AC electrical characterisation and insight to charge transfer mechanisms in DNA molecular wires through temperature and UV effects.

PubMed

Kassegne, Sam; Wibowo, Denni; Chi, James; Ramesh, Varsha; Narenji, Alaleh; Khosla, Ajit; Mokili, John

2015-06-01

In this study, AC characterisation of DNA molecular wires, effects of frequency, temperature and UV irradiation on their conductivity is presented. λ-DNA molecular wires suspended between high aspect-ratio electrodes exhibit highly frequency-dependent conductivity that approaches metal-like behaviour at high frequencies (∼MHz). Detailed temperature dependence experiments were performed that traced the impedance response of λ-DNA until its denaturation. UV irradiation experiments where conductivity was lost at higher and longer UV exposures helped to establish that it is indeed λ-DNA molecular wires that generate conductivity. The subsequent renaturation of λ-DNA resulted in the recovery of current conduction, providing yet another proof of the conducting DNA molecular wire bridge. The temperature results also revealed hysteretic and bi-modal impedance responses that could make DNA a candidate for nanoelectronics components like thermal transistors and switches. Further, these experiments shed light on the charge transfer mechanism in DNA. At higher temperatures, the expected increase in thermal-induced charge hopping may account for the decrease in impedance supporting the 'charge hopping mechanism' theory. UV light, on the other hand, causes damage to GC base-pairs and phosphate groups reducing the path available both for hopping and short-range tunneling mechanisms, and hence increasing impedance--this again supporting both the 'charge hopping' and 'tunneling' mechanism theories.

DNA-Based Single-Molecule Electronics: From Concept to Function.

PubMed

Wang, Kun

2018-01-17

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I-V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

DNA-Based Single-Molecule Electronics: From Concept to Function

PubMed Central

2018-01-01

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed. PMID:29342091

Novel Molecular Architectures Developed for Improved Solid Polymer Electrolytes for Lithium Polymer Batteries

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B.; Kinder, James D.; Bennett, William R.

2002-01-01

Lithium-based polymer batteries for aerospace applications need the ability to operate in temperatures ranging from -70 to 70 C. Current state-of-the-art solid polymer electrolytes (based on amorphous polyethylene oxide, PEO) have acceptable ionic conductivities (10-4 to 10-3 S/cm) only above 60 C. Higher conductivity can be achieved in the current systems by adding solvent or plasticizers to the solid polymer to improve ion transport. However, this can compromise the dimensional and thermal stability of the electrolyte, as well as compatibility with electrode materials. One of NASA Glenn Research Center's objectives in the PERS program is to develop new electrolytes having unique molecular architectures and/or novel ion transport mechanisms, leading to good ionic conductivity at room temperature and below without solvents or plasticizers.

Conductance of three-terminal molecular bridge based on tight-binding theory

NASA Astrophysics Data System (ADS)

Wang, Li-Guang; Li, Yong; Yu, Ding-Wen; Katsunori, Tagami; Masaru, Tsukada

2005-05-01

The quantum transmission characteristic of three-benzene ring nano-molecular bridge is investigated theoretically by using Green's function approach based on tight-binding theory with only a π orbital per carbon atom at the site. The transmission probabilities that electrons transport through the molecular bridge from one terminal to the other two terminals are obtained. The electronic current distributions inside the molecular bridge are calculated and shown in graphical analogy by the current density method based on Fisher-Lee formula at the energy points E = ±0.42, ±1.06 and ±1.5, respectively, where the transmission spectra appear peaks. We find that the transmission spectra are related to the incident electronic energy and the molecular levels strongly and the current distributions agree well with Kirchhoff quantum current momentum conservation law.

Self-assembled nanogaps for molecular electronics.

PubMed

Tang, Qingxin; Tong, Yanhong; Jain, Titoo; Hassenkam, Tue; Wan, Qing; Moth-Poulsen, Kasper; Bjørnholm, Thomas

2009-06-17

A nanogap for molecular devices was realized using solution-based self-assembly. Gold nanorods were assembled to gold nanoparticle-coated conducting SnO2:Sb nanowires via thiol end-capped oligo(phenylenevinylene)s (OPVs). The molecular gap was easily created by the rigid molecule itself during self-assembly and the gap length was determined by the molecule length. The gold nanorods and gold nanoparticles, respectively covalently bonded at the two ends of the molecule, had very small dimensions, e.g. a width of approximately 20 nm, and hence were expected to minimize the screening effect. The ultra-long conducting SnO2:Sb nanowires provided the bridge to connect one of the electrodes of the molecular device (gold nanoparticle) to the external circuit. The tip of the atomic force microscope (AFM) was contacted onto the other electrode (gold nanorod) for the electrical measurement of the OPV device. The conductance measurement confirmed that the self-assembly of the molecules and the subsequent self-assembly of the gold nanorods was a feasible method for the fabrication of the nanogap of the molecular devices.

Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

PubMed

Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

2011-07-21

In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

Noncovalent Molecular Electronics.

