory Committee report found that 4 out of the 5 top five fusion knowledge gaps were related to PSI. The time is appropriate to develop a concentrated and synergistic science effort that would expand, exploit and integrate the wealth of laboratory ion-beam and plasma research, as well as exciting new computational tools, towards the goal of bridging the PSI knowledge gap. This effort would broadly advance plasma and material sciences,more » while providing critical knowledge towards progress in fusion PSI. This project involves the development of a Science Center focused on a new approach to PSI science; an approach that both exploits access to state-of-the-art PSI experiments and modeling, as well as confinement devices. The organizing principle is to develop synergistic experimental and modeling tools that treat the truly coupled multi-scale aspect of the PSI issues in confinement devices. This is motivated by the simple observation that while typical lab experiments and models allow independent manipulation of controlling variables, the confinement PSI environment is essentially self-determined with few outside controls. This means that processes that may be treated independently in laboratory experiments, because they involve vastly different physical and time scales, will now affect one another in the confinement environment. Also, lab experiments cannot simultaneously match all exposure conditions found in confinement devices typically forcing a linear extrapolation of lab results. At the same time programmatic limitations prevent confinement experiments alone from answering many key PSI questions. The resolution to this problem is to usefully exploit access to PSI science in lab devices, while retooling our thinking from a linear and de-coupled extrapolation to a multi-scale, coupled approach. The PSI Plasma Center consisted of three equal co-centers; one located at the MIT Plasma Science and Fusion Center, one at UC San Diego Center for Energy Research and one at the UC Berkeley Department of Nuclear Engineering, which moved to the University of Tennessee, Knoxville (UTK) with Professor Brian Wirth in July 2010. The Center had three co-directors: Prof. Dennis Whyte led the MIT co-center, the UCSD co-center was led by Dr. Russell Doerner, and Prof. Brian Wirth led the UCB/UTK center. The directors have extensive experience in PSI and material research, and have been internationally recognized in the magnetic fusion, materials and plasma research fields. The co-centers feature keystone PSI experimental and modeling facilities dedicated to PSI science: the DIONISOS/CLASS facility at MIT, the PISCES facility at UCSD, and the state-of-the-art numerical modeling capabilities at UCB/UTK. A collaborative partner in the center is Sandia National Laboratory at Livermore (SNL/CA), which has extensive capabilities with low energy ion beams and surface diagnostics, as well as supporting plasma facilities, including the Tritium Plasma Experiment, all of which significantly augment the Center. Interpretive, continuum material models are available through SNL/CA, UCSD and MIT. The participating institutions of MIT, UCSD, UCB/UTK, SNL/CA and LLNL brought a formidable array of experimental tools and personnel abilities into the PSI Plasma Center. Our work has focused on modeling activities associated with plasma surface interactions that are involved in effects of He and H plasma bombardment on tungsten surfaces. This involved performing computational material modeling of the surface evolution during plasma bombardment using molecular dynamics modeling. The principal outcomes of the research efforts within the combined experimental – modeling PSI center are to provide a knowledgebase of the mechanisms of surface degradation, and the influence of the surface on plasma conditions.« less

Deciphering the morphology of ice films on metal surfaces

NASA Astrophysics Data System (ADS)

Thürmer, Konrad

2011-03-01

Although extensive research has been aimed at the structure of ice films, questions regarding basic processes that govern film evolution remain. Recently we discovered how ice films as many as 30 molecular layers thick can be imaged with STM. The observed morphology yields new insights about water-solid interactions and how they affect the structure of ice films. This talk gives an overview of this progress for crystalline ice films on Pt(111) [2-5]. STM reveals a first molecular water layer very different from bulk ice: besides the usual hexagons it also contains pentagons and heptagons. Slightly thicker films (~ 1 nm, at T> 120 K) arecomprisedof ~ 3 nm - highcrystallites , surroundedbytheone - molecule - thickwettinglayer . Thesecrystalsdewetbynucleatinglayersontheirtopfacets [ 4 ] . Measurementsofthenucleationrateasafunctionofcrystalheightprovideestimatesoftheenergyoftheice - Ptinterface . ForT > 115 Ksurfacediffusionisfastenoughthatsurfacesmoothingand 2 D - islandripeningisobservable [ 5 ] . ByquantifyingtheT - dependentripeningofislandarrayswedeterminedtheactivationenergyforsurfaceself - diffusion . Theshapeofthese 2 Dislandsvariesstronglywithfilmthickness . Weattributethistoatransitionfrompolarizediceatthesubstratetowardsprotondisorderatlargerfilmthicknesses . Despitefastsurfacediffusionicemultilayersareoftenfarfromequilibrium . Forexample , icegrowsbetween ~ 120 and ~ 160 K in its cubic variant rather than in its equilibrium hexagonal form. We found this to be a consequence of the mismatch in the atomic Pt-step height and the ice-bilayer separation and propose a mechanism of cubic-ice formation via growth spirals around screw dislocations. Joint work with N.C. Bartelt and S. Nie, Sandia Natl. Labs, CA. This work was supported by the Office of Basic Energy Sciences, Division of Materials Sciences, U.S. DOE under Contracts No. DEAC04-94AL85000.

Comparison of blue-green response between transmission-mode GaAsP- and GaAs-based photocathodes grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Gang-Cheng, Jiao; Zheng-Tang, Liu; Hui, Guo; Yi-Jun, Zhang

2016-04-01

In order to develop the photodetector for effective blue-green response, the 18-mm-diameter vacuum image tube combined with the transmission-mode Al0.7Ga0.3As0.9 P 0.1/GaAs0.9 P 0.1 photocathode grown by molecular beam epitaxy is tentatively fabricated. A comparison of photoelectric property, spectral characteristic and performance parameter between the transmission-mode GaAsP-based and blue-extended GaAs-based photocathodes shows that the GaAsP-based photocathode possesses better absorption and higher quantum efficiency in the blue-green waveband, combined with a larger surface electron escape probability. Especially, the quantum efficiency at 532 nm for the GaAsP-based photocathode achieves as high as 59%, nearly twice that for the blue-extended GaAs-based one, which would be more conducive to the underwater range-gated imaging based on laser illumination. Moreover, the simulation results show that the favorable blue-green response can be achieved by optimizing the emission-layer thickness in a range of 0.4 μm-0.6 μm. Project supported by the National Natural Science Foundation of China (Grant No. 61301023) and the Science and Technology on Low-Light-Level Night Vision Laboratory Foundation, China (Grant No. BJ2014001).

Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

PubMed

Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

2014-04-28

Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

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

PubMed

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.

Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge

PubMed Central

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

2015-01-01

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. PMID:26435758

Detecting Fermi-level shifts by Auger electron spectroscopy in Si and GaAs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Debehets, J.; Homm, P.; Menghini, M.

In this paper, changes in surface Fermi-level of Si and GaAs, caused by doping and cleaning, are investigated by Auger electron spectroscopy. Based on the Auger voltage contrast, we compared the Auger transition peak energy but with higher accuracy by using a more accurate detector and an improved peak position determination method. For silicon, a peak shift as large as 0.46 eV was detected when comparing a cleaned p-type and n-type wafer, which corresponds rather well with the theoretical difference in Fermi-level. If no cleaning was applied, the peak position did not differ significantly for both wafer types, indicating Fermi-levelmore » pinning in the band gap. For GaAs, peak shifts were detected after cleaning with HF and (NH4)2S-solutions in an inert atmosphere (N2-gas). Although the (NH4)2S-cleaning in N2 is very efficient in removing the oxygen from the surface, the observed Ga- and As-peak shifts are smaller than those obtained after the HF-cleaning. It is shown that the magnitude of the shift is related to the surface composition. After Si-deposition on the (NH4)2S-cleaned surface, the Fermi-level shifts back to a similar position as observed for an as-received wafer, indicating that this combination is not successful in unpinning the Fermi-level of GaAs. This work has been funded by J.D.'s PhD fellowship of the Fund of Scientific Research-Flanders (FWO-V) (Dossier No. 11U4516N). P.H. acknowledges support from Becas Chile-CONICYT. This research was also supported by the FWO Odysseus Program, the Belgian Hercules Stichting with the Project No. Her/08/25 and AKUL/13/19 and the KU Leuven project GOA "Fundamental challenges in Semiconductor Research". The authors would also like to thank Bastiaan Opperdoes and Ludwig Henderix for technical support. The work was supported by the U.S. Department of Energy (USDOE), Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, and performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). Battelle operates PNNL for the USDOE under contract DE-AC05-76RL01830.« less

Understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates

NASA Technical Reports Server (NTRS)

Etters, R. D.

1985-01-01

Work directed toward understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates is reported. The motivation, apart from expanding our basic knowledge about these systems, was to understand and predict the properties of new materials synthesized at high pressure, including pressure induced metallic and superconducting states. As a consequence, information about the states of matter of the Jovian planets and their satellites, which are natural high pressure laboratories was also provided. The work on molecular surfaces and finite two and three dimensional clusters of atoms and molecules was connected with the composition and behavior of planetary atmospheres and on the processes involved in forming surface layers, which is vital to the development of composite materials and microcircuitry.

Membrane Desalination: Where Are We, and What Can We Learn from Fundamentals?

PubMed

Imbrogno, Joseph; Belfort, Georges

2016-06-07

Although thermal desalination technology provides potable water in arid regions (e.g., Israel and the Gulf), its relatively high cost has limited application to less arid regions with large populations (e.g., California). Energy-intensive distillation is currently being replaced with less costly pressure- and electrically driven membrane-based processes. Reverse osmosis (RO) is a preferred membrane technology owing to process and pre- and posttreatment improvements that have significantly reduced energy requirements and cost. Further technical advances will require a deeper understanding of the fundamental science underlying RO. This includes determining the mechanism for water selectivity; elucidating the behavior of molecular water near polar and apolar surfaces, as well as the advantages and limitations of hydrophobic versus hydrophilic pores; learning the rules of selective water transport from nature; and designing synthetic analogs for selective water transport. Molecular dynamics simulations supporting experiments will play an important role in advancing these efforts. Finally, future improvements in RO are limited by inherent technical mass transfer limitations.

Heat conductance, diffusion theory and intracellular metabolic regulation.

PubMed

Wheatley, D N; Malone, P C

1993-01-01

Diffusion theory played a major role in the development of biology as an exact science. The question is raised, however, as to its relevance and applicability in the molecular interactions which occur in metabolism in the living cell. This review looks at diffusion theory from its inception and subsequent introduction into biology, its shortcomings with regard not only to whole-body physiology, but more pertinently at the intracellular level, with its failure to offer a rational basis for metabolic regulation in the internum of the cell. The conclusion is reached that although diffusion inevitably occurs within cells, its role is of little importance with regard to most metabolic activity. In comparison, perfusion of the internal surfaces of the cell by streaming of the fluid compartment of the cytoplasm seems to be the modus operandi which allows molecular interactions to occur at rates far beyond those that diffusion would permit, and at the same time offers a mechanism which permits sensitive control of metabolic activity.

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex.

PubMed

Lee, Kwangkook; Zhong, Xiaofen; Gu, Shenyan; Kruel, Anna Magdalena; Dorner, Martin B; Perry, Kay; Rummel, Andreas; Dong, Min; Jin, Rongsheng

2014-06-20

How botulinum neurotoxins (BoNTs) cross the host intestinal epithelial barrier in foodborne botulism is poorly understood. Here, we present the crystal structure of a clostridial hemagglutinin (HA) complex of serotype BoNT/A bound to the cell adhesion protein E-cadherin at 2.4 angstroms. The HA complex recognizes E-cadherin with high specificity involving extensive intermolecular interactions and also binds to carbohydrates on the cell surface. Binding of the HA complex sequesters E-cadherin in the monomeric state, compromising the E-cadherin-mediated intercellular barrier and facilitating paracellular absorption of BoNT/A. We reconstituted the complete 14-subunit BoNT/A complex using recombinantly produced components and demonstrated that abolishing either E-cadherin- or carbohydrate-binding of the HA complex drastically reduces oral toxicity of BoNT/A complex in vivo. Together, these studies establish the molecular mechanism of how HAs contribute to the oral toxicity of BoNT/A. Copyright © 2014, American Association for the Advancement of Science.

Special Issue: European Conference on Surface Science 2014

NASA Astrophysics Data System (ADS)

Opila, Robert L.; Ertas, Gulay

2015-11-01

The present Special Issue of Applied Surface Science is intended to provide a collection of peer-reviewed contributions presented at the Symposium "European Conference on Surface Science" held in Antalya (Turkey), August 31-September 5, 2014. This conference is organized annually through the joint efforts of the Surface Science Division of IUVSTA and the Surface and Interface Section of the European Physical Society (EPS). The ECOSS conference series started in 1978 in Amsterdam, Netherlands, and has been held in various cities throughout Europe during the past years. This is the first time that an ECOSS conference was held in Turkey, with the chairmanship of Prof. Sefik Suzer of Bilkent University, Ankara.

Science Education Future. Proceedings of the Arctic Science Conference (39th, Fairbanks, Alaska, October 7-10, 1988).

ERIC Educational Resources Information Center

American Association for the Advancement of Science, Fairbanks, AK. Arctic Div.

This catalog includes abstracts of each of the papers delivered at the Arctic Science Conference. The conference was divided into the following symposia: (1) "Biochemistry and Molecular Biology"; (2) "An Update of Alaskan Science and Discovery"; (3) "Science Education for the Public"; (4) "Hubbard Glacier,…

Surface analysis of lipids by mass spectrometry: more than just imaging.

PubMed

Ellis, Shane R; Brown, Simon H; In Het Panhuis, Marc; Blanksby, Stephen J; Mitchell, Todd W

2013-10-01

Mass spectrometry is now an indispensable tool for lipid analysis and is arguably the driving force in the renaissance of lipid research. In its various forms, mass spectrometry is uniquely capable of resolving the extensive compositional and structural diversity of lipids in biological systems. Furthermore, it provides the ability to accurately quantify molecular-level changes in lipid populations associated with changes in metabolism and environment; bringing lipid science to the "omics" age. The recent explosion of mass spectrometry-based surface analysis techniques is fuelling further expansion of the lipidomics field. This is evidenced by the numerous papers published on the subject of mass spectrometric imaging of lipids in recent years. While imaging mass spectrometry provides new and exciting possibilities, it is but one of the many opportunities direct surface analysis offers the lipid researcher. In this review we describe the current state-of-the-art in the direct surface analysis of lipids with a focus on tissue sections, intact cells and thin-layer chromatography substrates. The suitability of these different approaches towards analysis of the major lipid classes along with their current and potential applications in the field of lipid analysis are evaluated. Copyright © 2013 Elsevier Ltd. All rights reserved.

In Situ Preparation of Biomimetic Thin Films and Their Surface-Shielding Effect for Organisms in High Vacuum

PubMed Central

Muranaka, Yoshinori; Shimomura, Masatsugu; Hariyama, Takahiko

2013-01-01

Self-standing biocompatible films have yet to be prepared by physical or chemical vapor deposition assisted by plasma polymerization because gaseous monomers have thus far been used to create only polymer membranes. Using a nongaseous monomer, we previously found a simple fabrication method for a free-standing thin film prepared from solution by plasma polymerization, and a nano-suit made by polyoxyethylene (20) sorbitan monolaurate can render multicellular organisms highly tolerant to high vacuum. Here we report thin films prepared by plasma polymerization from various monomer solutions. The films had a flat surface at the irradiated site and were similar to films produced by vapor deposition of gaseous monomers. However, they also exhibited unique characteristics, such as a pinhole-free surface, transparency, solvent stability, flexibility, and a unique out-of-plane molecular density gradient from the irradiated to the unirradiated surface of the film. Additionally, covering mosquito larvae with the films protected the shape of the organism and kept them alive under the high vacuum conditions in a field emission-scanning electron microscope. Our method will be useful for numerous applications, particularly in the biological sciences. PMID:24236023

From bedside to blackboard: the benefits of teaching molecular biology within a medical context.

PubMed

Sitaraman, Ramakrishnan

2012-01-01

Courses in molecular biology are part of practically every degree program in medicine and the life sciences. Historically, many basic discoveries in this field have resulted from investigations by doctors into the nature of diseases. This essay suggests that medical educators deliberately incorporate such material, whether historical or contemporaneous, into their molecular and cell biology courses. An example of such usage, an early report of the detection of bacteriophage activity on pathogenic bacteria, is discussed in detail. Such an approach can potentially narrow the perceived gap between "basic" and "applied" science. As medicine is so intimately and obviously linked with human welfare, this also provides an avenue for educators to discuss issues of scientific integrity and ethics within a "pure science" course.

Contamination of agricultural lands by polycyclic aromatic hydrocarbons (Tver region, Russia)

NASA Astrophysics Data System (ADS)

Zhidkin, Andrey; Koshovskii, Timur; Gennadiev, Alexander

2016-04-01

It is important to study sources and concentrations of polycyclic aromatic hydrocarbons (PAHs) in the agriculture soils within areas without intensive contaminations. Our studied object was soil and snow cover in the taiga zone (Tver region, Russia). A total of 52 surface (0-30 cm) and 31 subsurface (30-50 cm) soil samples, and 13 snow samples were collected in 35 soil pits, located in forest, crop and layland soils. Studied concentrations of the following 11 individual compounds: two-ring compounds (diphenyl and naphthalene homologues); three-ring compounds (fluorene, phenanthrene, anthracene); four-ring compounds (chrysene, pyrene, tetraphene); five-ring compounds (perylene, benzo[a]pyrene); and six-ring compounds (benzo[ghi]perylene). Analyses made by specrtofluorometry method at the temperature of liquid nitrogen. The total concentrations of all PAHs in soil samples ranged from 9 to 770 ng*g-1 with a median of 96 ng*g-1. The sum of high molecular weight PAHs was significantly lower than the sum of low molecular weight PAHs in the studied soils. The phenanthrene concentration was highest and ranged from 1.2 to 720 ng*g-1 (medium 72 ng*g-1). Compared PAHs reserves in snow cover (μg*m-2) with the reserves in topsoil layer (μg*m-2 in the upper 30 cm). Low molecular weight PAHs (fluorene, phenanthrene, diphenyl, naphthalene) reserves in snow was less than 20% from the reserves in the soil surface layer. High molecular weight PAHs (benzo[a]pyrene, chrysene, perylene, pyrene and tetraphene) reserves in snow was about 50-70% from the reserves in soil surface layer. High molecular weight PAHs (benzo[ghi]perylene and anthracene) reserves in snow was more than in topsoil. PAHs vertical distribution in soil profiles was statistically examined. The total concentration of all PAHs decreased with depth in all studied forest soils. In the arable soils was no significant trend in domination of PAHs total concentrations in the plowing and subsoil layers. The ratio of topsoil to subsoil concentrations of PAHs is different for differ congeners. Contents of phenanthrene and fluorene predominantly increase with the depth. Content of high molecular weight PAHs (benzo[a]pyrene, anthracene, tetraphene, perylene and pyrene) predominantly decreased with the depth. Other PAHs congeners have indistinct profile distributions in studied pits. Based on studied results PAHs divided to associations with different concentrations, sources and vertical distribution in soils: a) phenanthrene and fluorine; b) naphthalene, diphenyl; c) pyrene, benzo(a)pyrene, tetraphene, perylene, chrysene; d) anthracene and benzo(ghi)perylene. Research is funded by Russian Science Foundation (Project 14-27-00083).

Bibliometric analysis of original molecular biology research in anaesthesia.

PubMed

Schreiber, K; Girard, T; Kindler, C H

2004-10-01

Molecular biology has expanded the horizons of anaesthesia during the last 20 years and has led to an increase of basic science articles that are published in the specialised anaesthetic journals or originate in anaesthetic institutions. We searched for and analysed the specific features, such as year of publication, publishing journal, and country of origin, of all such molecular biology articles stored in the MEDLINE database during the period 1986-2002. We identified 1265 original articles that used molecular biology techniques; 223 (18%) of these articles were published in anaesthetic journals and 1042 (82%) articles in 556 other biomedical journals. While in the late 1980s only a few molecular biology articles were published each year by anaesthetic institutions, worldwide this number reached approximately 200 basic science articles by the end of 2002. The USA clearly dominates the field of anaesthesia with respect to molecular biology research with 839 (66%) such articles.

Helium Ion Microscopy: A Promising Tool for Probing Biota-Mineral Interfaces

NASA Astrophysics Data System (ADS)

Lybrand, R.; Zaharescu, D. G.; Gallery, R. E.