PubMed

Gryn'ova, G; Corminboeuf, C

2018-05-03

Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

Novel Solid-State Solar Cell Based on Hole-Conducting MOF-Sensitizer Demonstrating Power Conversion Efficiency of 2.1.

PubMed

Ahn, Do Young; Lee, Deok Yeon; Shin, Chan Yong; Bui, Hoa Thi; Shrestha, Nabeen K; Giebeler, Lars; Noh, Yong-Young; Han, Sung-Hwan

2017-04-19

This work reports on designing of first successful MOF-sensitizer based solid-state photovoltaic device, perticularly with a meaningful output power conversion efficiency. In this study, an intrinsically conductive cobalt-based MOFs (Co-DAPV) formed by the coordination between Co (II) ions and a redox active di(3-diaminopropyl)-viologen (i.e., DAPV) ligand is investigated as sensitizer. Hall-effect measurement shows p-type conductivity of the Co-DAPV film with hole mobility of 0.017 cm 2 V -1 s -1 , suggesting its potential application as hole transporting sensitizer. Further, the energy levels of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of Co-DAPV are well-matched to be suitably employed for sensitizing TiO 2 . Thus, by layer-by-layer deposition of hole conducting MOF-sensitizer onto mesoporous TiO 2 film, a power conversion efficiency of as high as 2.1% is achieved, which exceeds the highest efficiency values of MOF-sensitized liquid-junction solar cells reported so far.

Conductance of carbon based macro-molecular structures

NASA Astrophysics Data System (ADS)

Stafström, S.; Hansson, A.; Paulsson, M.

2000-11-01

Electron transport through metallic nanotubes and stacks of wide bandgap polyaromatic hydrocarbons (PAH) are studied theoretically using the Landauer formalism. These two systems constitute examples of different types of carbon based nanostructured materials of potential use in molecular electronics. The studies are carried out for structures with finite length that bridge two contact pads. In the case of perfect metallic nanotubes, the current is observed to increase stepwise with the applied voltage and the resistance is independent on the length of the tube. In the PAH stacks, the off resonance tunneling conductance decreases exponentially with the number of molecules in the stack and shows a near linear increase with the number of carbon atoms in each molecule.

Photon Upconversion and Molecular Solar Energy Storage by Maximizing the Potential of Molecular Self-Assembly.

PubMed

Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki

2016-11-29

The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.

Highly Conductive Thin Uniform Gold-Coated DNA Nanowires.

PubMed

Stern, Avigail; Eidelshtein, Gennady; Zhuravel, Roman; Livshits, Gideon I; Rotem, Dvir; Kotlyar, Alexander; Porath, Danny

2018-06-01

Over the past decades, DNA, the carrier of genetic information, has been used by researchers as a structural template material. Watson-Crick base pairing enables the formation of complex 2D and 3D structures from DNA through self-assembly. Various methods have been developed to functionalize these structures for numerous utilities. Metallization of DNA has attracted much attention as a means of forming conductive nanostructures. Nevertheless, most of the metallized DNA wires reported so far suffer from irregularity and lack of end-to-end electrical connectivity. An effective technique for formation of thin gold-coated DNA wires that overcomes these drawbacks is developed and presented here. A conductive atomic force microscopy setup, which is suitable for measuring tens to thousands of nanometer long molecules and wires, is used to characterize these DNA-based nanowires. The wires reported here are the narrowest gold-coated DNA wires that display long-range conductivity. The measurements presented show that the conductivity is limited by defects, and that thicker gold coating reduces the number of defects and increases the conductive length. This preparation method enables the formation of molecular wires with dimensions and uniformity that are much more suitable for DNA-based molecular electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improving the leakage current of polyimide-based resistive memory by tuning the molecular chain stack of the polyimide film

NASA Astrophysics Data System (ADS)

Wu, Chi-Chang; Hsiao, Yu-Ping; You, Hsin-Chiang; Lin, Guan-Wei; Kao, Min-Fang; Manga, Yankuba B.; Yang, Wen-Luh

2018-02-01

We have developed an organic-based resistive random access memory (ReRAM) by using spin-coated polyimide (PI) as the resistive layer. In this study, the chain distance and number of chain stacks of PI molecules are investigated. We employed different solid contents of polyamic acid (PAA) to synthesize various PI films, which served as the resistive layer of ReRAM, the electrical performance of which was evaluated. By tuning the PAA solid content, the intermolecular interaction energy of the PI films is changed without altering the molecular structure. Our results show that the leakage current in the high-resistance state and the memory window of the PI-based ReRAM can be substantially improved using this technique. The superior properties of the PI-based ReRAM are ascribed to fewer molecular chain stacks in the PI films when the PAA solid content is decreased, hence suppressing the leakage current. In addition, a device retention time of more than 107 s can be achieved using this technique. Finally, the conduction mechanism in the PI-based ReRAM was analyzed using hopping and conduction models.

Quantum Point Contact Single-Nucleotide Conductance for DNA and RNA Sequence Identification.