2017-12-01

The study of biogeochemical interfaces in soil requires powerful technologies that can enhance our ability to characterize mineral surfaces and interacting organisms at micro- to nanoscale resolutions. We aim to demonstrate potential applications of Helium Ion Microscopy in the earth and ecological sciences using, as an example, samples from a field experiment. We assessed samples deployed for one year along climatic and topographic gradients in two Critical Zone Observatories (CZOs): a desert to mixed conifer forest gradient (Catalina CZO) and a humid hardwood forest (Calhoun CZO). Sterile ground rock (basalt, quartz, and granite; 53-250 µm) was sealed into nylon mesh bags and buried in the surface soils of both CZOs. We employed helium ion and scanning electron microscopies to compare retrieved ground rock samples with sterile unreacted mineral controls in conjunction with the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory, USA. Our work showed early colonization of mesh bag materials by fungal and bacterial organisms from the field systems and identified morphological changes in mineral grains following exposure to the soil environment. Biological specimens observed on grain surfaces exhibited contrasting features depending on mineral type and ecosystem location, including fungal hyphae that varied in length, diameter, and surface morphologies. We also present imagery that provides evidence for incipient stages of mineral transformation at the fungal-mineral interface. Our findings demonstrate that helium ion microscopy can be successfully used to characterize grain features and biological agents of weathering in experimental field samples, representing a promising avenue for research in the biogeosciences. Future directions of this work will couple high resolution imaging with measures of aqueous and solid geochemistry, fungal morphological characterization, and microbial profiling to better understand mineral transformation along gradients of climate and topography.

Surface chemistry characterization of hydrodesulfurization and methanol synthesis model nanocatalysts

NASA Astrophysics Data System (ADS)

Komarneni, Mallikharjuna Rao

Surface science investigations of model catalysts have contributed significantly to heterogeneous catalysis over the past several decades. The unique properties of nanomaterials are being exploited in catalysis for the development of highly active and selective catalysts. Surface science investigations of model catalysts such as inorganic fullerene-like (IF) nanoparticles (NP), inorganic nanotubes (INT), and the oxide-supported nanoclusters are included in this dissertation. Thermal desorption spectroscopy and molecular beam scattering were respectively utilized to study the adsorption kinetics and dynamics of gas phase molecules on catalyst surfaces. In addition, ambient pressure kinetics experiments were performed to characterize the catalytic activity of hydrodesulfurization (HDS) nanocatalysts. The nanocatalysts were characterized with a variety of techniques, including Auger electron spectroscopy, x-ray photoelectron spectroscopy, electron microscopy, and x-ray diffraction. The adsorption kinetics studies of thiophene on novel HDS catalysts provided the first evidence for the presence of different adsorption sites on INT-WS2. Additionally, the adsorption sites on IF-MoS2 NP and silica-supported Mo clusters (Mo/silica) were characterized. Furthermore, the C-S bond activation energy of thiophene on Mo/silica was determined. These studies finally led to the fabrication of Ni/Co coated INT-WS2, which showed good catalytic activity towards HDS of thiophene. The studies of methanol synthesis catalysts include the adsorption kinetics and dynamics studies of CO and CO2 on Cu/silica and silica-supported EBL-fabricated Cu/CuOx nanoclusters. The adsorption dynamics of CO on Cu/silica are modeled within the frame work of the capture zone model (CZM), and the active sites of the silica-supported Au/Cu catalysts are successfully mapped. Studies on EBL model catalysts identify the rims of the CuOx nanoclusters as catalytically active sites. This observation has implications for new methanol catalyst design.

Driving and controlling molecular surface rotors with a terahertz electric field.

PubMed

Neumann, Jan; Gottschalk, Kay E; Astumian, R Dean

2012-06-26

Great progress has been made in the design and synthesis of molecular motors and rotors. Loosely inspired by biomolecular machines such as kinesin and the FoF1 ATPsynthase, these molecules are hoped to provide elements for construction of more elaborate structures that can carry out tasks at the nanoscale corresponding to the tasks accomplished by elementary machines in the macroscopic world. Most of the molecular motors synthesized to date suffer from the drawback that they operate relatively slowly (less than kHz). Here we show by molecular dynamics studies of a diethyl sulfide rotor on a gold(111) surface that a high-frequency oscillating electric field normal to the surface can drive directed rotation at GHz frequencies. The maximum directed rotation rate is 10(10) rotations per second, significantly faster than the rotation of previously reported directional molecular rotors. Understanding the fundamental basis of directed motion of surface rotors is essential for the further development of efficient externally driven artificial rotors. Our results represent a step toward the design of a surface-bound molecular rotary motor with a tunable rotation frequency and direction.

Better Spectrometers, Beautiful Spectra and Confusion for All

NASA Technical Reports Server (NTRS)

Pearson, J. C.; Brauer, C. S.; Drouin, B. J.; Yu, S.

2009-01-01

The confluence of enormous improvements in submillimeter receivers and the development of powerful large scale observatories is about to force astrophysics and the sciences that support it to develop novel approaches for interpretation of data. The historical method of observing one or two lines and carefully analyzing them in the context of a simple model is now only applicable for distant objects where only a few lines are strong enough to be observable. Modern observatories collect many GHz of high signal-to-noise spectra in a single observation and in many cases, at sufficiently high spatial resolution to start resolving chemically distinct regions. The observatories planned for the near future and the inevitable upgrades of existing facilities will make large spectral data sets the rule rather than the exception in many areas of molecular astrophysics. The methodology and organization required to fully extract the available information and interpret these beautiful spectra represents a challenge to submillimeter astrophysics similar in magnitude to the last few decades of effort in improving receivers. The quality and abundance of spectra effectively prevents line-by-line analysis from being a time efficient proposition, however, global analysis of complex spectra is a science in its infancy. Spectroscopy at several other wavelengths have developed a number of techniques to analyze complex spectra, which can provide a great deal of guidance to the molecular astrophysics community on how to attack the complex spectrum problem. Ultimately, the challenge is one of organization, similar to building observatories, requiring teams of specialists combining their knowledge of dynamical, structural, chemical and radiative models with detailed knowledge in molecular physics and gas and grain surface chemistry to extract and exploit the enormous information content of complex spectra. This paper presents a spectroscopists view of the necessary elements in a tool for complex spectral analysis.

Quantitative Chemical Analysis of Enceladus' Plume Composition.

NASA Astrophysics Data System (ADS)

Peter, J.; Nordheim, T.; Hofmann, A.; Hand, K. P.

2017-12-01

Analyses of data from Cassini's Ion and Neutral Mass Spectrometer (INMS) taken during several close flybys of Enceladus suggest the presence of a potentially habitable ocean underneath the ice shell [1,2]. Proper identification of the molecular species sampled from Enceladus' plumes by INMS is of utmost importance for characterizing the ocean's chemical composition. Data from Cassini's Cosmic Dust Analyzer (CDA) and Visible and Infrared Mapping Spectrometer (VIMS) have provided clues for possible plume chemistry, but further analysis of the INMS data is necessary [3,4]. Here we present a novel automated algorithm for comparing INMS spectra and analogue laboratory spectra to a vast library of sample spectra provided by the National Institute of Standards and Technology (NIST). The algorithm implements a Monte Carlo simulation that computes the angular similarity between the spectrum of interest and a random sample of synthetic spectra generated at arbitrary mixing ratios of molecular species. The synthetic spectra with the highest similarity scores are then averaged to produce a convergent estimate of the mixing ratio of the spectrum of interest. Here we will discuss the application of this technique to INMS and laboratory data and the implication of our preliminary results for the ocean chemistry and habitability of Enceladus. 1. Waite, J., et al., 2009. Liquid Water on Enceladus From Observations of Ammonia and 40Ar in the Plume. Nature 460, 487-498. 2. Waite, J., et al. 2017. Cassini Finds Molecular Hydrogen in the Enceladus Plume: Evidence for Hydrothermal Processes. Science 356, 155-159. 3. Postberg, F., et al., 2008. The E Ring in the Vicinity of Enceladus II: Signatures of Enceladus in the Elemental Composition of E-Ring Particles. Icarus 193(2), 438-454. 4. Brown, R., et al., 2006. Composition and Physical Properties of Enceladus' Surface. Science 311, 1425-1428.

Customized Peptide Biomaterial Synthesis via an Environment-Reliant Auto-Programmer Stigmergic Approach

PubMed Central

Choonara, Yahya E.; du Toit, Lisa C.; Bijukumar, Divya; Chejara, Dharmesh R.

2018-01-01

Stigmergy, a form of self-organization, was employed here to engineer a self-organizing peptide capable of forming a nano- or micro-structure and that can potentially be used in various drug delivery and biomedical applications. These self-assembling peptides exhibit several desirable qualities for drug delivery, tissue engineering, cosmetics, antibiotics, food science, and biomedical surface engineering. In this study, peptide biomaterial synthesis was carried out using an environment-reliant auto-programmer stigmergic approach. A model protein, α-gliadin (31, 36, and 38 kD), was forced to attain a primary structure with free –SH groups and broken down enzymatically into smaller fragments using chymotrypsin. This breakdown was carried out at different environment conditions (37 and 50 °C), and the fragments were allowed to self-organize at these temperatures. The new peptides so formed diverged according to the environmental conditions. Interestingly, two peptides (with molecular weights of 13.8 and 11.8 kD) were isolated when the reaction temperature was maintained at 50 °C, while four peptides with molecular weights of 54, 51, 13.8, and 12.8 kD were obtained when the reaction was conducted at 37 °C. Thus, at a higher temperature (50 °C), the peptides formed, compared to the original protein, had lower molecular weights, whereas, at a lower temperature (37 °C), two peptides had higher molecular weights and two had lower molecular weights. PMID:29659507

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

NASA Astrophysics Data System (ADS)

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 temporal release of the encapsulated drugs. In addition to acoustic energy, self-assembled surfaces experience order-disorder transition and have a transition temperature higher than body temperature if longer alkyl chains (C18) are used. The C18-assembled surface barrier membrane exhibits a relatively superior impermeable coating than the shorter C12 chains. The versatility of derivatizing the terminal groups of the self-assembled molecular structures is illustrated by attaching poly (ethyleneoxide) oligomers to the alkyl chains to minimize nonspecific protein adsorption. This study lays an important foundation for future work in conjugating other biomolecules to develop surface-based diagnostics and biomaterials. With much success, this original research work of forming self-assembled crystalline structures on synthetic materials still allows for numerous opportunities for new applications and possibly even more new discoveries.

Reflectron Time-of-Flight Mass Spectrometer (REMAS) Instrumentation

NASA Technical Reports Server (NTRS)

Brinckerhoff, W. B.; McEntire, R. W.; Cheng, A. F.

2000-01-01

The restricted mass and power budgets of landed science missions present a challenge to obtaining detailed analyses of planetary bodies. In situ studies, whether alone or as reconnaissance for sample return, must rely on highly miniaturized and autonomous instrumentation. Such devices must still produce useful data sets from a minimum of measurements. The great desire to understand the surfaces and interiors of planets, moons, and small bodies had driven the development of small, robotic techniques with ever-increasing capabilities. One of the most important goals on a surface mission is to study composition in many geological contexts. The mineralogical, molecular, elemental, and isotopic content of near-surface materials (regolith, rocks, soils, dust, etc.) at a variety of sites can complement broader imaging to describe the makeup and formative history of the body in question. Instruments that perform this site-to-site analysis must be highly transportable and work as a suite. For instance, a camera, microscope, spectrophotometer, and mass spectrometer can share several components and operate under a parallel command structure. Efficient use of multiple systems on a small rover has been demonstrated on the Mars Pathfinder mission.

Surface-charge-governed electrolyte transport in carbon nanotubes

NASA Astrophysics Data System (ADS)

Xue, Jian-Ming; Guo, Peng; Sheng, Qian

2015-08-01

The transport behavior of pressure-driven aqueous electrolyte solution through charged carbon nanotubes (CNTs) is studied by using molecular dynamics simulations. The results reveal that the presence of charges around the nanotube can remarkably reduce the flow velocity as well as the slip length of the aqueous solution, and the decreasing of magnitude depends on the number of surface charges and distribution. With 1-M KCl solution inside the carbon nanotube, the slip length decreases from 110 nm to only 14 nm when the number of surface charges increases from 0 to 12 e. This phenomenon is attributed to the increase of the solid-liquid friction force due to the electrostatic interaction between the charges and the electrolyte particles, which can impede the transports of water molecules and electrolyte ions. With the simulation results, we estimate the energy conversion efficiency of nanofluidic battery based on CNTs, and find that the highest efficiency is only around 30% but not 60% as expected in previous work. Project supported by the National Natural Science Foundation of China (Grant Nos. 11375031 and 11335003).

Life sciences and environmental sciences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

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,more » applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.« less

A guide to using case-based learning in biochemistry education.

PubMed

Kulak, Verena; Newton, Genevieve

2014-01-01

Studies indicate that the majority of students in undergraduate biochemistry take a surface approach to learning, associated with rote memorization of material, rather than a deep approach, which implies higher cognitive processing. This behavior relates to poorer outcomes, including impaired course performance and reduced knowledge retention. The use of case-based learning (CBL) into biochemistry teaching may facilitate deep learning by increasing student engagement and interest. Abundant literature on CBL exists but clear guidance on how to design and implement case studies is not readily available. This guide provides a representative review of CBL uses in science and describes the process of developing CBL modules to be used in biochemistry. Included is a framework to implement a directed CBL assisted with lectures in a content-driven biochemistry course regardless of class size. Moreover, this guide can facilitate adopting CBL to other courses. Consequently, the information presented herein will be of value to undergraduate science educators with an interest in active learning pedagogies. © 2014 The International Union of Biochemistry and Molecular Biology.

Real-space imaging of interfacial water with submolecular resolution

NASA Astrophysics Data System (ADS)

Jiang, Ying; Peking University Team

2014-03-01

Water/solid interfaces are vital to our daily lives and also a central theme across an incredibly wide range of scientific disciplines. Resolving the internal structure, i.e. the O-H directionality, of water molecules adsorbed on solid surfaces has been one of the key issues of water science yet remains challenging. Using a low-temperature scanning tunneling microscope (STM), we report the submolecular-resolution imaging of individual water monomers and tetramers on NaCl(001) films supported by a Au(111) substrate at 5 K. The frontier molecular orbitals of adsorbed water were directly visualized, which allowed discriminating the orientation of the monomers and the H-bond directionality of the tetramers in real space. Comparison with ab initio density functional theory calculations reveals that the ability to access the orbital structures of water stems from the electronic decoupling effect provided by the NaCl films and the precisely tunable tip-water coupling. Supported by National Basic Research Programs of China and National Science Foundation of China.

PREFACE: Special issue: CAMOP-MOLEC XVII Special issue: CAMOP-MOLEC XVII

NASA Astrophysics Data System (ADS)

Vasyutinskii, Oleg

2009-10-01

This special issue of CAMOP/Physica Scripta presents highlights from the scientific contributions presented at the European Conference on Dynamics of Molecular Systems (MOLEC XVII) held on 23-29 August 2008 at St Petersburg, Russia. This meeting was the seventeenth in a series of biannual meetings that started in 1976, when the first conference was held in Trento, Italy. Subsequent meetings were held at Brandbjerg Hojskole (Denmark), Oxford (UK), Nijmegen (The Netherlands), Jerusalem (Israel), Aussois (France), Assisi (Italy), Bernkastel-Kues (Germany), Prague (Czech Republic), Salamanca (Spain), Nyborg Strand (Denmark), Bristol (UK), Jerusalem (Israel), Istanbul (Turkey), Nunspeet (The Netherlands) and Trento (Italy). In 2008, the meeting was jointly organized by scientists from the Ioffe Institute, Russian Academy of Sciences, St Petersburg, Herzen State University, St Petersburg, Moscow State University, St Petersburg Polytechnical University, and St Petersburg State University. About 150 scientists from 21 countries visited Pushkin, a beautiful suburb of St Petersburg near the famous palace of Empress Catherine II, and discussed the state of the art and trends in the field, as well as new methods and applications, during 24 plenary lectures, 36 hot topic talks and two evening poster sessions. A special event was the presentation of the MOLEC XVII award to Professor Grabriel Balint-Kurti for his outstanding contributions to the theory of reaction dynamics and molecular photodissociation. Further information is available from the homepage of the meeting: http://www.ioffe.ru/MOLEC17/. This special issue covers different aspects of atomic and molecular interactions, with emphasis on both experimental and theoretical studies of the dynamics of elastic, inelastic and reactive encounters between atoms, molecules, ions, clusters and surfaces. More specifically, it includes molecular collisions in different environments; plasma, atmospheric, interstellar and combustion processes, gas-surface processes, and biologically relevant systems; ab initio calculations of molecular dynamics; photon-matter interactions: spectroscopy, photodissociation and photo-induced reactions including femtosecond dynamics; interaction between ultra-cold molecules and atoms and processes in He droplets; and steric effects and vector correlations in reactive processes and in photodissociation. The organizers are pleased to acknowledge the support of LENTRANSGAS, Russian Foundation for Basic Research, and the Russian Academy of Sciences. We are very grateful to all members of the Local Organizing Committee, especially Alexei Podlaskin, Irina Krassovskaya, Oleg Rojdestvenski, Peter Shternin, Andrey Smolin, Irina Beletskaya, Alexei Verkhovtsev and Ekaterina Khadikova, whose hard work made the conference so successful. I very much hope that you will enjoy reading this special issue and that many of the articles presented will catch your attention. Perhaps we will meet at MOLEC XVIII in 2010, in Coimbra, Portugal.

78 FR 9689 - Notification of a Public Meeting of the Chartered Science Advisory Board

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-11

... advances in molecular biology, chemistry and innovative computer science to more effectively and... Science Advisory Board AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: The Environmental Protection Agency (EPA) Science Advisory Board (SAB) Staff Office announces a public meeting of...

Middle School Regional Science Bowl Competition | Argonne National

Science.gov Websites

biology, chemistry, earth science, physics, energy, and math. The winner of the academic portion of the Biology IMEInstitute for Molecular Engineering JCESRJoint Center for Energy Storage Research MCSGMidwest Science and Engineering RISCRisk and Infrastructure Science Center SBCStructural Biology Center Energy.gov

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

NASA Astrophysics Data System (ADS)

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.

PubMed

López-Moreno, S; Romero, A H

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 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 force microscopy – looking at mechanosensors on the cell surface

PubMed Central

Heinisch, Jürgen J.; Lipke, Peter N.; Beaussart, Audrey; El Kirat Chatel, Sofiane; Dupres, Vincent; Alsteens, David; Dufrêne, Yves F.

2012-01-01

Summary Living cells use cell surface proteins, such as mechanosensors, to constantly sense and respond to their environment. However, the way in which these proteins respond to mechanical stimuli and assemble into large complexes remains poorly understood at the molecular level. In the past years, atomic force microscopy (AFM) has revolutionized the way in which biologists analyze cell surface proteins to molecular resolution. In this Commentary, we discuss how the powerful set of advanced AFM techniques (e.g. live-cell imaging and single-molecule manipulation) can be integrated with the modern tools of molecular genetics (i.e. protein design) to study the localization and molecular elasticity of individual mechanosensors on the surface of living cells. Although we emphasize recent studies on cell surface proteins from yeasts, the techniques described are applicable to surface proteins from virtually all organisms, from bacteria to human cells. PMID:23077172

Pragmatic precision oncology: the secondary uses of clinical tumor molecular profiling

PubMed Central

Thota, Ramya; Staggs, David B; Johnson, Douglas B; Warner, Jeremy L

2016-01-01

Background Precision oncology increasingly utilizes molecular profiling of tumors to determine treatment decisions with targeted therapeutics. The molecular profiling data is valuable in the treatment of individual patients as well as for multiple secondary uses. Objective To automatically parse, categorize, and aggregate clinical molecular profile data generated during cancer care as well as use this data to address multiple secondary use cases. Methods A system to parse, categorize and aggregate molecular profile data was created. A naÿve Bayesian classifier categorized results according to clinical groups. The accuracy of these systems were validated against a published expertly-curated subset of molecular profiling data. Results Following one year of operation, 819 samples have been accurately parsed and categorized to generate a data repository of 10,620 genetic variants. The database has been used for operational, clinical trial, and discovery science research. Conclusions A real-time database of molecular profiling data is a pragmatic solution to several knowledge management problems in the practice and science of precision oncology. PMID:27026612

A Rational Reconstruction of the Kinetic Molecular Theory of Gases Based on History and Philosophy of Science and Its Implications for Chemistry Textbooks.

ERIC Educational Resources Information Center

Niaz, Mansoor

2000-01-01

Describes a study that was designed to develop a framework for examining the way in which chemistry textbooks describe the kinetic theory and related issues. The framework was developed by a rational reconstruction of the kinetic molecular theory of gases based on historians and philosophers of science. (Contains 102 references.)(Author/LRW)

Benefits of applying low-temperature plasma treatment to wound care and hemostasis from the viewpoints of physics and pathology

NASA Astrophysics Data System (ADS)

Shimizu, Tetsuji; Ikehara, Yuzuru

2017-12-01

Over the last decade, low-temperature plasma (LTP) technology has reached the life sciences and introduced the benefits of using such technology at atmospheric pressure for medical applications. The active elements from LTP, such as reactive molecular species, charged particles and photons, appear to react with biomolecules on wounds and at bleeding points. This action by LTP might be analogous with semiconductor fabrication techniques such as etching and surface modification. From this perspective, we discuss the general aspects and principles of LTP devices used at atmospheric pressure in wound care and hemostasis as an interdisciplinary fusion of applied physics and pathology.

An experimental study to support the search for organics at Mars

NASA Astrophysics Data System (ADS)

Poch, Olivier; Stalport, Fabien; Noblet, Audrey; Szopa, Cyril; Coll, Patrice

2012-07-01

Several evidences suggest that early Mars offered favorable conditions for long-term sustaining water. As a consequence, we can assume that processes related to prebiotic chemistry, and even the emergence of life, may have occurred on early Mars. In those days, organic matter may have been widespread on Mars, due to exogenous delivery from small bodies, or endogenous chemical processes. The search for these organic relics is one of the main objectives of Mars exploration missions to come. But for about 3 Gy, due to the harsh environmental conditions of the Mars surface (UV radiation, oxidants etc.), the inventory of organic compounds at the current surface or subsurface of Mars may have been narrowed. Two major questions raised by this putative evolution are: What is the evolution pattern of organics in the Martian environment? What types of molecules would have been preserved, and if so, in which conditions? We address these questions using an experimental device dedicated to simulate the processes susceptible to have an effect on organic matter in the current environmental conditions of the Mars surface and subsurface. This experimental setup is part of a project called MOMIE, for Mars Organic Molecules Irradiation and Evolution. We study the evolution of some of the most likely molecular compounds potentially synthesized or brought to Mars (amino acids, hydrocarbons, nucleobases etc.). Nanometers thin deposits of a molecular compound or of a mineral in which the molecular compound has been embedded are allowed to evolve at mean Martian pressure and temperature, under a UV radiation environment similar to the Martian one. Qualitative and quantitative changes of the sample are monitored during the simulation, especially using infrared spectroscopy. We will present and compare the evolution of several organics submitted to these conditions. These experiments will provide essential insights to guide and discuss in situ analyses at Mars, particularly during the upcoming exploration of Gale Crater by Curiosity, the rover of the NASA Mars Science Laboratory mission.

Surface induced molecular dynamics of thin lipid films confined to submicron cavities: A 1H multiple-quantum NMR study

NASA Astrophysics Data System (ADS)

Jagadeesh, B.; Prabhakar, A.; Demco, D. E.; Buda, A.; Blümich, B.

2005-03-01

The dynamics and molecular order of thin lipid (lecithin) films confined to 200, 100 and 20 nm cylindrical pores with varying surface coverage, were investigated by 1H multiple-quantum NMR. The results show that the molecular dynamics in the surface controlled layers are less hindered compared to those in the bulk. Dynamic heterogeneity among terminal CH 3 groups is evident. Enhanced dynamic freedom is observed for films with area per molecule, ˜ 128 Å 2. The results are discussed in terms of changes in the lipid molecular organization with respect to surface concentration, its plausible motional modes and dynamic heterogeneity.

Coupling molecular catalysts with nanostructured surfaces for efficient solar fuel production

NASA Astrophysics Data System (ADS)

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 photosensitizers. In Chapter 3, effective coupling of the macrocyclic Co(III) complex with titanium dioxide (TiO¬2) nanoparticles was achieved by two deposition methods. The synthesized hybrid photocatalysts were thoroughly characterized with a variety of techniques. Upon UV light irradiation, photoexcited electrons in TiO2 nanoparticles were transferred to the surface Co(III) catalyst for CO2 reduction. Production of carbon monoxide (CO) from CO2 was confirmed by isotope labeling combined with infrared spectroscopy. Deposition of the Co(III) catalyst through Ti-O-Co linkages was essential for the photo-induced electron transfer and CO2-reduction activity using the hybrid photocatalysts. In Chapter 4, molecular Re(I) and Co(II) catalysts were coupled with silicon-based photoelectrodes, including a silicon nanowire (SiNW) photoelectrode, to achieve photoelectrochemical CO2 reduction. Photovoltages between 300-600 mV were obtained using the molecular catalysts on the silicon photoelectrodes. SiNWs exhibited enhanced properties, including significantly higher photovoltages than a planar silicon photoelectrode, the ability to protect one of the molecular catalysts from photo-induced decomposition, and excellent selectivity towards CO production in CO2 reduction. Recent theoretical and experimental work have demonstrated low-energy, binuclear pathways for CO2-to-CO conversion using several molecular catalysts. In such binuclear pathways, two metal centers work cooperatively to achieve two-electron CO2 reduction. Chapter 5 describes our effort to promote the binuclear pathway by grafting the molecular Co(III) catalyst onto silica surfaces. Different linking strategies were attempted to achieve this goal by planting the surface Co(III) sites in close proximity.

Physical re-examination of parameters on a molecular collisions-based diffusion model for diffusivity prediction in polymers.

PubMed

Ohashi, Hidenori; Tamaki, Takanori; Yamaguchi, Takeo

2011-12-29

Molecular collisions, which are the microscopic origin of molecular diffusive motion, are affected by both the molecular surface area and the distance between molecules. Their product can be regarded as the free space around a penetrant molecule defined as the "shell-like free volume" and can be taken as a characteristic of molecular collisions. On the basis of this notion, a new diffusion theory has been developed. The model can predict molecular diffusivity in polymeric systems using only well-defined single-component parameters of molecular volume, molecular surface area, free volume, and pre-exponential factors. By consideration of the physical description of the model, the actual body moved and which neighbor molecules are collided with are the volume and the surface area of the penetrant molecular core. In the present study, a semiempirical quantum chemical calculation was used to calculate both of these parameters. The model and the newly developed parameters offer fairly good predictive ability. © 2011 American Chemical Society

Prediction of Sliding Friction Coefficient Based on a Novel Hybrid Molecular-Mechanical Model.

PubMed

Zhang, Xiaogang; Zhang, Yali; Wang, Jianmei; Sheng, Chenxing; Li, Zhixiong

2018-08-01

Sliding friction is a complex phenomenon which arises from the mechanical and molecular interactions of asperities when examined in a microscale. To reveal and further understand the effects of micro scaled mechanical and molecular components of friction coefficient on overall frictional behavior, a hybrid molecular-mechanical model is developed to investigate the effects of main factors, including different loads and surface roughness values, on the sliding friction coefficient in a boundary lubrication condition. Numerical modelling was conducted using a deterministic contact model and based on the molecular-mechanical theory of friction. In the contact model, with given external loads and surface topographies, the pressure distribution, real contact area, and elastic/plastic deformation of each single asperity contact were calculated. Then asperity friction coefficient was predicted by the sum of mechanical and molecular components of friction coefficient. The mechanical component was mainly determined by the contact width and elastic/plastic deformation, and the molecular component was estimated as a function of the contact area and interfacial shear stress. Numerical results were compared with experimental results and a good agreement was obtained. The model was then used to predict friction coefficients in different operating and surface conditions. Numerical results explain why applied load has a minimum effect on the friction coefficients. They also provide insight into the effect of surface roughness on the mechanical and molecular components of friction coefficients. It is revealed that the mechanical component dominates the friction coefficient when the surface roughness is large (Rq > 0.2 μm), while the friction coefficient is mainly determined by the molecular component when the surface is relatively smooth (Rq < 0.2 μm). Furthermore, optimal roughness values for minimizing the friction coefficient are recommended.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

NASA Astrophysics Data System (ADS)

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-cystine surfaces. Collectively, these findings identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal step sites, thereby articulating a strategy for stone prevention based on molecular design. The second part of this thesis describes the crystal growth and inhibition of a P2X3 receptor antagonist, denoted as DAPSA, recently reported as a non-opioid treatment of chronic pain. The low solubility of this compound results in the formation of drug-induced renal calculi (a.k.a. xenostones). in situ AFM of the morphologically significant (011) DAPSA surface revealed dislocation-actuated growth spirals with an anisotropic morphology, behavior that can be attributed to the non-uniform rate of solute attachment to eight crystallographically unique steps of the spiral, a direct consequence of the dissymmetry of this crystal surface. Eighteen molecular imposters were selected from the screening library to systematically investigate the roles of imposter substitute position, size, and functionality on the step velocities along the eight unique crystallographic directions. A non-uniform reduction in step velocities was observed, signaling site discrimination of imposter binding that can be attributed to stereochemical recognition of the imposters at specific crystal sites. The anisotropy of growth inhibition observed in the presence of the various imposters is consistent with binding energies calculated for the thirty-two crystallographically unique kink sites on steps advancing along predominant growth directions. These results provide insight to the design of growth inhibitors for molecular crystalline solids with complex and dissymmetric surfaces, while also suggesting a strategy for formulations containing congeners that can prevent harmful crystal growth in human renal structures. The last two crystalline systems discussed in this thesis are two isomorphous crystal systems that are ideal for the study of impurity incorporation at dissymmetric surfaces because their morphology is dominated by dissymmetric {101} growth faces. Growth processes on the dissymmetric (101) surfaces of these crystalline systems were investigated using metadynamics simulations to determine the free energy of adsorption for solute and impurity attachment to different flat, stepped, and kinked (101) surface terminations. Results suggest that growth occurs via a non-Kossel crystal growth mechanism, and highlights the need for dissymmetric surface structures (i.e. steps and kinks) for a higher fidelity in the orientation of adsorbed molecules. Overall, the results presented in this thesis suggest that growth of molecular crystals, particularly at dissymmetric surfaces, is complex and requires the combination of several experimental and computational techniques to decipher the mechanisms responsible for growth phenomena. The use of molecular imposters to inhibit growth can be useful for the development of therapeutics for pathological crystals, but can also inform processes by which crystal growth occurs at complex surfaces as a result of their site selectivity.

Workshop on Surface Science and Technology Held in Ann Arbor, Michigan on 7-9 November 1990

DTIC Science & Technology

1992-03-01

assess the state of the art of surface science and technology as well as to identify new research opportunities essential for the understanding and control...The objective of this workshop was to review and assess the state of the art of surface science and technology as well as to identify new research...AD-A253 566 ’ # 4 - m~~i n~nl lInIir ~~ na Ri1 ?epoi’rt: EN 1Workshop on Surface Science and Technology DTIC ft , L-CTE I OUG0 3192 Ann Arbor

Adsorption--from theory to practice.

PubMed

Dabrowski, A

2001-10-08

Adsorption at various interfaces has concerned scientists since the beginning of this century. This phenomenon underlies a number of extremely important processes of utilitarian significance. The technological, environmental and biological importance of adsorption can never be in doubt. Its practical applications in industry and environmental protection are of paramount importance. The adsorption of substrates is the first stage in many catalytic processes. The methods for separation of mixtures on a laboratory and on an industrial scale are increasingly based on utilising the change in concentration of components at the interface. Moreover, such vital problems as purification of water, sewages, air and soil are involved here too. On the other hand, many areas in which technological innovation has covered adsorption phenomena have been expanded more through art and craft than through science. A basic understanding of the scientific principles is far behind; in part because the study of interfaces requires extremely careful experimentation if meaningful and reproducible results are to be obtained. In recent years, however, considerable effort has been increasingly directed toward closing the gap between theory and practice. Crucial progress in theoretical description of the adsorption has been achieved, mainly through the development of new theoretical approaches formulated on a molecular level, by means of computer simulation methods and owing to new techniques which examine surface layers or interfacial regions. Moreover, during the last 15 years new classes of solid adsorbents have been developed, such as activated carbon fibres and carbon molecular sieves, fullerenes and heterofullerenes, microporous glasses and nanoporous--both carbonaceous and inorganic--materials. Nanostructured solids are very popular in science and technology and have gained extreme interest due to their sorption, catalytic, magnetic, optical and thermal properties. Although the development of adsorption up to the 1918s has been following rather a zig-zag path, this arm of surface science is now generally considered to have become a well-defined branch of physical science representing an intrinsically interdisciplinary area between chemistry, physics, biology and engineering. This review presents in brief the history of adsorption and highlights the progress in theoretical description of the phenomenon under consideration. The paper deals with the above problems critically, showing the development of adsorption, presenting some of the latest important results and giving a source of up-to-date literature on it. Moreover, in this paper the most important aspects are overviewed referring to today's trends and visions in application of adsorption science in industry, environmental protection and in environmental analysis. The relationship between development of adsorption theory and adsorption practice is pointed out. Current understanding and perspectives pertaining to applications of adsorption phenomena on laboratory and on industrial scale as well as environmental protection are discussed and illustrated by means of a few spectacular examples.

[Precision medicine: new opportunities and challenges for molecular epidemiology].

PubMed

Song, Jing; Hu, Yonghua

2016-04-01

Since the completion of the Human Genome Project in 2003 and the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in January 2015, human beings have initially completed the " three steps" of " genomics to biology, genomics to health as well as genomics to society". As a new inter-discipline, the emergence and development of precision medicine have relied on the support and promotion from biological science, basic medicine, clinical medicine, epidemiology, statistics, sociology and information science, etc. Meanwhile, molecular epidemiology is considered to be the core power to promote precision medical as a cross discipline of epidemiology and molecular biology. This article is based on the characteristics and research progress of medicine and molecular epidemiology respectively, focusing on the contribution and significance of molecular epidemiology to precision medicine, and exploring the possible opportunities and challenges in the future.

Bringing the physical sciences into your cell biology research

PubMed Central

Robinson, Douglas N.; Iglesias, Pablo A.

2012-01-01

Historically, much of biology was studied by physicists and mathematicians. With the advent of modern molecular biology, a wave of researchers became trained in a new scientific discipline filled with the language of genes, mutants, and the central dogma. These new molecular approaches have provided volumes of information on biomolecules and molecular pathways from the cellular to the organismal level. The challenge now is to determine how this seemingly endless list of components works together to promote the healthy function of complex living systems. This effort requires an interdisciplinary approach by investigators from both the biological and the physical sciences. PMID:23112230

Bringing the physical sciences into your cell biology research.

PubMed

Robinson, Douglas N; Iglesias, Pablo A

2012-11-01

Historically, much of biology was studied by physicists and mathematicians. With the advent of modern molecular biology, a wave of researchers became trained in a new scientific discipline filled with the language of genes, mutants, and the central dogma. These new molecular approaches have provided volumes of information on biomolecules and molecular pathways from the cellular to the organismal level. The challenge now is to determine how this seemingly endless list of components works together to promote the healthy function of complex living systems. This effort requires an interdisciplinary approach by investigators from both the biological and the physical sciences.

Science | Argonne National Laboratory

Science.gov Websites

Publications Researchers Postdocs Exascale Computing Institute for Molecular Engineering at Argonne Work with Scientific Publications Researchers Postdocs Exascale Computing Institute for Molecular Engineering at understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels

78 FR 26378 - Center for Scientific Review; Notice of Closed Meetings

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2013-05-06

..., Genomes, and Genetics Integrated Review Group; Prokaryotic Cell and Molecular Biology Study Section. Date..., Kidney and Urological Systems Integrated Review Group; Clinical, Integrative and Molecular... Respiratory Sciences Integrated Review Group; Lung Cellular, Molecular, and Immunobiology Study Section. Date...

Marc Snir | Argonne National Laboratory

Science.gov Websites

Molecular biology Proteomics Environmental science & technology Air quality Atmospheric & climate , H.S., Jr., Demonstrating the scalability of a molecular dynamics application on a Petaflop computer Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Engineering JCESRJoint

First-Principles Thermodynamics Study of Spinel MgAl 2 O 4 Surface Stability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Qiuxia; Wang, Jian-guo; Wang, Yong

The surface stability of all possible terminations for three low-index (111, 110, 100) structures of the spinel MgAl2O4 has been studied using first-principles based thermodynamic approach. The surface Gibbs free energy results indicate that the 100_AlO2 termination is the most stable surface structure under ultra-high vacuum at T=1100 K regardless of Al-poor or Al-rich environment. With increasing oxygen pressure, the 111_O2(Al) termination becomes the most stable surface in the Al-rich environment. The oxygen vacancy formation is thermodynamically favorable over the 100_AlO2, 111_O2(Al) and the (111) structure with Mg/O connected terminations. On the basis of surface Gibbs free energies for bothmore » perfect and defective surface terminations, the 100_AlO2 and 111_O2(Al) are the most dominant surfaces in Al-rich environment under atmospheric condition. This is also consistent with our previously reported experimental observation. This work was supported by a Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL). The computing time was granted by the National Energy Research Scientific Computing Center (NERSC). Part of computing time was also granted by a scientific theme user proposal in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington.« less

Virtual Special Issue on Catalysis at the U.S. Department of Energy’s National Laboratories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruski, Marek; Sadow, Aaron; Slowing, Igor

Catalysis research at the U.S. Department of Energy's (DOE's) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/ molecular catalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE’s mission to ensure America’s security and prosperity by addressing its energy, environmental, and nuclear challenges through trans-formative science and technology solutions. The catalysis research carried out at the DOE National Laboratories ranges from very fundamental catalysis science, funded by DOE’s Office of Basic Energy Sciences (BES), to applied research and development (R&D)more » in areas such as biomass conversion to fuels and chemicals, fuel cells, and vehicle emission control with primary funding from DOE’s Office of Energy Efficiency and Renewable Energy. National Laboratories are home to many DOE Office of Science national scientific user facilities that provide researchers with the most advanced tools of modern science, including accelerators, colliders, supercomputers, light sources, and neutron sources, as well as facilities for studying the nanoworld and the terrestrial environment. National Laboratory research programs typically feature teams of researchers working closely together, often joining scientists from different disciplines to attack scientific and technical problems using a variety of tools and techniques available at the DOE national scientific user facilities. Along with collaboration between National Laboratory scientists, interactions with university colleagues are common in National Laboratory catalysis R&D. In some cases, scientists have joint appoint-ments at a university and a National Laboratory.« less

Virtual Special Issue on Catalysis at the U.S. Department of Energy’s National Laboratories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruski, Marek; Sadow, Aaron D.; Slowing, Igor I.

Catalysis research at the U.S. Department of Energy’s (DOE’s) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/molecular catalysis, biocatalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE’s mission to ensure America’s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. The catalysis research carried out at the DOE National Laboratories ranges from very fundamental catalysis science, funded by DOE’s Office of Basic Energy Sciences (BES), to applied research and development (R&D)more » in areas such as biomass conversion to fuels and chemicals, fuel cells, and vehicle emission control with primary funding from DOE’s Office of Energy Efficiency and Renewable Energy. National Laboratories are home to many DOE Office of Science national scientific user facilities that provide researchers with the most advanced tools of modern science, including accelerators, colliders, supercomputers, light sources, and neutron sources, as well as facilities for studying the nanoworld and the terrestrial environment. National Laboratory research programs typically feature teams of researchers working closely together, often joining scientists from different disciplines to tackle scientific and technical problems using a variety of tools and techniques available at the DOE national scientific user facilities. Along with collaboration between National Laboratory scientists, interactions with university colleagues are common in National Laboratory catalysis R&D. In some cases, scientists have joint appointments at a university and a National Laboratory.« less

eScience for molecular-scale simulations and the eMinerals project.

PubMed

Salje, E K H; Artacho, E; Austen, K F; Bruin, R P; Calleja, M; Chappell, H F; Chiang, G-T; Dove, M T; Frame, I; Goodwin, A L; Kleese van Dam, K; Marmier, A; Parker, S C; Pruneda, J M; Todorov, I T; Trachenko, K; Tyer, R P; Walker, A M; White, T O H

2009-03-13

We review the work carried out within the eMinerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

Surface enhanced Raman scattering on Tardigrada--towards monitoring and imaging molecular structures in live cryptobiotic organisms.

PubMed

Kneipp, Harald; Møbjerg, Nadja; Jørgensen, Aslak; Bohr, Henrik G; Hélix-Nielsen, Claus; Kneipp, Janina; Kneipp, Katrin

2013-10-01

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 supported by plasmonic gold nanoparticles can measure molecular constituents and their local distribution in live tardigrades. Surface enhanced Raman signatures allow to differentiate between two species and indicate molecular structural differences between tardigrades in water and in a dry state. This opens new avenues for exploring cryptobiosis by studying molecular changes in live cryptobiotic organisms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A molecular catalyst for water oxidation that binds to metal oxide surfaces

PubMed Central

Sheehan, Stafford W.; Thomsen, Julianne M.; Hintermair, Ulrich; Crabtree, Robert H.; Brudvig, Gary W.; Schmuttenmaer, Charles A.

2015-01-01

Molecular catalysts are known for their high activity and tunability, but their solubility and limited stability often restrict their use in practical applications. Here we describe how a molecular iridium catalyst for water oxidation directly and robustly binds to oxide surfaces without the need for any external stimulus or additional linking groups. On conductive electrode surfaces, this heterogenized molecular catalyst oxidizes water with low overpotential, high turnover frequency and minimal degradation. Spectroscopic and electrochemical studies show that it does not decompose into iridium oxide, thus preserving its molecular identity, and that it is capable of sustaining high activity towards water oxidation with stability comparable to state-of-the-art bulk metal oxide catalysts. PMID:25757425

Autonomous molecular cascades for evaluation of cell surfaces

NASA Astrophysics Data System (ADS)

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.

Comparison of the Photodesorption Activities of cis-Butene, trans-Butene and Isobutene on the Rutile TiO 2(110) Surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, Michael A.

2013-10-17

The chemical and photochemical properties of three butene molecules (cis-butene, trans-butene and isobutene) were explored on the clean rutile TiO 2(110) surface using temperature programmed desorption (TPD) and photon simulated desorption (PSD). At the low coverage limit, trans-butene was the most strongly bound butene on the TiO 2(110) surface, desorbing at ~ 210 K, however increased intermolecular repulsions between trans-butene molecules at higher coverage diminished its binding. Both cis-butene and isobutene saturated the first layer on TiO 2(110) at a coverage of ~0.50 ML in a single TPD feature at 184 and 192 K, respectively. In contrast, the maximum coveragemore » that trans-butene could achieve in its 210 K peak was ~1/3 ML, with higher coverages resulting a low temperature desorption at ~137 K. Coverages of these molecules above 0.50 ML resulted in population of second layer and multilayer states. The instability of trans-butene at a coverage of 0.5 ML on the surface was linked to the inversion center in its symmetry. In the absence of coadsorbed oxygen, the primary photochemical pathway of each butene molecule on TiO 2(110) was photodesorption. The photoactivities of these molecules on TiO 2(110) at an initial coverage of 0.50 ML followed the trend: isobutene > cis-butene > trans-butene. In contrast, the photoactivities of low coverages of cis-butene and trans-butene exceeded those measured at 0.50 ML. These data suggest that intermolecular interactions (repulsions) play a significant role in diminishing the photoactivities of weakly bound molecules on TiO 2 photocatalysts. Work reported here was supported by the U.S. Department of Energy, Office of Basic Energy Science, Division of Chemical Sciences, Geosciences, and Biosciences, and performed in the Williams R. Wiley Environmental Molecular Science Laboratory (EMSL), a Department of Energy user facility funded by the Office of Biological and Environmental Research. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for the U.S. Department of Energy by the Battelle Memorial Institute under contract DEAC05-76RL01830.« less

Authentication of forensic DNA samples.

PubMed

Frumkin, Dan; Wasserstrom, Adam; Davidson, Ariane; Grafit, Arnon

2010-02-01

Over the past twenty years, DNA analysis has revolutionized forensic science, and has become a dominant tool in law enforcement. Today, DNA evidence is key to the conviction or exoneration of suspects of various types of crime, from theft to rape and murder. However, the disturbing possibility that DNA evidence can be faked has been overlooked. It turns out that standard molecular biology techniques such as PCR, molecular cloning, and recently developed whole genome amplification (WGA), enable anyone with basic equipment and know-how to produce practically unlimited amounts of in vitro synthesized (artificial) DNA with any desired genetic profile. This artificial DNA can then be applied to surfaces of objects or incorporated into genuine human tissues and planted in crime scenes. Here we show that the current forensic procedure fails to distinguish between such samples of blood, saliva, and touched surfaces with artificial DNA, and corresponding samples with in vivo generated (natural) DNA. Furthermore, genotyping of both artificial and natural samples with Profiler Plus((R)) yielded full profiles with no anomalies. In order to effectively deal with this problem, we developed an authentication assay, which distinguishes between natural and artificial DNA based on methylation analysis of a set of genomic loci: in natural DNA, some loci are methylated and others are unmethylated, while in artificial DNA all loci are unmethylated. The assay was tested on natural and artificial samples of blood, saliva, and touched surfaces, with complete success. Adopting an authentication assay for casework samples as part of the forensic procedure is necessary for maintaining the high credibility of DNA evidence in the judiciary system.

The birth and evolution of surface science: child of the union of science and technology.

PubMed

Duke, C B

2003-04-01

This article is an account of the birth and evolution of surface science as an interdisciplinary research area. Surface science emanated from the confluence of concepts and tools in physics and chemistry with technological innovations that made it possible to determine the structure and properties of surfaces and interfaces and the dynamics of chemical reactions at surfaces. The combination in the 1960s and 1970s of ultra-high-vacuum (i.e., P < 10(-7) Pascal or 10(-9) Torr) technology with the recognition that electrons in the energy range from 50 to 500 eV exhibited inelastic collision mean free paths of the order of a few angstroms fostered an explosion of activity. The results were a reformulation of the theory of electron solid scattering, the nearly universal use of electron spectroscopies for surface characterization, the rise of surface science as an independent interdisciplinary research area, and the emergence of the American Vacuum Society (AVS) as a major international scientific society. The rise of microelectronics in the 1970s and 1980s resulted in huge increases in computational power. These increases enabled more complex experiments and the utilization of density functional theory for the quantitative prediction of surface structure and dynamics. Development of scanning-probe microscopies in the 1990s led to atomic-resolution images of macroscopic surfaces and interfaces as well as videos of atoms moving about on surfaces during growth and diffusion. Scanning probes have since brought solid-liquid interfaces into the realm of atomic-level surface science, expanding its scope to more complex systems, including fragile biological materials and processes.

Compression of self-assembled nano-objects: 2D/3D transitions in films of (perfluoroalkyl)alkanes--persistence of an organized array of surface micelles.

PubMed

de Gracia Lux, Caroline; Gallani, Jean-Louis; Waton, Gilles; Krafft, Marie Pierre

2010-06-25

Understanding and controlling the molecular organization of amphiphilic molecules at interfaces is essential for materials and biological sciences. When spread on water, the model amphiphiles constituted by C(n)F(2n+1)C(m)H(2m+1) (FnHm) diblocks spontaneously self-assemble into surface hemimicelles. Therefore, compression of monolayers of FnHm diblocks is actually a compression of nanometric objects. Langmuir films of F8H16, F8H18, F8H20, and F10H16 can actually be compressed far beyond the "collapse" of their monolayers at approximately 30 A(2). For molecular areas A between 30 and 10 A(2), a partially reversible, 2D/3D transition occurs between a monolayer of surface micelles and a multilayer that coexist on a large plateau. For A<10 A(2), surface pressure increases again, reaching up to approximately 48 mN m(-1) before the film eventually collapses. Brewster angle microscopy and AFM indicate a several-fold increase in film thickness when scanning through the 2D/3D coexistence plateau. Compression beyond the plateau leads to a further increase in film thickness and, eventually, to film disruption. Reversibility was assessed by using compression-expansion cycles. AFM of F8H20 films shows that the initial monolayer of micelles is progressively covered by one (and eventually two) bilayers, which leads to a hitherto unknown organized composite arrangement. Compression of films of the more rigid F10H16 results in crystalline-like inflorescences. For both diblocks, a hexagonal array of surface micelles is consistently seen, even when the 3D structures eventually disrupt, which means that this monolayer persists throughout the compression experiments. Two examples of pressure-driven transformations of films of self-assembled objects are thus provided. These observations further illustrate the powerful self-assembling capacity of perfluoroalkyl chains.

USSR Report, Life Sciences Biomedical and Behavioral Sciences.

DTIC Science & Technology

1983-09-13

created by the lengthy pro- cesses of evolution and selection, as well as methods for selecting and evaluating plants at the first stages of the...27 May 83) 17 Soviets-American Symposium in Alma-Ata on Plant Proteins and Nutrition (N. Idrisov? KAZAKHSTANSKAYA PRAVDA, 26 Feb 83).., 19...MIKROBIOLOGIYA, Nov-Dec 82),.,,. 38 MOLECULAR BIOLOGY New Research Institute of Plant Molecular Biology and Biochemistry in Alma-Ata (Murat

Titan Lifting Entry & Atmospheric Flight (T-LEAF) Science Mission

NASA Astrophysics Data System (ADS)

Lee, G.; Sen, B.; Ross, F.; Sokol, D.

2016-12-01

Northrop Grumman has been developing the Titan Lifting Entry & Atmospheric Flight (T-LEAF) sky rover to roam the lower atmosphere and observe at close quarters the lakes and plains of Saturn's ocean moon, Titan. T-LEAF also supports surface exploration and science by providing precision delivery of in-situ instruments to the surface of Titan. T-LEAF is a highly maneuverable sky rover and its aerodynamic shape (i.e., a flying wing) does not restrict it to following prevailing wind patterns on Titan, but allows mission operators to chart its course. This freedom of mobility allows T-LEAF to follow the shorelines of Titan's methane lakes, for example, or to target very specific surface locations. We will present a straw man concept of T-LEAF, including size, mass, power, on-board science payloads and measurement, and surface science dropsonde deployment CONOPS. We will discuss the various science instruments and their vehicle level impacts, such as meteorological and electric field sensors, acoustic sensors for measuring shallow depths, multi-spectral imagers, high definition cameras and surface science dropsondes. The stability of T-LEAF and its long residence time on Titan will provide for time to perform a large aerial survey of select prime surface targets deployment of dropsondes at selected locations surface measurements that are coordinated with on-board remote measurements communication relay capabilities to orbiter (or Earth). In this context, we will specifically focus upon key factors impacting the design and performance of T-LEAF science: science payload accommodation, constraints and opportunities characteristics of flight, payload deployment and measurement CONOPS in the Titan atmosphere. This presentation will show how these factors provide constraints as well as enable opportunities for novel long duration scientific studies of Titan's surface.

Basic Energy Science | NREL

Science.gov Websites

scientific understanding-of molecular, nanoscale, semiconductor, and biological materials, systems, and molecular, nanoscale, and semiconductor systems to capture, control, and convert solar radiation with high

Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.

2014-01-15

Possible proton channels in Clostridium pasteurianum [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to discern proposed channels, compare their properties, evaluate the functional channel, and to provide insight into the features of an active proton channel. Our simulations suggest that protons are not transported through water wires. Instead, a five-residue motif (E282, S319, E279, HOH, C299) was found to be the likely channel, consistent with experimental observations. This channel connects the surface of the enzyme and the di-thiomethylamine bridge of the catalytic H-cluster, permitting the transport of protons. The channel was found to have a persistentmore » hydrogen bonded core (residues E279 to S319), with less persistent hydrogen bonds at the ends of the channel. The hydrogen bond occupancy in this network was found to be sensitive to the protonation state of the residues in the channel, with different protonation states enhancing or stabilizing hydrogen bonding in different regions of the network. Single site mutations to non-hydrogen bonding residues break the hydrogen bonding network at that residue, consistent with experimental observations showing catalyst inactivation. In many cases, these mutations alter the hydrogen bonding in other regions of the channel which may be equally important in catalytic failure. A correlation between the protein dynamics near the proton channel and the redox partner binding regions was also found as a function of protonation state. The likely mechanism of proton movement in [FeFe]-hydrogenases is discussed based on the structural analysis presented here. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory, and a portion of the research was performed using PNNL Institutional Computing at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Multiscale Computation. Needs and Opportunities for BER Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scheibe, Timothy D.; Smith, Jeremy C.

2015-01-01

The Environmental Molecular Sciences Laboratory (EMSL), a scientific user facility managed by Pacific Northwest National Laboratory for the U.S. Department of Energy, Office of Biological and Environmental Research (BER), conducted a one-day workshop on August 26, 2014 on the topic of “Multiscale Computation: Needs and Opportunities for BER Science.” Twenty invited participants, from various computational disciplines within the BER program research areas, were charged with the following objectives; Identify BER-relevant models and their potential cross-scale linkages that could be exploited to better connect molecular-scale research to BER research at larger scales and; Identify critical science directions that will motivate EMSLmore » decisions regarding future computational (hardware and software) architectures.« less

77 FR 2739 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-19

... . Name of Committee: Genes, Genomes, and Genetics Integrated Review Group; Molecular Genetics A Study... Urological Systems Integrated Review Group; Kidney Molecular Biology and Genitourinary Organ Development... Sciences Integrated Review Group; Molecular and Cellular Endocrinology Study Section. Date: February 13...

Electrostatically self-assembled polyoxometalates on molecular-dye-functionalized diamond.

PubMed

Zhong, Yu Lin; Ng, Wibowo; Yang, Jia-Xiang; Loh, Kian Ping

2009-12-30

We have successfully immobilized phosphotungstic acid (PTA), a polyoxometalate, on the surface of boron-doped diamond (BDD) surface through electrostatic self-assembly of PTA on pyridinium dye-functionalized-BDD. The inorganic/organic bilayer structure on BDD is found to exhibit fast surface-confined reversible electron transfer. The molecular dye-grafted BDD can undergo controllable electrical stripping and regeneration of PTA which can be useful for electronics or sensing applications. Furthermore, we have demonstrated the use of PTA as a molecular switch in which the direction of photocurrent from diamond to methyl viologen is reversed by the surface bound PTA. Robust photocurrent converter based on such molecular system-diamond platform can operate in corrosive medium which is not tolerated by indium tin oxide electrodes.

MODELING THE INTERACTION OF AGROCHEMICALS WITH ENVIRONMENTAL SURFACES: PESTICIDES ON RUTILE AND ORGANO-RUTILE SURFACES

EPA Science Inventory

Non-bonded interactions between model pesticides and organo-mineral surfaces have been studied using molecular mechanical conformational calculations and molecular dynamics simulations. The minimum energy conformations and relative binding energies for the interaction of atrazine...

Wetting of crystalline polymer surfaces: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Fan, Cun Feng; Caǧin, Tahir

1995-11-01

Molecular dynamics has been used to study the wetting of model polymer surfaces, the crystal surfaces of polyethylene (PE), poly(tetrafluoroethylene) (PTFE), and poly(ethylene terephthalate) (PET) by water and methylene iodide. In the simulation a liquid droplet is placed on a model surface and constant temperature, rigid body molecular dynamics is carried out while the model surface is kept fixed. A generally defined microscopic contact angle between a liquid droplet and a solid surface is quantitatively calculated from the volume of the droplet and the interfacial area between the droplet and the surface. The simulation results agree with the trend in experimental data for both water and methylene iodide. The shape of the droplets on the surface is analyzed and no obvious anisotropy of the droplets is seen in the surface plane, even though the crystal surfaces are highly oriented. The surface free energies of the model polymer surfaces are estimated from their contact angles with the two different liquid droplets.

The 2011 Dynamics of Molecular Collisions Conference

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nesbitt, David J.

The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical &more » experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor Yuan T. Lee & Professor George Schatz. Professor Lee’s research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lee’s work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatz’s research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed to encouraging women & minorities as well as encourage the field of Chemical Physics in scientifically developing countries. For example, it has been a tradition of the DMC meeting to offer of order 40 scholarships for students & postdocs to defray registration & travel costs. The benefits of increased graduate student & post doctoral attendance at the meeting cannot be over emphasized. First, these young scientists have the opportunity to present their work by means of the poster session & to a gathering of experts in their field. Secondly the limited size of the meeting allows student & young postdocs to meet & interact directly with experts in their area, to network with their peers at other institutions & become aware of career opportunities. Graduate students & post doctoral fellows are the life blood of our field. Support of their attendance at this & other similar meetings will ensure a continued flow of young talent into many areas of research represented by the DMC meeting & important to DOE.« less

76 FR 80952 - Request for Nominations for Voting Members on a Public Advisory Committee; Food Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-27

... life science, food science, risk assessment, nutrition, food technology, molecular biology, and other... chemistry or food science to serve on the Food Advisory Committee, Center for Food Safety and Applied Nutrition, Office of Regulations, Policy, and Social Sciences. FDA has a special interest in ensuring that...

Surface chemistry at Swiss Universities of Applied Sciences.

PubMed

Brodard, Pierre; Pfeifer, Marc E; Adlhart, Christian D; Pieles, Uwe; Shahgaldian, Patrick

2014-01-01

In the Swiss Universities of Applied Sciences, a number of research groups are involved in surface science, with different methodological approaches and a broad range of sophisticated characterization techniques. A snapshot of the current research going on in different groups from the University of Applied Sciences and Arts Western Switzerland (HES-SO), the Zurich University of Applied Sciences (ZHAW) and the University of Applied Sciences and Arts Northwestern Switzerland (FHNW) is given.

Saturn Magnetospheric Impact on Surface Molecular Chemistry and Astrobiological Potential of Enceladus

NASA Technical Reports Server (NTRS)

Cooper, Paul D.; Cooper, John F.; Sittler, Edward C.; Burger, Matthew H.; Sturner, Steven J.; Rymer, Abigail M.

2008-01-01

The active south polar surface of Enceladus is exposed to strong chemical processing by direct interaction with charged plasma and energetic particles in the local magnetospheric environment of this icy moon. Chemical oxidation activity is suggested by detection of H202 at the surface in this region and less directly by substantial presence of C02, CO, and N2 in the plume gases. Molecular composition of the uppermost surface, including ejecta from plume activity, is radiolytically transformed mostly by penetrating energetic electrons with lesser effects from more depleted populations of energetic protons. The main sources of molecular plasma ions and E-ring dust grains in the magnetospheric environment are the cryovolcanic plume emissions from Enceladus. These molecular ions and the dust grains are chemically processed by magnetospheric interactions that further impact surface chemistry on return to Enceladus. For example, H20 neutrals dominating the emitted plume gas return to the surface mostly as H30+ ions after magnetospheric processing. Surface oxidant loading is further increased by return of radiolytically processed ice grains from the E-ring. Plume frost deposition and micrometeoroid gardening protect some fraction of newly produced molecular species from destruction by further irradiation. The evident horizontal and vertical mobility of surface ices in the south polar region drive mixing of these processed materials into the moon interior with potential impacts on deep ice molecular chemistry and plume gas production. Similarly as suggested previously for Europa, the externally driven source of radiolytic oxidants could affect evolution of life in any subsurface liquid water environments of Enceladus.

Thermodynamic Control of Two-Dimensional Molecular Ionic Nanostructures on Metal Surfaces

DOE PAGES

Jeon, Seokmin; Doak, Peter W.; Sumpter, Bobby G.; ...

2016-07-26

Bulk molecular ionic solids exhibit fascinating electronic properties, including electron correlations, phase transitions and superconducting ground states. In contrast, few of these phenomena have so far been observed in low-dimensional molecular structures, including thin films, nanoparticles and molecular blends, not in the least because most of such structures have so far been composed of nearly closed-shell molecules. It is therefore desirable to develop low-dimensional molecular structures of ionic molecules toward fundamental studies and potential applications. Here we present detailed analysis of monolayer-thick structures of the canonical TTF-TCNQ (tetrathiafulvalene 7,7,8,8-tetracyanoquinodimethane) system grown on low-index gold and silver surfaces. The most distinctivemore » property of the epitaxial growth is the wide abundance of stable TTF/TCNQ ratios, in sharp contrast to the predominance of 1:1 ratio in the bulk. We propose the existence of the surface phase-diagram that controls the structures of TTF-TCNQ on the surfaces, and demonstrate phase-transitions that occur upon progressively increasing the density of TCNQ while keeping the surface coverage of TTF fixed. Based on direct observations, we propose the binding motif behind the stable phases and infer the dominant interactions that enable the existence of the rich spectrum of surface structures. Finally, we also show that the surface phase diagram will control the epitaxy beyond monolayer coverage. Multiplicity of stable surface structures, the corollary rich phase diagram and the corresponding phase-transitions present an interesting opportunity for low-dimensional molecular systems, particularly if some of the electronic properties of the bulk can be preserved or modified in the surface phases.« less

Partners | Argonne National Laboratory

Science.gov Websites

Biology IMEInstitute for Molecular Engineering JCESRJoint Center for Energy Storage Research MCSGMidwest Science and Engineering RISCRisk and Infrastructure Science Center SBCStructural Biology Center Energy.gov

Energy | Argonne National Laboratory

Science.gov Websites

Biology IMEInstitute for Molecular Engineering JCESRJoint Center for Energy Storage Research MCSGMidwest Science and Engineering RISCRisk and Infrastructure Science Center SBCStructural Biology Center Energy.gov

Science Syllabus for Middle and Junior High Schools. Block D, The Earth's Changing Surface.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Bureau of General Education Curriculum Development.

This syllabus begins with a list of program objectives and performance criteria for the study of three general topic areas in earth science and a list of 22 science processes. Following this information is a listing of concepts and understandings for subtopics within the general topic areas: (1) the earth's surface--surface features, rock…

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.

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,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 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 CeO 2 (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.« less

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

DOE PAGES

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.; ...

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,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 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 CeO 2 (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.« less

Facile Isolation of Adsorbent-Free Long and Highly-Pure Chirality-Selected Semiconducting Single-Walled Carbon Nanotubes Using A Hydrogen-bonding Supramolecular Polymer.

PubMed

Toshimitsu, Fumiyuki; Nakashima, Naotoshi

2015-12-14

The ideal form of semiconducting-single-walled carbon nanotubes (sem-SWNTs) for science and technology is long, defect-free, chirality pure and chemically pure isolated narrow diameter tubes. While various techniques to solubilize and purify sem-SWNTs have been developed, many of them targeted only the chiral- or chemically-purity while sacrificing the sem-SWNT intrinsic structural identities by applying strong ultra-sonication and/or chemical modifications. Toward the ultimate purification of the sem-SWNTs, here we report a mild-conditioned extraction of the sem-SWNTs using removable supramolecular hydrogen-bonding polymers (HBPs) that are composed of dicarboxylic- or diaminopyridyl-fluorenes with ~70%-(8,6)SWNT selective extraction. Replacing conventional strong sonication techniques by a simple shaking using HPBs was found to provide long sem-SWNTs (>2.0 μm) with a very high D/G ratio, which was determined by atomic force microscopy observations. The HBPs were readily removed from the nanotube surfaces by an outer stimulus, such as a change in the solvent polarities, to provide chemically pure (8,6)-enriched sem-SWNTs. We also describe molecular mechanics calculations to propose possible structures for the HBP-wrapped sem-SWNTs, furthermore, the mechanism of the chiral selectivity for the sorted sem-SWNTs is well explained by the relationship between the molecular surface area and mass of the HBP/SWNT composites.

Advances in Molecular Rotational Spectroscopy for Applied Science

NASA Astrophysics Data System (ADS)

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.

The contour-buildup algorithm to calculate the analytical molecular surface.

PubMed

Totrov, M; Abagyan, R

1996-01-01

A new algorithm is presented to calculate the analytical molecular surface defined as a smooth envelope traced out by the surface of a probe sphere rolled over the molecule. The core of the algorithm is the sequential build up of multi-arc contours on the van der Waals spheres. This algorithm yields substantial reduction in both memory and time requirements of surface calculations. Further, the contour-buildup principle is intrinsically "local", which makes calculations of the partial molecular surfaces even more efficient. Additionally, the algorithm is equally applicable not only to convex patches, but also to concave triangular patches which may have complex multiple intersections. The algorithm permits the rigorous calculation of the full analytical molecular surface for a 100-residue protein in about 2 seconds on an SGI indigo with R4400++ processor at 150 Mhz, with the performance scaling almost linearly with the protein size. The contour-buildup algorithm is faster than the original Connolly algorithm an order of magnitude.

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

77 FR 31030 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-24

... Review Group; Cellular, Molecular and Integrative Reproduction Study Section. Date: June 21, 2012. Time...: Endocrinology, Metabolism, Nutrition and Reproductive Sciences Integrated Review Group; Molecular and Cellular..., Bethesda, MD 20892, 301-827- 7915, [email protected] . Name of Committee: Molecular, Cellular and...

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

PubMed

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.

Studies of Scientific Disciplines. An Annotated Bibliography.

ERIC Educational Resources Information Center

Weisz, Diane; Kruytbosch, Carlos

Provided in this bibliography are annotated lists of social studies of science literature, arranged alphabetically by author in 13 disciplinary areas. These areas include astronomy; general biology; biochemistry and molecular biology; biomedicine; chemistry; earth and space sciences; economics; engineering; mathematics; physics; political science;…

A Surface Science Paradigm for a Post-Huygens Titan Mission

NASA Technical Reports Server (NTRS)

Zimmerman, Wayne F.; Lunine, Jonathan; Lorenz, Ralph

2005-01-01

With the Cassini-Huygens atmospheric probe drop-off mission fast approaching, it is essential that scientists and engineers start scoping potential follow-on surface science missions. This paper provides a summary of the first year of a two year design study which examines in detail the desired surface science measurements and resolution, potential instrument suite, and complete payload delivery system. Also provided are design concepts for both an aerial inflatable mobility platform and deployable instrument sonde. The tethered deployable sonde provides the capability to sample near surface atmosphere, sub-surface liquid (if it exists), and surface solid material. Actual laboratory tests of the amphibious sonde prototype are also presented.

Teacher Programs | Argonne National Laboratory

Science.gov Websites

Biology IMEInstitute for Molecular Engineering JCESRJoint Center for Energy Storage Research MCSGMidwest Science and Engineering RISCRisk and Infrastructure Science Center SBCStructural Biology Center Energy.gov

Educational Programs | Argonne National Laboratory

Science.gov Websites

Biology IMEInstitute for Molecular Engineering JCESRJoint Center for Energy Storage Research MCSGMidwest Science and Engineering RISCRisk and Infrastructure Science Center SBCStructural Biology Center Energy.gov

Exploring the Surface Sensitivity of ToF-SIMS by Measuring the Implantation and Sampling Depths of Bin and C60 Ions in Organic Films

PubMed Central

Muramoto, Shin; Brison, Jeremy; Castner, David G.

2011-01-01

The surface sensitivity of Binq+ (n = 1, 3, 5, q = 1, 2) and C60q+ (q = 1, 2) primary ions in static time-of-flight secondary ion mass spectrometry (ToF-SIMS) experiments were investigated for molecular trehalose and polymeric tetraglyme organic films. Parameters related to surface sensitivity (impact crater depth, implantation depth, and molecular escape depths) were measured. Under static ToF-SIMS conditions (primary ion doses of 1 × 1012 ions/cm2), the 25 keV Bi1+ primary ions were the most surface sensitive with a molecular escape depth of 1.8 nm for protein films with tetraglyme overlayers, but they had the deepest implantation depth (~18 and 26 nm in trehalose and tetraglyme films, respectively). The 20 keV C60++ primary ions were the second most surface sensitive with a slightly larger molecular escape depth of 2.3 nm. The most important factor that determined the surface sensitivity of the primary ion was its impact crater depth, or the amount of surface erosion. The most surface sensitive primary ions, Bi1+ and C60++, created impact craters with depths of 0.3 and 1.0 nm, respectively, in tetraglyme films. In contrast, Bi5++ primary ions created impact craters with a depth of 1.8 nm in tetraglyme films and were the least surface sensitive with a molecular escape depth of 4.7 nm. PMID:22084828

Wetting properties of molecularly rough surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Svoboda, Martin; Lísal, Martin, E-mail: lisal@icpf.cas.cz; Department of Physics, Institute of Science, J. E. Purkinje University, 400 96 Ústí n. Lab.

2015-09-14

We employ molecular dynamics simulations to study the wettability of nanoscale rough surfaces in systems governed by Lennard-Jones (LJ) interactions. We consider both smooth and molecularly rough planar surfaces. Solid substrates are modeled as a static collection of LJ particles arranged in a face-centered cubic lattice with the (100) surface exposed to the LJ fluid. Molecularly rough solid surfaces are prepared by removing several strips of LJ atoms from the external layers of the substrate, i.e., forming parallel nanogrooves on the surface. We vary the solid-fluid interactions to investigate strongly and weakly wettable surfaces. We determine the wetting properties bymore » measuring the equilibrium droplet profiles that are in turn used to evaluate the contact angles. Macroscopic arguments, such as those leading to Wenzel’s law, suggest that surface roughness always amplifies the wetting properties of a lyophilic surface. However, our results indicate the opposite effect from roughness for microscopically corrugated surfaces, i.e., surface roughness deteriorates the substrate wettability. Adding the roughness to a strongly wettable surface shrinks the surface area wet with the liquid, and it either increases or only marginally affects the contact angle, depending on the degree of liquid adsorption into the nanogrooves. For a weakly wettable surface, the roughness changes the surface character from lyophilic to lyophobic due to a weakening of the solid-fluid interactions by the presence of the nanogrooves and the weaker adsorption of the liquid into the nanogrooves.« less

Fluorescence-correlation spectroscopy study of molecular transport within reversed-phase chromatographic particles compared to planar model surfaces.

PubMed

Cooper, Justin; Harris, Joel M

2014-12-02

Reversed-phase liquid chromatography (RPLC) is a widely used technique for molecular separations. Stationary-phase materials for RPLC generally consist of porous silica-gel particles functionalized with n-alkane ligands. Understanding motions of molecules within the interior of these particles is important for developing efficient chromatographic materials and separations. To characterize these dynamics, time-resolved spectroscopic methods (photobleach recovery, fluorescence correlation, single-molecule imaging) have been adapted to measure molecular diffusion rates, typically at n-alkane-modified planar silica surfaces, which serve as models of chromatographic interfaces. A question arising from these studies is how dynamics of molecules on a planar surface relate to motions of molecules within the interior of a porous chromatographic particle. In this paper, imaging-fluorescence-correlation spectroscopy is used to measure diffusion rates of a fluorescent probe molecule 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) within authentic RPLC porous silica particles and compared with its diffusion at a planar C18-modified surface. The results show that surface diffusion on the planar C18 substrate is much faster than the diffusion rate of the probe molecule through a chromatographic particle. Surface diffusion within porous particles, however, is governed by molecular trajectories along the tortuous contours of the interior surface of the particles. By accounting for the greater surface area that a molecule must explore to diffuse macroscopic distances through the particle, the molecular-scale diffusion rates on the two surfaces can be compared, and they are virtually identical. These results provide support for the relevance of surface-diffusion measurements made on planar model surfaces to the dynamic behavior of molecules on the internal surfaces of porous chromatographic particles.

Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding

NASA Astrophysics Data System (ADS)

Bush, Derek B.; Knotts, Thomas A.

2017-04-01

Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces. To overcome this limitation, this study uses molecular simulation and an advanced, experimentally validated, coarse-grain, protein-surface model to compare fab-lysozyme binding in bulk solution and when the fab is tethered to hydrophobic and hydrophilic surfaces. The results show that the tether site in the fab, as well as the surface hydrophobicity, significantly impacts the binding process and suggests that the optimal design involves tethering fabs upright on a hydrophilic surface. The results offer an unprecedented, molecular-level picture of the binding process and give hope that the rational design of protein-microarrays is possible.

The birth and evolution of surface science: Child of the union of science and technology

PubMed Central

Duke, C. B.

2003-01-01

This article is an account of the birth and evolution of surface science as an interdisciplinary research area. Surface science emanated from the confluence of concepts and tools in physics and chemistry with technological innovations that made it possible to determine the structure and properties of surfaces and interfaces and the dynamics of chemical reactions at surfaces. The combination in the 1960s and 1970s of ultra-high-vacuum (i.e., P < 10−7 Pascal or 10−9 Torr) technology with the recognition that electrons in the energy range from 50 to 500 eV exhibited inelastic collision mean free paths of the order of a few angstroms fostered an explosion of activity. The results were a reformulation of the theory of electron solid scattering, the nearly universal use of electron spectroscopies for surface characterization, the rise of surface science as an independent interdisciplinary research area, and the emergence of the American Vacuum Society (AVS) as a major international scientific society. The rise of microelectronics in the 1970s and 1980s resulted in huge increases in computational power. These increases enabled more complex experiments and the utilization of density functional theory for the quantitative prediction of surface structure and dynamics. Development of scanning-probe microscopies in the 1990s led to atomic-resolution images of macroscopic surfaces and interfaces as well as videos of atoms moving about on surfaces during growth and diffusion. Scanning probes have since brought solid–liquid interfaces into the realm of atomic-level surface science, expanding its scope to more complex systems, including fragile biological materials and processes. PMID:12651946

Design and Evaluation of a Digital Module with Guided Peer Feedback for Student Learning Biotechnology and Molecular Life Sciences, Attitudinal Change, and Satisfaction

ERIC Educational Resources Information Center

Noroozi, Omid; Mulder, Martin

2017-01-01

This study aims to investigate the impacts of a digital learning module with guided peer feedback on students' domain-specific knowledge gain and their attitudinal change in the field of biotechnology and molecular life sciences. The extent to which the use of this module is appreciated by students is studied as well. A pre-test, post-test design…

Mass spectrometry in life science research.

PubMed

Lehr, Stefan; Markgraf, Daniel

2016-12-01

Investigating complex signatures of biomolecules by mass spectrometry approaches has become indispensable in molecular life science research. Nowadays, various mass spectrometry-based omics technologies are available to monitor qualitative and quantitative changes within hundreds or thousands of biological active components, including proteins/peptides, lipids and metabolites. These comprehensive investigations have the potential to decipher the pathophysiology of disease development at a molecular level and to monitor the individual response of pharmacological treatment or lifestyle intervention.

Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction

NASA Astrophysics Data System (ADS)

Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

2014-01-01

DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag+-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 ofmore » 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).« less

Mapping the Materials Genome through Combinatorial Informatics

NASA Astrophysics Data System (ADS)

Rajan, Krishna

2012-02-01

The recently announced White House Materials Genome Initiative provides an exciting challenge to the materials science community. To meet that challenge one needs to address a critical question, namely what is the materials genome? Some guide on how to the answer this question can be gained by recognizing that a ``gene'' is a carrier of information. In the biological sciences, discovering how to manipulate these genes has generated exciting discoveries in fundamental molecular biology as well as significant advances in biotechnology. Scaling that up to molecular, cellular length scales and beyond, has spawned from genomics, fields such as proteomics, metabolomics and essentially systems biology. The ``omics'' approach requires that one needs to discover and track these ``carriers of information'' and then correlate that information to predict behavior. A similar challenge lies in materials science, where there is a diverse array of modalities of materials ``discovery'' ranging from new materials chemistries and molecular arrangements with novel properties, to the development and design of new micro- and mesoscale structures. Hence to meaningfully adapt the spirit of ``genomics'' style research in materials science, we need to first identify and map the ``genes'' across different materials science applications On the experimental side, combinatorial experiments have opened a new approach to generate data in a high throughput manner, but without a clear way to link that to models, the full value of that data is not realized. Hence along with experimental and computational materials science, we need to add a ``third leg'' to our toolkit to make the ``Materials Genome'' a reality, the science of Materials Informatics. In this presentation we provide an overview of how information science coupled to materials science can in fact achieve the goal of mapping the ``Materials Genome''.

Human Mars Surface Science Operations

NASA Technical Reports Server (NTRS)

Bobskill, Marianne R.; Lupisella, Mark L.

2014-01-01

Human missions to the surface of Mars will have challenging science operations. This paper will explore some of those challenges, based on science operations considerations as part of more general operational concepts being developed by NASA's Human Spaceflight Architecture (HAT) Mars Destination Operations Team (DOT). The HAT Mars DOT has been developing comprehensive surface operations concepts with an initial emphasis on a multi-phased mission that includes a 500-day surface stay. This paper will address crew science activities, operational details and potential architectural and system implications in the areas of (a) traverse planning and execution, (b) sample acquisition and sample handling, (c) in-situ science analysis, and (d) planetary protection. Three cross-cutting themes will also be explored in this paper: (a) contamination control, (b) low-latency telerobotic science, and (c) crew autonomy. The present traverses under consideration are based on the report, Planning for the Scientific Exploration of Mars by Humans1, by the Mars Exploration Planning and Analysis Group (MEPAG) Human Exploration of Mars-Science Analysis Group (HEM-SAG). The traverses are ambitious and the role of science in those traverses is a key component that will be discussed in this paper. The process of obtaining, handling, and analyzing samples will be an important part of ensuring acceptable science return. Meeting planetary protection protocols will be a key challenge and this paper will explore operational strategies and system designs to meet the challenges of planetary protection, particularly with respect to the exploration of "special regions." A significant challenge for Mars surface science operations with crew is preserving science sample integrity in what will likely be an uncertain environment. Crewed mission surface assets -- such as habitats, spacesuits, and pressurized rovers -- could be a significant source of contamination due to venting, out-gassing and cleanliness levels associated with crew presence. Low-latency telerobotic science operations has the potential to address a number of contamination control and planetary protection issues and will be explored in this paper. Crew autonomy is another key cross-cutting challenge regarding Mars surface science operations, because the communications delay between earth and Mars could as high as 20 minutes one way, likely requiring the crew to perform many science tasks without direct timely intervention from ground support on earth. Striking the operational balance between crew autonomy and earth support will be a key challenge that this paper will address.

Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

NASA Astrophysics Data System (ADS)

Sinha, Sumona; Wang, C.-H.; Mukherjee, M.

2017-07-01

This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation as well as orientation and surface morphology of deposited rubrene thin film at rubrene/Ag interfaces and are beneficial for the improvement of the device performance.

Applying Molecular Bonding Concepts to the Solid State

NASA Astrophysics Data System (ADS)

Dunnington, Benjamin D.

In this thesis, we describe the extension and application of Natural Bond Orbital (NBO) analysis to periodic systems. This enables the translation of rigorous, quantum mechanical calculation results of solid systems into the localized lone pairs and two-center bonds of Lewis structures. Such localized bonding descriptions form the basic language of chemistry, and application of these ideas to solids allows for the understanding of complex phenomena in bulk systems using readily accessible concepts from molecular science. In addition to the algorithmic adjustments needed for to account for periodic boundary conditions in the NBO process, we also discuss methodology to interface the ubiquitous plane wave basis sets of the solid state with the atom-centered basis functions needed as input for NBO analysis. We will describe one method using projection of the plane wave eigenstates, and a second projection-free method that involves the direct calculation of matrix elements of the plane wave Hamiltonian in an atom-centered basis. The reliance of many localized, post-computational analysis techniques on an atom-centered description of the orbitals, means these interfaces will have applicability beyond our NBO development. An ideal area for application of such molecular descriptions of periodic systems is heterogeneous catalysis, where reactants from a gas/liquid phase react on a solid catalyst surface. Previous studies of these systems have originated from the delocalized perspective of the bulk catalyst. NBO provides an explicit description of the perturbative effect of the catalyst on the covalent bonds of the reactant, which is correlated with the catalytic activity of the material. Such a shift to an adsorbate focused description of surface reactivity will enable understanding of catalysis across a variety of materials.

Growth and Characterization of Large Scale (Sb1-xBix)2 Te3 Thin Films on Mica

NASA Astrophysics Data System (ADS)

Ni, Yan; Zhang, Zhen; Jiles, David

2015-03-01

Topological insulators (TIs) attract attentions for both fundamental science and potential applications because of their bulk band inversion arising from the strong spin orbital coupling. However, it is necessary to tune the Fermi level and Dirac cone in 3D TI (Sb1-xBix)2 Te3 to make an ideal system for TI applications. In this work, we report high quality (Sb1-xBix)2 Te3 thin films grown on mica substrate by molecular beam epitaxy. The surface roughness of the thin film can reach as low as 0.7 nm in a large area by van der Waals epitaxy. (Sb1-xBix)2 Te3 thin film with x = 0.04 shows a local maxima in the room temperature sheet resistance, which indicates a minimization of the carrier density due to band structure engineering. Moreover, for higher Bi concentration, due to an increase of the surface roughness and corresponding reduction of electron mobility, the sheet resistance increases. Our results on the feasibility of depositing (Sb1-xBix)2 Te3 in wide Bi range on mica substrate will helpful for the application of TI at room temperature and flexible electronics. Authors would like to thank the financial support from the U.S. National Science Foundation under the Award No. 1201883.

[Analysis of hot spots and trend of molecular pharmacognosy research based on project supported by National Natural Science Foundation of 1995-2014].

PubMed

Wang, Jun-Wen; Liu, Yang; Tong, Yuan-Yuan; Yang, Ce; Li, Hai-Yan

2016-05-01

This study collected 1995-2014 molecular pharmacognosy study, a total of 595 items, funded by Natural Science Foundation of China (NSFC). TDA and Excel software were used to analyze the data of the projects about general situation, hot spots of research with rank analytic and correlation analytic methods. Supported by NSFC molecular pharmacognosy projects and funding a gradual increase in the number of, the proportion of funds for pharmaceutical research funding tends to be stable; mainly supported by molecular biology methods of genuine medicinal materials, secondary metabolism and Germplasm Resources Research; hot drugs including Radix Salviae Miltiorrhizae, Radix Rehmanniae, Cordyceps sinensis, hot contents including tanshinone biosynthesis, Rehmannia glutinosa continuous cropping obstacle. Copyright© by the Chinese Pharmaceutical Association.

The effect of grain size and surface area on organic matter, lignin and carbohydrate concentration, and molecular compositions in Peru Margin sediments

USGS Publications Warehouse

Bergamaschi, B.A.; Tsamakis, E.; Keil, R.G.; Eglinton, T.I.; Montlucon, D.B.; Hedges, J.I.

1997-01-01

A C-rich sediment sample from the Peru Margin was sorted into nine hydrodynamically-determined grain size fractions to explore the effect of grain size distribution and sediment surface area on organic matter content and composition. The neutral monomeric carbohydrate composition, lignin oxidation product yields, total organic carbon, and total nitrogen contents were determined independently for each size fraction, in addition to sediment surface area and abundance of biogenic opal. The percent organic carbon and percent total nitrogen were strongly related to surface area in these sediments. In turn, the distribution of surface area closely followed mass distribution among the textural size classes, suggesting hydrodynamic controls on grain size also control organic carbon content. Nevertheless, organic compositional distinctions were observed between textural size classes. Total neutral carbohydrate yields in the Peru Margin sediments were found to closely parallel trends in total organic carbon, increasing in abundance among grain size fractions in proportion to sediment surface area. Coincident with the increases in absolute abundance, rhamnose and mannose increased as a fraction of the total carbohydrate yield in concert with surface area, indicating these monomers were preferentially represented in carbohydrates associated with surfaces. Lignin oxidation product yields varied with surface area when normalized to organic carbon, suggesting that the terrestrially-derived component may be diluted by sorption of marine derived material. Lignin-based parameters suggest a separate source for terrestrially derived material associated with sand-size material as opposed to that associated with silts and clays. Copyright ?? 1997 Elsevier Science Ltd.

Progress on the Surface Nanobubble Story: What is in the bubble? Why does it exist?

PubMed

Peng, Hong; Birkett, Greg R; Nguyen, Anh V

2015-08-01

Interfaces between aqueous solutions and hydrophobic solid surfaces are important in various areas of science and technology. Many researchers have found that forces between hydrophobic surfaces in aqueous solution are significantly different from the classical DLVO theory. Long-range attractive forces (non-DLVO forces) are thought to be affected by nanoscopic gaseous domains at the interfaces. This is a review of the latest research on nanobubbles at hydrophobic surfaces from experimental and simulation studies. The review focusses on non-intrusive optical view of surface nanobubbles and gas enrichment on solid surfaces by imaging and force mapping. By use of these recent experimental data in conjunction with molecular simulation work, all major theories on surface nanobubble formation and stability are critically reviewed. Even though the current body of research cannot comprehensively explain all properties of surface nanobubbles observed, the fundamental understanding has been significantly improved. Line tension has been shown to be incapable of explaining the contact angle of nanobubbles. Dense gas layer theory provides a new explanation on both large contact angle and long-time stability. The high density of gas in these domains may significantly affect the gas-water interface which is in line with some observation made on bulk nanobubbles. Along this line of inquiry, experimental and simulation effort should be focussed on measuring the density within surface nanobubbles and the properties of the gas water interface which may be the key to explaining the stability of these nanobubbles. Copyright © 2014 Elsevier B.V. All rights reserved.

Faculty | Argonne National Laboratory

Science.gov Websites

Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Engineering JCESRJoint Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

Competitions | Argonne National Laboratory

Science.gov Websites

Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Engineering JCESRJoint Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

First principles calculations of thermal conductivity with out of equilibrium molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Puligheddu, Marcello; Gygi, Francois; Galli, Giulia

The prediction of the thermal properties of solids and liquids is central to numerous problems in condensed matter physics and materials science, including the study of thermal management of opto-electronic and energy conversion devices. We present a method to compute the thermal conductivity of solids by performing ab initio molecular dynamics at non equilibrium conditions. Our formulation is based on a generalization of the approach to equilibrium technique, using sinusoidal temperature gradients, and it only requires calculations of first principles trajectories and atomic forces. We discuss results and computational requirements for a representative, simple oxide, MgO, and compare with experiments and data obtained with classical potentials. This work was supported by MICCoM as part of the Computational Materials Science Program funded by the U.S. Department of Energy (DOE), Office of Science , Basic Energy Sciences (BES), Materials Sciences and Engineering Division under Grant DOE/BES 5J-30.

Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

DOE PAGES

Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

2015-07-28

Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

Secondary Ion Mass Spectrometry SIMS XI

NASA Astrophysics Data System (ADS)

Gillen, G.; Lareau, R.; Bennett, J.; Stevie, F.

2003-05-01

This volume contains 252 contributions presented as plenary, invited and contributed poster and oral presentations at the 11th International Conference on Secondary Ion Mass Spectrometry (SIMS XI) held at the Hilton Hotel, Walt Disney World Village, Orlando, Florida, 7 12 September, 1997. The book covers a diverse range of research, reflecting the rapid growth in advanced semiconductor characterization, ultra shallow depth profiling, TOF-SIMS and the new areas in which SIMS techniques are being used, for example in biological sciences and organic surface characterization. Papers are presented under the following categories: Isotopic SIMS Biological SIMS Semiconductor Characterization Techniques and Applications Ultra Shallow Depth Profiling Depth Profiling Fundamental/Modelling and Diffusion Sputter-Induced Topography Fundamentals of Molecular Desorption Organic Materials Practical TOF-SIMS Polyatomic Primary Ions Materials/Surface Analysis Postionization Instrumentation Geological SIMS Imaging Fundamentals of Sputtering Ion Formation and Cluster Formation Quantitative Analysis Environmental/Particle Characterization Related Techniques These proceedings provide an invaluable source of reference for both newcomers to the field and experienced SIMS users.

Surface and Thin Film Analysis during Metal Organic Vapour Phase Epitaxial Growth

NASA Astrophysics Data System (ADS)

Richter, Wolfgang

2007-06-01

In-situ analysis of epitaxial growth is the essential ingredient in order to understand the growth process, to optimize growth and last but not least to monitor or even control the epitaxial growth on a microscopic scale. In MBE (molecular beam epitaxy) in-situ analysis tools existed right from the beginning because this technique developed from Surface Science technology with all its electron based analysis tools (LEED, RHEED, PES etc). Vapour Phase Epitaxy, in contrast, remained for a long time in an empirical stage ("alchemy") because only post growth characterisations like photoluminescence, Hall effect and electrical conductivity were available. Within the last two decades, however, optical techniques were developed which provide similar capabilities as in MBE for Vapour Phase growth. I will discuss in this paper the potential of Reflectance Anisotropy Spectroscopy (RAS) and Spectroscopic Ellipsometry (SE) for the growth of thin epitaxial semiconductor layers with zincblende (GaAs etc) and wurtzite structure (GaN etc). Other techniques and materials will be also mentioned.

Effect of polar surfaces on organic molecular crystals

NASA Astrophysics Data System (ADS)

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.

76 FR 22907 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-25

...: Genes, Genomes, and Genetics Integrated Review Group; Molecular Genetics B Study Section. Date: June 1-2... . Name of Committee: Genes, Genomes, and Genetics Integrated Review Group; Molecular Genetics A Study... Reproductive Sciences; Integrated Review Group. Molecular and Cellular Endocrinology Study Section. Date: June...

NREL Receives Editors' Choice Awards for Supercomputer Research | News |

Science.gov Websites

function," Beckham said. "We followed up these molecular simulations with experimental work to Award. The awards recognize outstanding research in computational molecular science and engineering Mechanisms of Cellulose-Active Enzymes Using Molecular Simulation" at the AIChE 2014 Annual Meeting

Impact of surface chemistry

PubMed Central

Somorjai, Gabor A.; Li, Yimin

2011-01-01

The applications of molecular surface chemistry in heterogeneous catalyst technology, semiconductor-based technology, medical technology, anticorrosion and lubricant technology, and nanotechnology are highlighted in this perspective. The evolution of surface chemistry at the molecular level is reviewed, and the key roles of surface instrumentation developments for in situ studies of the gas–solid, liquid–solid, and solid–solid interfaces under reaction conditions are emphasized. PMID:20880833

Tradition in Science

ERIC Educational Resources Information Center

Heisenberg, Werner

1973-01-01

Discusses the influence of tradition in science on selection of scientific problems and methods and on the use of concepts as tools for research work. Indicates that future research studies will be directed toward the change of fundamental concepts in such fields as astrophysics, molecular biology, and environmental science. (CC)

EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

NASA Astrophysics Data System (ADS)

Weinelt, Martin; von Oppen, Felix

2012-10-01

In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on metal surfaces, focusing on electronic and vibrational spectroscopy in one case and scanning tunneling microscopy studies in the other. Original research articles describe results in many aspects of the field, including: Self-assembly, self-organization, and controlled growth of molecular layers on various substrates. Highly-ordered arrays provide model systems with extraordinary structural properties, allowing one to adjust interactions between molecules and between molecule and substrate, and can be robustly prepared from solution, an essential prerequisite for applications. Conformational or electronic switching of molecules adsorbed at metal and semiconductor surfaces. These studies highlight the elementary processes governing molecular switching at surfaces as well as the wide range of possible stimuli. Carbon-based substrates such as graphene or carbon nanotubes. These substrates are attractive due to their effective two-dimensionality which implies that switching of adsorbed molecules can effect a significant back-action on the substrate. Mechanisms of conformational switching. Several contributions study the role of electron-vibron coupling and heating in current-induced conformational switching. We hope that the collection of articles presented here will stimulate and encourage researchers in surface physics and interfacial chemistry to contribute to the still emerging field of molecular switches at surfaces. We wish to acknowledge the support and input from many colleagues in preparing this special section. A significant part of this work has been conducted in the framework of the Sonderforschungsbereich 658 Elementary Processes in Molecular Switches at Surfaces of the Deutsche Forschungsgemeinschaft, to which we are grateful for financial support. Molecular surfaces at switches contents Molecular switches at surfacesMartin Weinelt and Felix von Oppen Optically and thermally induced molecular switching processes at metal surfacesPetra Tegeder Effects of electron-vibration coupling in transport through single moleculesKatharina J Franke and Jose Ignacio Pascual Vibrational heating in single-molecule switches: an energy-dependent density-of-states approachT Brumme, R Gutierrez and G Cuniberti Reversible switching of single tin phthalocyanine molecules on the InAs(111)A surfaceC Nacci, K Kanisawa and S Fölsch Tuning the interaction between carbon nanotubes and dipole switches: the influence of the change of the nanotube-spiropyran distanceP Bluemmel, A Setaro, C Maity, S Hecht and S Reich Carbon nanotubes as substrates for molecular spiropyran-based switchesE Malic, A Setaro, P Bluemmel, Carlos F Sanz-Navarro, Pablo Ordejón, S Reich and A Knorr Ultrafast dynamics of dithienylethenes differently linked to the surface of TiO2 nanoparticlesLars Dworak, Marc Zastrow, Gehad Zeyat, Karola Rück-Braun and Josef Wachtveitl Switching the electronic properties of Co-octaethylporphyrin molecules on oxygen-covered Ni films by NO adsorptionC F Hermanns, M Bernien, A Krüger, J Miguel and W Kuch STM-switching of organic molecules on semiconductor surfaces: an above threshold density matrix model for 1,5 cyclooctadiene on Si(100)K Zenichowski, Ch Nacci, S Fölsch, J Dokić, T Klamroth and P Saalfrank A switch based on self-assembled thymineFatih Kalkan, Michael Mehlhorn and Karina Morgenstern The growth and electronic structure of azobenzene-based functional molecules on layered crystalsJ Iwicki, E Ludwig, J Buck, M Kalläne, F Köhler, R Herges, L Kipp and K Rossnagel Voltage-dependent conductance states of a single-molecule junctionY F Wang, N Néel, J Kröger, H Vázquez, M Brandbyge, B Wang and R Berndt Molecules with multiple switching units on a Au(111) surface: self-organization and single-molecule manipulationJohannes Mielke, Sofia Selvanathan, Maike Peters, Jutta Schwarz, Stefan Hecht and Leonhard Grill Preparing and regulating a bi-stable molecular switch by atomic manipulationS Sakulsermsuk, R E Palmer and P A Sloan Mixed self-assembled monolayers of azobenzene photoswitches with trifluoromethyl and cyano end groupsDaniel Brete, Daniel Przyrembel, Christian Eickhoff, Robert Carley, Wolfgang Freyer, Karsten Reuter, Cornelius Gahl and Martin Weinelt Reversible electron-induced cis-trans isomerization mediated by intermolecular interactionsCh Lotze, Y Luo, M Corso, K J Franke, R Haag and J I Pascual Transport properties of graphene functionalized with molecular switchesNiels Bode, Eros Mariani and Felix von Oppen

Electron spin resonance. Part two: a diagnostic method in the environmental sciences.

PubMed

Rhodes, Christopher J

2011-01-01

A review is presented of some of the ways in which electron spin resonance (ESR) spectroscopy may be useful to investigate systems of relevance to the environmental sciences. Specifically considered are: quantititave ESR, photocatalysis for pollution control; sorption and mobility of molecules in zeolites; free radicals produced by mechanical action and by shock waves from explosives; measurement of peroxyl radicals and nitrate radicals in air; determination of particulate matter polyaromatic hydrocarbons (PAH), soot and black carbon in air; estimation of nitrate and nitrite in vegetables and fruit; lipid-peroxidation by solid particles (silica, asbestos, coal dust); ESR of soils and other biogenic substances: formation of soil organic matter carbon capture and sequestration (CCS) and no-till farming; detection of reactive oxygen species in the photosynthetic apparatus of higher plants under light stress; molecular mobility and intracellular glasses in seeds and pollen; molecular mobility in dry cotton; characterisation of the surface of carbon black used for chromatography; ESR dating for archaeology and determining seawater levels; measurement of the quality of tea-leaves by ESR; green-catalysts and catalytic media; studies of petroleum (crude oil); fuels; methane hydrate; fuel cells; photovoltaics; source rocks; kerogen; carbonaceous chondrites to find an ESR-based marker for extraterrestrial origin; samples from the Moon taken on the Apollo 11 and Apollo 12 missions to understand space-weathering; ESR studies of organic matter in regard to oil and gas formation in the North Sea; solvation by ionic liquids as green solvents, ESR in food and nutraceutical research.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

NASA Astrophysics Data System (ADS)

Mrugalla, Florian; Kast, Stefan M.

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

PubMed

Mrugalla, Florian; Kast, Stefan M

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc05720a Click here for additional data file.

PubMed Central

Smith, J. S.

2017-01-01

Deep learning is revolutionizing many areas of science and technology, especially image, text, and speech recognition. In this paper, we demonstrate how a deep neural network (NN) trained on quantum mechanical (QM) DFT calculations can learn an accurate and transferable potential for organic molecules. We introduce ANAKIN-ME (Accurate NeurAl networK engINe for Molecular Energies) or ANI for short. ANI is a new method designed with the intent of developing transferable neural network potentials that utilize a highly-modified version of the Behler and Parrinello symmetry functions to build single-atom atomic environment vectors (AEV) as a molecular representation. AEVs provide the ability to train neural networks to data that spans both configurational and conformational space, a feat not previously accomplished on this scale. We utilized ANI to build a potential called ANI-1, which was trained on a subset of the GDB databases with up to 8 heavy atoms in order to predict total energies for organic molecules containing four atom types: H, C, N, and O. To obtain an accelerated but physically relevant sampling of molecular potential surfaces, we also proposed a Normal Mode Sampling (NMS) method for generating molecular conformations. Through a series of case studies, we show that ANI-1 is chemically accurate compared to reference DFT calculations on much larger molecular systems (up to 54 atoms) than those included in the training data set. PMID:28507695

Contact Us | Argonne National Laboratory

Science.gov Websites

Chemical Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Infrastructure Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

Classroom Resources | Argonne National Laboratory

Science.gov Websites

Chemical Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Infrastructure Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

Learning Center | Argonne National Laboratory

Science.gov Websites

Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Engineering JCESRJoint Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

First-principles Study of Phenol Hydrogenation on Pt and Ni Catalysts in Aqueous Phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, Yeohoon; Rousseau, Roger J.; Weber, Robert S.

2014-07-23

The effects of aqueous phase on the reactivity of phenol hydrogenation over Pt and Ni catalysts were investigated using density functional theory based ab initio molecular dynamics (AIMD) calculations. The adsorption of phenol and the first hydrogenation steps via three carbon positions (ortho, meta and para) with respect to the phenolic OH group were studied in both vacuum and liquid phase conditions. To gain insight into how the aqueous phase affects the metal catalyst surface, increasing water environments including singly adsorbed water molecule, mono- (9 water molecules), double layers (24 water molecules), and the bulk liquid water which (52 watermore » molecules) on the Pt(111) and the Ni(111) surfaces were modeled. Compared to the vacuum/metal interfaces, AIMD simulation results suggest that the aqueous Pt(111) and Ni(111) interfaces have a lower metal work function in the order of 0.8 - 0.9 eV, thus, making the metals in aqueous phase stronger reducing agents and poorer oxidizing agents. Phenol adsorption from the aqueous phase is found to be slightly weaker that from the vapor phase. The first hydrogenation step of phenol at the ortho position of the phenolic ring is slightly favored over the other two positions. The polarization induced by the surrounding water molecules and the solvation effect play important roles in stabilizing the transition states associated with phenol hydrogenation by lowering the barriers of 0.1 - 0.4 eV. The detailed discussion on the basis of the interfacial electrostatics from the current study is very useful to understand the nature of a broader class of metal catalyzed reactions in liquid solution phase. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences and Office of Energy Efficiency and Renewable Energy. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Nanomaterials for Cancer Precision Medicine.

PubMed

Wang, Yilong; Sun, Shuyang; Zhang, Zhiyuan; Shi, Donglu

2018-04-01

Medical science has recently advanced to the point where diagnosis and therapeutics can be carried out with high precision, even at the molecular level. A new field of "precision medicine" has consequently emerged with specific clinical implications and challenges that can be well-addressed by newly developed nanomaterials. Here, a nanoscience approach to precision medicine is provided, with a focus on cancer therapy, based on a new concept of "molecularly-defined cancers." "Next-generation sequencing" is introduced to identify the oncogene that is responsible for a class of cancers. This new approach is fundamentally different from all conventional cancer therapies that rely on diagnosis of the anatomic origins where the tumors are found. To treat cancers at molecular level, a recently developed "microRNA replacement therapy" is applied, utilizing nanocarriers, in order to regulate the driver oncogene, which is the core of cancer precision therapeutics. Furthermore, the outcome of the nanomediated oncogenic regulation has to be accurately assessed by the genetically characterized, patient-derived xenograft models. Cancer therapy in this fashion is a quintessential example of precision medicine, presenting many challenges to the materials communities with new issues in structural design, surface functionalization, gene/drug storage and delivery, cell targeting, and medical imaging. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tuning the deposition of molecular graphene nanoribbons by surface functionalization.

PubMed

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

2015-08-14

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.

Tuning the deposition of molecular graphene nanoribbons by surface functionalization

NASA Astrophysics Data System (ADS)

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.

Preparation of a silicon surface for subsequent growth of dilute nitride alloys by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Lazarenko, A. A.; Berezovskaya, T. N.; Denisov, D. V.; Sobolev, M. S.; Pirogov, E. V.; Nikitina, E. V.

2017-11-01

This article discusses the process of preparation of a silicon surface for subsequent growth of dilute nitride alloys by molecular-beam epitaxy. The method of preparation of Si (100) and Si (111) substrates was developed. This method provides reproducible high-quality silicon surface for molecular-beam epitaxy of Si-GaP heterostructures. As a result, it managed to reduce the eviction oxide temperature below 800 °C, which is an important parameter for the MBE technology.

Modeling adsorption: Investigating adsorbate and adsorbent properties

NASA Astrophysics Data System (ADS)

Webster, Charles Edwin

1999-12-01

Surface catalyzed reactions play a major role in current chemical production technology. Currently, 90% of all chemicals are produced by heterogeneously catalyzed reactions. Most of these catalyzed reactions involve adsorption, concentrating the substrate(s) (the adsorbate) on the surface of the solid (the adsorbent). Pore volumes, accessible surface areas, and the thermodynamics of adsorption are essential in the understanding of solid surface characteristics fundamental to catalyst and adsorbent screening and selection. Molecular properties such as molecular volumes and projected molecular areas are needed in order to convert moles adsorbed to surface volumes and areas. Generally, these molecular properties have been estimated from bulk properties, but many assumptions are required. As a result, different literature values are employed for these essential molecular properties. Calculated molar volumes and excluded molecular areas are determined and tabulated for a variety of molecules. Molecular dimensions of molecules are important in the understanding of molecular exclusion as well as size and shape selectivity, diffusion, and adsorbent selection. Molecular dimensions can also be used in the determination of the effective catalytic pore size of a catalyst. Adsorption isotherms, on zeolites, (crystalline mineral oxides) and amorphous solids, can be analyzed with the Multiple Equilibrium Analysis (MEA) description of adsorption. The MEA produces equilibrium constants (Ki), capacities (ni), and thermodynamic parameters (enthalpies, ΔHi, and entropies, ΔSi) of adsorption for each process. Pore volumes and accessible surface areas are calculated from the process capacities. Adsorption isotherms can also be predicted for existing and new adsorbate-adsorbent systems with the MEA. The results show that MEA has the potential of becoming a standard characterization method for microporous solids that will lead to an increased understanding of their behavior in gas adsorption and catalysis. These studies are also applicable to environmental cleanup applications, such as waste stream purification and separation procedures as well as decontamination of chemical warfare agents.

The Effect of Interactive, Three Dimensional, High Speed Simulations on High School Science Students' Conceptions of the Molecular Structure of Water.

ERIC Educational Resources Information Center

Hakerem, Gita; And Others

The Water and Molecular Networks (WAMNet) Project uses graduate student written Reduced Instruction Set Computing (RISC) computer simulations of the molecular structure of water to assist high school students learn about the nature of water. This study examined: (1) preconceptions concerning the molecular structure of water common among high…

Analysis of structural changes in active site of luciferase adsorbed on nanofabricated hydrophilic Si surface by molecular-dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishiyama, Katsuhiko; Hoshino, Tadatsugu; Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522

2007-05-21

Interactions between luciferase and a nanofabricated hydrophilic Si surface were explored by molecular-dynamics simulations. The structural changes in the active-site residues, the residues affecting the luciferin binding, and the residues affecting the bioluminescence color were smaller on the nanofabricated hydrophilic Si surface than on both a hydrophobic Si surface and a hydrophilic Si surface. The nanofabrication and wet-treatment techniques are expected to prevent the decrease in activity of luciferase on the Si surface.

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

PubMed

Ilott, Andrew J; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R

2013-10-10

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

A Course in Colloid and Surface Science.

ERIC Educational Resources Information Center

Scamehorn, John F.

1984-01-01

Describes a course for chemical engineers, chemists, and petroleum engineers that focuses on colloid and surface science. Major topic areas in the course include capillarity, surface thermodynamics, adsorption contact angle, micelle formation, solubilization in micelles, emulsions, foams, and applications. (JN)

Lunar Science Enabled by the Deep Space Gateway and PHASR Rover

NASA Astrophysics Data System (ADS)

Bakambu, J. N.; Shaw, A.; Fulford, P.; Osinski, G.; Bourassa, M.; Rehmatullah, F.; Zanetti, M.; Rembala, R.

2018-02-01

The Deep Space Gateway will be a tremendous boon to lunar surface science. It will enable the PHASR Rover, a concept for a Canadian rover system, with international contributions and the goal of sample acquisition and lunar surface science.

Developing Science Operations Concepts for the Future of Planetary Surface Exploration

NASA Astrophysics Data System (ADS)

Young, K. E.; Bleacher, J. E.; Rogers, A. D.; McAdam, A.; Evans, C. A.; Graff, T. G.; Garry, W. B.; Whelley, P. L.; Scheidt, S.; Carter, L.; Coan, D.; Reagan, M.; Glotch, T.; Lewis, R.

2017-02-01

Human exploration of other planetary bodies is crucial in answering critical science questions about our solar system. As we seek to put humans on other surfaces by 2050, we must understand the science operations concepts needed for planetary EVA.

Materials chemistry. Composition-matched molecular "solders" for semiconductors.

PubMed

Dolzhnikov, Dmitriy S; Zhang, Hao; Jang, Jaeyoung; Son, Jae Sung; Panthani, Matthew G; Shibata, Tomohiro; Chattopadhyay, Soma; Talapin, Dmitri V

2015-01-23

We propose a general strategy to synthesize largely unexplored soluble chalcogenidometallates of cadmium, lead, and bismuth. These compounds can be used as "solders" for semiconductors widely used in photovoltaics and thermoelectrics. The addition of solder helped to bond crystal surfaces and link nano- or mesoscale particles together. For example, CdSe nanocrystals with Na2Cd2Se3 solder was used as a soluble precursor for CdSe films with electron mobilities exceeding 300 square centimeters per volt-second. CdTe, PbTe, and Bi2Te3 powders were molded into various shapes in the presence of a small additive of composition-matched chalcogenidometallate or chalcogel, thus opening new design spaces for semiconductor technologies. Copyright © 2015, American Association for the Advancement of Science.

Impacting the Science Community through Teacher Development: Utilizing Virtual Learning.

PubMed

Boulay, Rachel; van Raalte, Lisa

2014-01-01

Commitment to the STEM (science, technology, engineering, math) pipeline is slowly declining despite the need for professionals in the medical field. Addressing this, the John A. Burns School of Medicine developed a summer teacher-training program with a supplemental technology-learning component to improve science teachers' knowledge and skills of Molecular Biology. Subsequently, students' skills, techniques, and application of molecular biology are impacted. Science teachers require training that will prepare them for educating future professionals and foster interest in the medical field. After participation in the program and full access to the virtual material, twelve high school science teachers completed a final written reflective statement to evaluate their experiences. Using thematic analysis, knowledge and classroom application were investigated in this study. Results were two-fold: teachers identified difference areas of gained knowledge from the teacher-training program and teachers' reporting various benefits in relation to curricula development after participating in the program. It is concluded that participation in the program and access to the virtual material will impact the science community by updating teacher knowledge and positively influencing students' experience with science.

Detailed methodology for high resolution scanning electron microscopy (SEM) of murine malaria parasitized-erythrocytes.

PubMed

Hayakawa, Eri H; Matsuoka, Hiroyuki

2016-10-01

Scanning electron microscopy (SEM) is a powerful tool used to investigate object surfaces and has been widely applied in both material science and biology. With respect to the study of malaria, SEM revealed that erythrocytes infected with Plasmodium falciparum, a human parasite, display 'knob-like' structures on their surface comprising parasitized proteins. However, detailed methodology for SEM studies of malaria parasites is lacking in the literature making such studies challenging. Here, we provide a step-by-step guide to preparing Plasmodium-infected erythrocytes from two mouse strains for SEM analysis with minimal structural deterioration. We tested three species of murine malaria parasites, P. berghei, P. yoelii, and P. chabaudi, as well as non-parasitized human erythrocytes and P. falciparum-infected erythrocytes for comparisons. Our data demonstrated that the surface structures of parasitized erythrocytes between the three species of murine parasites in the two different strains of mice were indistinguishable and no surface alterations were observed in P. falciparum-erythrocytes. Our SEM observations contribute towards an understanding of the molecular mechanisms of parasite maturation in the erythrocyte cytoplasm and, along with future studies using our detailed methodology, may help to gain insight into the clinical phenomena of human malaria. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Shape optimization of self-avoiding curves

NASA Astrophysics Data System (ADS)

Walker, Shawn W.

2016-04-01

This paper presents a softened notion of proximity (or self-avoidance) for curves. We then derive a sensitivity result, based on shape differential calculus, for the proximity. This is combined with a gradient-based optimization approach to compute three-dimensional, parameterized curves that minimize the sum of an elastic (bending) energy and a proximity energy that maintains self-avoidance by a penalization technique. Minimizers are computed by a sequential-quadratic-programming (SQP) method where the bending energy and proximity energy are approximated by a finite element method. We then apply this method to two problems. First, we simulate adsorbed polymer strands that are constrained to be bound to a surface and be (locally) inextensible. This is a basic model of semi-flexible polymers adsorbed onto a surface (a current topic in material science). Several examples of minimizing curve shapes on a variety of surfaces are shown. An advantage of the method is that it can be much faster than using molecular dynamics for simulating polymer strands on surfaces. Second, we apply our proximity penalization to the computation of ideal knots. We present a heuristic scheme, utilizing the SQP method above, for minimizing rope-length and apply it in the case of the trefoil knot. Applications of this method could be for generating good initial guesses to a more accurate (but expensive) knot-tightening algorithm.

What Is Psychosis?

MedlinePlus

... our Questions & Answers page. Share Science News About Schizophrenia Disorders Share Molecular Signatures March 1, 2018 Molecular ... Dish as in Brain August 18, 2017 More Schizophrenia Research Clinical Trials: Current Studies on Schizophrenia PubMed: ...

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

Seth M. Noone | NREL

Science.gov Websites

Education M.S., Biomedical Basic Science, Department of Biochemistry and Molecular Genetics, University of Interaction with Histones H3 and H4," Molecular and Cellular Biology (2013) "The Lysine 48 and Cerevisiae," Molecular and Cellular Biology (2007) View all NREL Publications for Seth M. Noone

76 FR 27652 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-12

... Integrated Review Group, Molecular Genetics C Study Section. Date: June 23-24, 2011. Time: 8 a.m. to 6 p.m... . Name of Committee: Interdisciplinary Molecular Sciences and Training Integrated Review Group, Enabling..., Bethesda, MD 20892, (301) 435-1782, [email protected] . Name of Committee: Molecular, Cellular and...

About Educational Programs | Argonne National Laboratory

Science.gov Websites

Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Engineering JCESRJoint Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

Education Staff Directory | Argonne National Laboratory

Science.gov Websites

Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Engineering JCESRJoint Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

Computer Analogies: Teaching Molecular Biology and Ecology.

ERIC Educational Resources Information Center

Rice, Stanley; McArthur, John

2002-01-01

Suggests that computer science analogies can aid the understanding of gene expression, including the storage of genetic information on chromosomes. Presents a matrix of biology and computer science concepts. (DDR)

Young Scientists Discuss Recent Advances, Future Challenges.

ERIC Educational Resources Information Center

Baum, Rudy M.

1989-01-01

Discusses a National Academy of Science forum at which a group of outstanding young researchers in astronomy, molecular and developmental biology, physics, chemistry, mathematics, atmospheric science, and materials science met for three days of formal presentations and informal conversations. Provides a short synopsis of major speakers. (MVL)

Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

PubMed

Chang, Chia-Ching; Sun, Kien Wen; Lee, Shang-Fan; Kan, Lou-Sing

2007-04-01

The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

Surface science studies of ethene containing model interstellar ices

NASA Astrophysics Data System (ADS)

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.

A Cu/Pt Near-Surface Alloy for Water-Gas Shift Catalysis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knudsen, Jan; Nilekar, Anand U.; Vang, Ronnie T.

2007-05-01

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The primary route to hydrogen production from fossil fuels involves the water-gas shift (WGS) reaction, and an improvement in the efficiency of WGS catalysts could therefore lead to a major leap forward in the realization of hydrogen economy. On the basis of a combination of high-resolution scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory (DFT) calculations, we suggestmore » the existence of a new thermodynamically stable Cu/Pt near-surface alloy (NSA). Temperature-programmed desorption and DFT reveal that this Cu/Pt NSA binds CO significantly more weakly than does Pt alone, thereby implying a considerable reduction in the potential for CO poisoning of the Cu/Pt NSA surface as compared to that of pure Pt. In addition, DFT calculations show that this Cu/Pt NSA is able to activate H2O easily, which is the rate-determining step for the WGS on several metal surfaces, and, at the same time, to bind the products of that reaction and formate intermediates rather weakly, thus avoiding possible poisoning of the catalyst surface. The Cu/Pt NSA is thus a promising candidate for an improved WGS catalyst.« less

Nanostructured Surfaces and Detection Instrumentation for Photonic Crystal Enhanced Fluorescence

PubMed Central

Chaudhery, Vikram; George, Sherine; Lu, Meng; Pokhriyal, Anusha; Cunningham, Brian T.

2013-01-01

Photonic crystal (PC) surfaces have been demonstrated as a compelling platform for improving the sensitivity of surface-based fluorescent assays used in disease diagnostics and life science research. PCs can be engineered to support optical resonances at specific wavelengths at which strong electromagnetic fields are utilized to enhance the intensity of surface-bound fluorophore excitation. Meanwhile, the leaky resonant modes of PCs can be used to direct emitted photons within a narrow range of angles for more efficient collection by a fluorescence detection system. The multiplicative effects of enhanced excitation combined with enhanced photon extraction combine to provide improved signal-to-noise ratios for detection of fluorescent emitters, which in turn can be used to reduce the limits of detection of low concentration analytes, such as disease biomarker proteins. Fabrication of PCs using inexpensive manufacturing methods and materials that include replica molding on plastic, nano-imprint lithography on quartz substrates result in devices that are practical for single-use disposable applications. In this review, we will describe the motivation for implementing high-sensitivity fluorescence detection in the context of molecular diagnosis and gene expression analysis though the use of PC surfaces. Recent efforts to improve the design and fabrication of PCs and their associated detection instrumentation are summarized, including the use of PCs coupled with Fabry-Perot cavities and external cavity lasers. PMID:23624689

Molecular insight into the nanoconfined calcite–solution interface

PubMed Central

Diao, Yijue; Espinosa-Marzal, Rosa M.

2016-01-01

Little is known about the influence of nanoconfinement on calcium carbonate mineralization. Here, colloidal probe atomic force microscopy is used to confine the calcite–solution interface with a silica microsphere and to measure Derjaguin–Landau–Verwey–Overbeek (DLVO) and non-DLVO forces as a function of the calcium concentration, also after charge reversal of both surfaces occurs. Through the statistical analysis of the oscillatory component of a strong hydration force, the subnanometer interfacial structure of the confined atomically flat calcite is resolved in aqueous solution. By applying a mechanical work, both water and hydrated counterions are squeezed out from the nanoconfined solution, leaving the calcite surface more negatively charged than the analogous unconfined surfaces. Layer size and applied work allow a distinction between the hydration states of the counterions in the Stern layer; we propose counterions to be inner- and outer-sphere calcium ions, with a population of inner-sphere calcium ions larger than on unconfined calcite surfaces. It is also shown that the composition of the nanoconfined solution can be tuned by varying calcium concentration. This is a fundamental study of DLVO and hydration forces, and of their connection, on atomically flat calcite. More broadly, our work scrutinizes the greatly unexplored relation between surface science and confined mineralization, with implications for diverse areas of inquiry, such as nanoconfined biomineralization, CO2 sequestration in porous aquifers, and pressure solution and crystallization in confined hydrosystems. PMID:27790988

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

PubMed Central

Raschke, Tanya M.; Tsai, Jerry; Levitt, Michael

2001-01-01

The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 ± 6 cal/mol⋅Å2. The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol⋅Å2. Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology. PMID:11353861

Technology Commercialization and Partnerships | Argonne National Laboratory

Science.gov Websites

Transformations IGSBInstitute for Genomics and Systems Biology IMEInstitute for Molecular Engineering JCESRJoint Science Center SBCStructural Biology Center Energy.gov U.S. Department of Energy Office of Science

Espionage scandal leads science news.

PubMed

Haley, S M

2001-05-18

Two Japanese molecular biologists are charged with espionage in a case that could strain scientific relations between the U.S. and Japan, report both Nature and Science in their top stories this week.

Self assembled molecular monolayers on high surface area materials as molecular getters

DOEpatents

King, David E.; Herdt, Gregory C.; Czanderna, Alvin W.

1997-01-01

The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium.

Self assembled molecular monolayers on high surface area materials as molecular getters

DOEpatents

King, D.E.; Herdt, G.C.; Czanderna, A.W.

1997-01-07

The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium. 9 figs.

Covalent Immobilization of Microtubules on Glass Surfaces for Molecular Motor Force Measurements and Other Single-Molecule Assays

PubMed Central

Nicholas, Matthew P.; Rao, Lu; Gennerich, Arne

2014-01-01

Rigid attachment of microtubules (MTs) to glass cover slip surfaces is a prerequisite for a variety of microscopy experiments in which MTs are used as substrates for MT-associated proteins, such as the molecular motors kinesin and cytoplasmic dynein. We present an MT-surface coupling protocol in which aminosilanized glass is formylated using the cross-linker glutaraldehyde, fluorescence-labeled MTs are covalently attached, and the surface is passivated with highly pure beta-casein. The technique presented here yields rigid MT immobilization while simultaneously blocking the remaining glass surface against nonspecific binding by polystyrene optical trapping microspheres. This surface chemistry is straightforward and relatively cheap and uses a minimum of specialized equipment or hazardous reagents. These methods provide a foundation for a variety of optical tweezers experiments with MT-associated molecular motors and may also be useful in other assays requiring surface-immobilized proteins. PMID:24633798

An advanced molecule-surface scattering instrument for study of vibrational energy transfer in gas-solid collisions.

PubMed

Ran, Qin; Matsiev, Daniel; Wodtke, Alec M; Auerbach, Daniel J

2007-10-01

We describe an advanced and highly sensitive instrument for quantum state-resolved molecule-surface energy transfer studies under ultrahigh vacuum (UHV) conditions. The apparatus includes a beam source chamber, two differential pumping chambers, and a UHV chamber for surface preparation, surface characterization, and molecular beam scattering. Pulsed and collimated supersonic molecular beams are generated by expanding target molecule mixtures through a home-built pulsed nozzle, and excited quantum state-selected molecules were prepared via tunable, narrow-band laser overtone pumping. Detection systems have been designed to measure specific vibrational-rotational state, time-of-flight, angular and velocity distributions of molecular beams coming to and scattered off the surface. Facilities are provided to clean and characterize the surface under UHV conditions. Initial experiments on the scattering of HCl(v = 0) from Au(111) show many advantages of this new instrument for fundamental studies of the energy transfer at the gas-surface interface.

A Surface Science Paradigm for a Post-Huygens Titan Mission

NASA Technical Reports Server (NTRS)

Zimmerman, Wayne; Lunine, Jonathan; Lorenz, Ralph

2004-01-01

With the Cassini-Huygens atmospheric probe drop-off mission fast approaching, it is essential that scientists and engineers start scoping potential follow-on surface science missions. This paper provides a summary of the first year of a two year design study which examines in detail the desired surface science measurements and resolution, potential instrument suite, and complete payload delivery system. Also provided are design concepts for both an aerial inflatable mobility platform and deployable instrument sonde. The tethered deployable sonde provides the capability to sample nearsurface atmosphere, sub-surface liquid (if it exists), and surface solid material. Actual laboratory tests of the amphibious sonde prototype are also presented.

Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23.

PubMed

Velazquez, Hector A; Riccardi, Demian; Xiao, Zhousheng; Quarles, Leigh Darryl; Yates, Charless Ryan; Baudry, Jerome; Smith, Jeremy C

2018-02-01

Ensemble docking is now commonly used in early-stage in silico drug discovery and can be used to attack difficult problems such as finding lead compounds which can disrupt protein-protein interactions. We give an example of this methodology here, as applied to fibroblast growth factor 23 (FGF23), a protein hormone that is responsible for regulating phosphate homeostasis. The first small-molecule antagonists of FGF23 were recently discovered by combining ensemble docking with extensive experimental target validation data (Science Signaling, 9, 2016, ra113). Here, we provide a detailed account of how ensemble-based high-throughput virtual screening was used to identify the antagonist compounds discovered in reference (Science Signaling, 9, 2016, ra113). Moreover, we perform further calculations, redocking those antagonist compounds identified in reference (Science Signaling, 9, 2016, ra113) that performed well on drug-likeness filters, to predict possible binding regions. These predicted binding modes are rescored with the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) approach to calculate the most likely binding site. Our findings suggest that the antagonist compounds antagonize FGF23 through the disruption of protein-protein interactions between FGF23 and fibroblast growth factor receptor (FGFR). © 2017 John Wiley & Sons A/S.

Accelerators for Discovery Science and Security applications

NASA Astrophysics Data System (ADS)

Todd, A. M. M.; Bluem, H. P.; Jarvis, J. D.; Park, J. H.; Rathke, J. W.; Schultheiss, T. J.

2015-05-01

Several Advanced Energy Systems (AES) accelerator projects that span applications in Discovery Science and Security are described. The design and performance of the IR and THz free electron laser (FEL) at the Fritz-Haber-Institut der Max-Planck-Gesellschaft in Berlin that is now an operating user facility for physical chemistry research in molecular and cluster spectroscopy as well as surface science, is highlighted. The device was designed to meet challenging specifications, including a final energy adjustable in the range of 15-50 MeV, low longitudinal emittance (<50 keV-psec) and transverse emittance (<20 π mm-mrad), at more than 200 pC bunch charge with a micropulse repetition rate of 1 GHz and a macropulse length of up to 15 μs. Secondly, we will describe an ongoing effort to develop an ultrafast electron diffraction (UED) source that is scheduled for completion in 2015 with prototype testing taking place at the Brookhaven National Laboratory (BNL) Accelerator Test Facility (ATF). This tabletop X-band system will find application in time-resolved chemical imaging and as a resource for drug-cell interaction analysis. A third active area at AES is accelerators for security applications where we will cover some top-level aspects of THz and X-ray systems that are under development and in testing for stand-off and portal detection.

Manipulating and Monitoring On-Surface Biological Reactions by Light-Triggered Local pH Alterations.

PubMed

Peretz-Soroka, Hagit; Pevzner, Alexander; Davidi, Guy; Naddaka, Vladimir; Kwiat, Moria; Huppert, Dan; Patolsky, Fernando

2015-07-08

Significant research efforts have been dedicated to the integration of biological species with electronic elements to yield smart bioelectronic devices. The integration of DNA, proteins, and whole living cells and tissues with electronic devices has been developed into numerous intriguing applications. In particular, the quantitative detection of biological species and monitoring of biological processes are both critical to numerous areas of medical and life sciences. Nevertheless, most current approaches merely focus on the "monitoring" of chemical processes taking place on the sensing surfaces, and little efforts have been invested in the conception of sensitive devices that can simultaneously "control" and "monitor" chemical and biological reactions by the application of on-surface reversible stimuli. Here, we demonstrate the light-controlled fine modulation of surface pH by the use of photoactive molecularly modified nanomaterials. Through the use of nanowire-based FET devices, we showed the capability of modulating the on-surface pH, by intensity-controlled light stimulus. This allowed us simultaneously and locally to control and monitor pH-sensitive biological reactions on the nanodevices surfaces, such as the local activation and inhibition of proteolytic enzymatic processes, as well as dissociation of antigen-antibody binding interactions. The demonstrated capability of locally modulating the on-surface effective pH, by a light stimuli, may be further applied in the local control of on-surface DNA hybridization/dehybridization processes, activation or inhibition of living cells processes, local switching of cellular function, local photoactivation of neuronal networks with single cell resolution and so forth.

Exploring the relationship between the engineering and physical sciences and the health and life sciences by advanced bibliometric methods.

PubMed

Waltman, Ludo; van Raan, Anthony F J; Smart, Sue

2014-01-01

We investigate the extent to which advances in the health and life sciences (HLS) are dependent on research in the engineering and physical sciences (EPS), particularly physics, chemistry, mathematics, and engineering. The analysis combines two different bibliometric approaches. The first approach to analyze the 'EPS-HLS interface' is based on term map visualizations of HLS research fields. We consider 16 clinical fields and five life science fields. On the basis of expert judgment, EPS research in these fields is studied by identifying EPS-related terms in the term maps. In the second approach, a large-scale citation-based network analysis is applied to publications from all fields of science. We work with about 22,000 clusters of publications, each representing a topic in the scientific literature. Citation relations are used to identify topics at the EPS-HLS interface. The two approaches complement each other. The advantages of working with textual data compensate for the limitations of working with citation relations and the other way around. An important advantage of working with textual data is in the in-depth qualitative insights it provides. Working with citation relations, on the other hand, yields many relevant quantitative statistics. We find that EPS research contributes to HLS developments mainly in the following five ways: new materials and their properties; chemical methods for analysis and molecular synthesis; imaging of parts of the body as well as of biomaterial surfaces; medical engineering mainly related to imaging, radiation therapy, signal processing technology, and other medical instrumentation; mathematical and statistical methods for data analysis. In our analysis, about 10% of all EPS and HLS publications are classified as being at the EPS-HLS interface. This percentage has remained more or less constant during the past decade.

Exploring the Relationship between the Engineering and Physical Sciences and the Health and Life Sciences by Advanced Bibliometric Methods

PubMed Central

Waltman, Ludo; van Raan, Anthony F. J.; Smart, Sue

2014-01-01

We investigate the extent to which advances in the health and life sciences (HLS) are dependent on research in the engineering and physical sciences (EPS), particularly physics, chemistry, mathematics, and engineering. The analysis combines two different bibliometric approaches. The first approach to analyze the ‘EPS-HLS interface’ is based on term map visualizations of HLS research fields. We consider 16 clinical fields and five life science fields. On the basis of expert judgment, EPS research in these fields is studied by identifying EPS-related terms in the term maps. In the second approach, a large-scale citation-based network analysis is applied to publications from all fields of science. We work with about 22,000 clusters of publications, each representing a topic in the scientific literature. Citation relations are used to identify topics at the EPS-HLS interface. The two approaches complement each other. The advantages of working with textual data compensate for the limitations of working with citation relations and the other way around. An important advantage of working with textual data is in the in-depth qualitative insights it provides. Working with citation relations, on the other hand, yields many relevant quantitative statistics. We find that EPS research contributes to HLS developments mainly in the following five ways: new materials and their properties; chemical methods for analysis and molecular synthesis; imaging of parts of the body as well as of biomaterial surfaces; medical engineering mainly related to imaging, radiation therapy, signal processing technology, and other medical instrumentation; mathematical and statistical methods for data analysis. In our analysis, about 10% of all EPS and HLS publications are classified as being at the EPS-HLS interface. This percentage has remained more or less constant during the past decade. PMID:25360616

Even More Brain-Powered Science: Teaching and Learning with Discrepant Events. Brain-Powered Science Series

ERIC Educational Resources Information Center

O'Brien, Thomas

2011-01-01

How can water and a penny demonstrate the power of mathematics and molecular theory? Do spelling and punctuation really matter to the human brain? The third of Thomas O'Brien's books designed for 5-12 grade science teachers, "Even More Brain-Powered Science" uses the questions above and 11 other inquiry-oriented discrepant events--experiments or…

A direct evidence of vibrationally delocalized response at ice surface.

PubMed

Ishiyama, Tatsuya; Morita, Akihiro

2014-11-14

Surface-specific vibrational spectroscopic responses at isotope diluted ice and amorphous ice are investigated by molecular dynamics (MD) simulations combined with quantum mechanics/molecular mechanics calculations. The intense response specific to the ordinary crystal ice surface is predicted to be significantly suppressed in the isotopically diluted and amorphous ices, demonstrating the vibrational delocalization at the ordinary ice surface. The collective vibration at the ice surface is also analyzed with varying temperature by the MD simulation.

InP and GaAs characterization with variable stoichiometry obtained by molecular spray

NASA Technical Reports Server (NTRS)

Massies, J.; Linh, N. T.; Olivier, J.; Faulconnier, P.; Poirier, R.

1979-01-01

Both InP and GaAs surfaces were studied in parallel. A molecular spray technique was used to obtain two semiconductor surfaces with different superficial compositions. The structures of these surfaces were examined by electron diffraction. Electron energy loss was measured spectroscopically in order to determine surface electrical characteristics. The results are used to support conclusions relative to the role of surface composition in establishing a Schottky barrier effect in semiconductor devices.

Surface chemistry and moisture sorption properties of wood coated with multifunctional alkoxysilanes by sol-gel process

Treesearch

Mandla A. Tshabalala; Peter Kingshott; Mark R. VanLandingham; David Plackett

2003-01-01

Sol-gel surface deposition of a hydrophobic polysiloxane coating on wood was accomplished by using a mixture of a low molecular weight multifunctional alkoxysilane, methyltrimethoxysilane (MTMOS), and a high molecular weight multifunctional alkoxysilane, hexadecyltrimethoxysilane (HDTMOS). Investigation of the surface chemistry and morphology of the wood specimens by...

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

NASA Astrophysics Data System (ADS)

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.

Ab Initio Study of KCl and AgCl Clusters.

NASA Astrophysics Data System (ADS)

McKeough, James; Hira, Ajit; Cathey, Tommy; Valdez, Alexandra

This paper presents a theoretical study of molecular clusters that examines the chemical and physical properties of small KnCln and AgnCln clusters (n = 2 - 24). Due to combinations of attractive and repulsive long-range forces, such clusters exhibit structural and dynamical behavior different from that of homogeneous clusters. The potentially important role of these molecular species in biochemical and medicinal processes is widely known. This work applies the hybrid ab initio methods to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations were performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. Potential design of new medicinal drugs is explored. We will also investigate model and material dependence of the results. AMP program of the National Science Foundation.

Molecular simulation of hydrophobin adsorption at an oil-water interface.

PubMed

Cheung, David L

2012-06-12

Hydrophobins are small, amphiphilic proteins expressed by strains of filamentous fungi. They fulfill a number of biological functions, often related to adsorption at hydrophobic interfaces, and have been investigated for a number of applications in materials science and biotechnology. In order to understand the biological function and applications of these proteins, a microscopic picture of the adsorption of these proteins at interfaces is needed. Using molecular dynamics simulations with a chemically detailed coarse-grained potential, the behavior of typical hydrophobins at the water-octane interface is studied. Calculation of the interfacial adsorption strengths indicates that the adsorption is essentially irreversible, with adsorption strengths of the order of 100 k(B)T (comparable to values determined for synthetic nanoparticles but significantly larger than small molecule surfactants and biomolecules). The protein structure at the interface is unchanged at the interface, which is consistent with the biological function of these proteins. Comparison of native proteins with pseudoproteins that consist of uniform particles shows that the surface structure of these proteins has a large effect on the interfacial adsorption strengths, as does the flexibility of the protein.

A cargo-sorting DNA robot.

PubMed

Thubagere, Anupama J; Li, Wei; Johnson, Robert F; Chen, Zibo; Doroudi, Shayan; Lee, Yae Lim; Izatt, Gregory; Wittman, Sarah; Srinivas, Niranjan; Woods, Damien; Winfree, Erik; Qian, Lulu

2017-09-15

Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their destinations allows for a simple robot design: a single-stranded DNA with one leg and two foot domains for walking, and one arm and one hand domain for picking up and dropping off cargos. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers them to specified destinations until all molecules are sorted into two distinct piles. The robot is designed to perform a random walk without any energy supply. Exploiting this feature, a single robot can repeatedly sort multiple cargos. Localization on DNA origami allows for distinct cargo-sorting tasks to take place simultaneously in one test tube or for multiple robots to collectively perform the same task. Copyright © 2017, American Association for the Advancement of Science.

Questions and Answers about Psychosis

MedlinePlus

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DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, A. A.; Hesjedal, T.; Diamond Light Source, Didcot OX11 0DE

We present a miniaturized molecular beam epitaxy (miniMBE) system with an outer diameter of 206 mm, optimized for flexible and high-throughput operation. The three-chamber system, used here for oxide growth, consists of a sample loading chamber, a storage chamber, and a growth chamber. The growth chamber is equipped with eight identical effusion cell ports with linear shutters, one larger port for either a multi-pocket electron beam evaporator or an oxygen plasma source, an integrated cryoshroud, retractable beam-flux monitor or quartz-crystal microbalance, reflection high energy electron diffraction, substrate manipulator, main shutter, and quadrupole mass spectrometer. The system can be combined withmore » ultrahigh vacuum (UHV) end stations on synchrotron and neutron beamlines, or equivalently with other complex surface analysis systems, including low-temperature scanning probe microscopy systems. Substrate handling is compatible with most UHV surface characterization systems, as the miniMBE can accommodate standard surface science sample holders. We introduce the design of the system, and its specific capabilities and operational parameters, and we demonstrate the epitaxial thin film growth of magnetoelectric Cr{sub 2}O{sub 3} on c-plane sapphire and ferrimagnetic Fe{sub 3}O{sub 4} on MgO (001)« less

Label-Enhanced Surface Plasmon Resonance: A New Concept for Improved Performance in Optical Biosensor Analysis

PubMed Central

Granqvist, Niko; Hanning, Anders; Eng, Lars; Tuppurainen, Jussi; Viitala, Tapani

2013-01-01

Surface plasmon resonance (SPR) is a well-established optical biosensor technology with many proven applications in the study of molecular interactions as well as in surface and material science. SPR is usually applied in the label-free mode which may be advantageous in cases where the presence of a label may potentially interfere with the studied interactions per se. However, the fundamental challenges of label-free SPR in terms of limited sensitivity and specificity are well known. Here we present a new concept called label-enhanced SPR, which is based on utilizing strongly absorbing dye molecules in combination with the evaluation of the full shape of the SPR curve, whereby the sensitivity as well as the specificity of SPR is significantly improved. The performance of the new label-enhanced SPR method was demonstrated by two simple model assays: a small molecule assay and a DNA hybridization assay. The small molecule assay was used to demonstrate the sensitivity enhancement of the method, and how competitive assays can be used for relative affinity determination. The DNA assay was used to demonstrate the selectivity of the assay, and the capabilities in eliminating noise from bulk liquid composition variations. PMID:24217357

Challenges in the Development of Functional Assays of Membrane Proteins

PubMed Central

Tiefenauer, Louis; Demarche, Sophie

2012-01-01

Lipid bilayers are natural barriers of biological cells and cellular compartments. Membrane proteins integrated in biological membranes enable vital cell functions such as signal transduction and the transport of ions or small molecules. In order to determine the activity of a protein of interest at defined conditions, the membrane protein has to be integrated into artificial lipid bilayers immobilized on a surface. For the fabrication of such biosensors expertise is required in material science, surface and analytical chemistry, molecular biology and biotechnology. Specifically, techniques are needed for structuring surfaces in the micro- and nanometer scale, chemical modification and analysis, lipid bilayer formation, protein expression, purification and solubilization, and most importantly, protein integration into engineered lipid bilayers. Electrochemical and optical methods are suitable to detect membrane activity-related signals. The importance of structural knowledge to understand membrane protein function is obvious. Presently only a few structures of membrane proteins are solved at atomic resolution. Functional assays together with known structures of individual membrane proteins will contribute to a better understanding of vital biological processes occurring at biological membranes. Such assays will be utilized in the discovery of drugs, since membrane proteins are major drug targets.

Cellular response of preosteoblasts to nanograined/ultrafine-grained structures.

PubMed

Misra, R D K; Thein-Han, W W; Pesacreta, T C; Hasenstein, K H; Somani, M C; Karjalainen, L P

2009-06-01

Metallic materials with submicron- to nanometer-sized grains provide surfaces that are different from conventional polycrystalline materials because of the large proportion of grain boundaries with high free energy. In the study described here, the combination of cellular and molecular biology, materials science and engineering advances our understanding of cell-substrate interactions, especially the cellular activity between preosteoblasts and nanostructured metallic surfaces. Experiments on the effect of nano-/ultrafine grains have shown that cell attachment, proliferation, viability, morphology and spread are favorably modulated and significantly different from conventional coarse-grained structures. Additionally, immunofluorescence studies demonstrated stronger vinculin signals associated with actin stress fibers in the outer regions of the cells and cellular extensions on nanograined/ultrafine-grained substrate. These observations suggest enhanced cell-substrate interaction and activity. The differences in the cellular response on nanograined/ultrafine-grained and coarse-grained substrates are attributed to grain size and degree of hydrophilicity. The outcomes of the study are expected to reduce challenges to engineer bulk nanostructured materials with specific physical and surface properties for medical devices with improved cellular attachment and response. The data lay the foundation for a new branch of nanostructured materials for biomedical applications.

Time-resolved molecular imaging

NASA Astrophysics Data System (ADS)

Xu, Junliang; Blaga, Cosmin I.; Agostini, Pierre; DiMauro, Louis F.

2016-06-01

Time-resolved molecular imaging is a frontier of ultrafast optical science and physical chemistry. In this article, we review present and future key spectroscopic and microscopic techniques for ultrafast imaging of molecular dynamics and show their differences and connections. The advent of femtosecond lasers and free electron x-ray lasers bring us closer to this goal, which eventually will extend our knowledge about molecular dynamics to the attosecond time domain.

Enhancing Return from Lunar Surface Missions via the Deep Space Gateway

NASA Astrophysics Data System (ADS)

Chavers, D. G.; Whitley, R. J.; Percy, T. K.; Needham, D. H.; Polsgrove, T. T.

2018-02-01

The Deep Space Gateway (DSG) will facilitate access to and communication with lunar surface assets. With a science airlock, docking port, and refueling capability in an accessible orbit, the DSG will enable high priority science across the lunar surface.

Transport of Ice on the Surface of Iapetus

NASA Astrophysics Data System (ADS)

Galuba, Götz G.

2014-11-01

The global black-and-white dichotomy as well as the dark floors and rims of equatorial craters on the Saturnian moon Iapetus can be explained by ice migration driven by a thermal feedback [1]. All icy moons in the Jovian and Saturnian systems are - with the exception of Titan - airless bodies. Yet it is unique, how these two types of surface features on Iapetus look. A physical model of the processes of absorption, sublimation and deposition was developed and a computational model that simulates ice migration of volatiles under these circumstances derived. The model tessellates the surfaces of an airless body into triangles of equal size that can each have different surface properties. These properties evolve while the model simulates a long-term development. A rate network of net migration is calculated from sublimation and redeposition under the assumptions ofa. a slowly rotating bodyb. undisturbed ballistic molecular trajectoriesc. isotropic emissiond. Maxwellian speed distributione. high sticking coefficients of the surfaces.The assumptions (b.) to (e.) are equally valid for all bigger outer solar system icy moons (except Titan). The very first assumption however is not equally valid throughout the moons of the outer solar system. Callisto being in many regards similar to Iapetus still has a five times higher rotation rate. So global effects depending on slow rotation are more profound on Iapetus. The computer model is complemented by a model for local ice migration from craters.First results show, that the global timescale of albedo change in our model is of the same order of magnitude as in the supporting material to [1] with a tendency towards slightly faster 2 Gyr instead of ~2.4 Gyr) darkening compared to the "Model B". The time rate of local crater darkening rates lies between the global darkening rate and rate of the opposing brightening effect as estimated in [2] to (τ between 10 and 100 MYr).[1] Formation of Iapetus’ Extreme Albedo Dichotomy by Exogenically Triggered Thermal Ice Migration, John R. Spencer , Tilmann Denk, Science 22, Vol. 327, January 2010.[2] Iapetus: Unique Surface Properties and a Global Color Dichotomy from Cassini Imaging T. Denk et al., Science 22, Vol. 327, January 2010.

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

NASA Astrophysics Data System (ADS)

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 review of molecular phase separation in binary self-assembled monolayers of thiols on gold surfaces

NASA Astrophysics Data System (ADS)

Ong, Quy; Nianias, Nikolaos; Stellacci, Francesco

2017-09-01

Binary self-assembled monolayers (SAMs) on gold surfaces have been known to undergo molecular phase separation to various degrees and have been subject to both experimental and theoretical studies. On gold nanoparticles in particular, binary SAMs ligand shells display intriguing morphologies. Consequently, unexpected behaviors of the nanoparticles with respect to their biological, chemical, and interfacial properties have been observed. It is critical that the phase separation of binary SAMs be understood at both molecular and macroscopic level to create, and then manipulate, the useful properties of the functionalized surfaces. We look into the current understanding of molecular phase separation of binary SAMs on gold surfaces, represented by Au(111) flat surfaces and Au nanoparticles, from both theoretical and experimental aspects. We point out shortcomings and describe several research strategies that will address them in the future. Contribution to the Focus Issue Self-assemblies of Inorganic and Organic Nanomaterials edited by Marie-Pule Pileni.

Surface-Water Quality-Assurance Plan for the USGS Wisconsin Water Science Center

USGS Publications Warehouse

Garn, H.S.

2007-01-01

This surface-water quality-assurance plan documents the standards, policies, and procedures used by the Wisconsin Water Science Center of the U.S. Geological Survey, Water Resources Discipline, for activities related to the collection, processing, storage, analysis, management, and publication of surface-water data. The roles and responsibilities of Water Science Center personnel in following these policies and procedures including those related to safety and training are presented.

A microelectronics approach for the ROSETTA surface science package

NASA Technical Reports Server (NTRS)

Sandau, Rainer (Editor); Alkalaj, Leon

1996-01-01

In relation to the Rosetta surface science package, the benefits of the application of advanced microelectronics packaging technologies and other output from the Mars environmental survey (MESUR) integrated microelectronics study are reported on. The surface science package will be designed to operate for tens of hours. Its limited mass and power consumption make necessary a highly integrated design with all the instruments and subunits operated from a centralized control and information management subsystem.

Molecular level studies on interfacial hydration of zwitterionic and other antifouling polymers in situ.

PubMed

Leng, Chuan; Sun, Shuwen; Zhang, Kexin; Jiang, Shaoyi; Chen, Zhan

2016-08-01

Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. Zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this review, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. Using SFG spectroscopy, we have measured the hydration layers of antifouling materials and found that strong hydrogen bonds are key to the formation of strong hydration layers preventing protein fouling at the polymer interfaces. Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. However, zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Moreover, although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this manuscript, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. All the SFG results indicate that strongly hydrogen-bonded water at the materials' surfaces (strong surface hydration) is closely correlated to the good antifouling properties of the materials. This review will be widely interested by readers of Acta Biomaterialia and will impact many different research fields in chemistry, materials, engineering, and beyond. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Correlation between the Knight shift of chemisorbed CO and the Fermi level local density of states at clean platinum catalyst surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tong, Y.Y.; Rice, C.; Godbout, N.

1999-04-07

Due to its fundamental importance in heterogeneous catalysis, as well as in electrocatalysis, the chemisorption and reaction of CO on transition metal surfaces has been an important focus of modern surface science. Here, the NMR spectroscopy of {sup 13}CO adsorbed onto transition metal surfaces has been shown to be a very powerful probe of molecular structure and dynamics of CO itself, as well as a probe of the electronic properties of the transition metal surfaces onto which it is adsorbed. The authors have investigated the {sup 195}Pt and {sup 13}C nuclear magnetic resonance (NMR) spectroscopy of clean-surface platinum catalysts andmore » of CO chemisorbed onto Pt catalysts surfaces. They use Knight shift, relaxation, and J-coupling data to deduce information about the Fermi level local density of states (E{sub f}-LDOS) at catalyst surfaces. There is a linear correlation between the Knight shifts of chemisorbed CO and the clean surface E{sub f}-LDOS of platinum onto which the CO is bound, as determined by {sup 13}C and {sup 195}Pt NMR. The correlation amounts to {approximately} 12 ppm/Ry{sup {minus}1} {center_dot} atom{sup {minus}1}, the same as that which can be deduced for CO on palladium, as well as from the electrode potential dependence of {sup 13}C Knight shifts and infrared vibrational frequencies, {nu}{sub CO}, and the relationship between {nu}{sub CO} and the E{sub f}-LDOS at clean platinum surfaces. The ability to now directly relate meal and adsorbate electronic properties opens up new avenues for investigating metal-ligand interactions in heterogeneous catalysis and electrocatalysis.« less