PubMed

Afsari, Sepideh; Korshoj, Lee E; Abel, Gary R; Khan, Sajida; Chatterjee, Anushree; Nagpal, Prashant

2017-11-28

Several nanoscale electronic methods have been proposed for high-throughput single-molecule nucleic acid sequence identification. While many studies display a large ensemble of measurements as "electronic fingerprints" with some promise for distinguishing the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine, and uracil), important metrics such as accuracy and confidence of base calling fall well below the current genomic methods. Issues such as unreliable metal-molecule junction formation, variation of nucleotide conformations, insufficient differences between the molecular orbitals responsible for single-nucleotide conduction, and lack of rigorous base calling algorithms lead to overlapping nanoelectronic measurements and poor nucleotide discrimination, especially at low coverage on single molecules. Here, we demonstrate a technique for reproducible conductance measurements on conformation-constrained single nucleotides and an advanced algorithmic approach for distinguishing the nucleobases. Our quantum point contact single-nucleotide conductance sequencing (QPICS) method uses combed and electrostatically bound single DNA and RNA nucleotides on a self-assembled monolayer of cysteamine molecules. We demonstrate that by varying the applied bias and pH conditions, molecular conductance can be switched ON and OFF, leading to reversible nucleotide perturbation for electronic recognition (NPER). We utilize NPER as a method to achieve >99.7% accuracy for DNA and RNA base calling at low molecular coverage (∼12×) using unbiased single measurements on DNA/RNA nucleotides, which represents a significant advance compared to existing sequencing methods. These results demonstrate the potential for utilizing simple surface modifications and existing biochemical moieties in individual nucleobases for a reliable, direct, single-molecule, nanoelectronic DNA and RNA nucleotide identification method for sequencing.

Ion conduction in high ion content PEO-based ionomers

NASA Astrophysics Data System (ADS)

Caldwell, David, II; Maranas, Janna

Solid Polymer Electrolytes (SPEs) can enable the design of batteries that are safer and have higher capacity than batteries with traditional volatile organic electrolytes. The current limitation for SPEs is their low conductivity, resulting from a conduction mechanism strongly coupled to the dynamics of the polymer host matrix. Our previous work indicated the possibility of a conduction mechanism through the use of ion aggregates. In order to investigate this mechanism, we performed a series of molecular dynamics simulations of PEO-based ionomers at high ion content. Our results indicate that conduction through ion aggregates are partially decoupled from polymer dynamics and could enable the development of higher conductive SPEs.

Conductance and thermopower in molecular nanojunctions

NASA Astrophysics Data System (ADS)

Sen, Arijit

2013-02-01

Electronic transport through short channels in a molecular junction is an intricate quantum scattering problem [1]. To garner insight on how the structure and the electrical properties of a nanoscale junction are correlated is thus of both fundamental and technological interest [1-3]. As observed experimentally in the last couple of years by several independent research groups [4-5], a two-terminal molecular junction comprising of a simple alkane chain with varying length can exhibit high as well as low conductance. However, what causes the simultaneous unveiling of multiple conductances remained largely obscure. We have recently demonstrated [6] that the binary conductance in these heterostructures is due mainly to two distinct electrode orientations that control the electrode-molecule coupling as well as the tunneling strength through quantum interference following diversity in the electrode band structures. Our detailed analysis on the transmission spectra indicates that even a single-molecule nanojunction can potentially serve as a realistic double-quantum-dot kind of system to yield tunable Fano resonance, as often desired for nanoscale switching. In this talk, I intend to give a brief account of molecular electronics and its future applications along with the challenges and possibilities in the current perspective. A few deliberations may as well include how the inter-dot tunneling strength may affect the non-equilibrium charge transport and thermoelectricity in a myriad of molecular junctions based on different molecular conformations and electrode structures. Finally, I shall try to touch upon the effect of electron-phonon interaction on the nanoscale charge transport, and also, the phonon-mediated thermal transport in molecular nanodevices.

A reversible single-molecule switch based on activated antiaromaticity

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

Yin, Xiaodong; Zang, Yaping; Zhu, Liangliang

Single-molecule electronic devices provide researchers with an unprecedented ability to relate novel physical phenomena to molecular chemical structures. Typically, conjugated aromatic molecular backbones are relied upon to create electronic devices, where the aromaticity of the building blocks is used to enhance conductivity. We capitalize on the classical physical organic chemistry concept of Hückel antiaromaticity by demonstrating a single-molecule switch that exhibits low conductance in the neutral state and, upon electrochemical oxidation, reversibly switches to an antiaromatic high-conducting structure. We form single-molecule devices using the scanning tunneling microscope–based break-junction technique and observe an on/off ratio of ~70 for a thiophenylidene derivativemore » that switches to an antiaromatic state with 6-4-6-p electrons. Through supporting nuclear magnetic resonance measurements, we show that the doubly oxidized core has antiaromatic character and we use density functional theory calculations to rationalize the origin of the high-conductance state for the oxidized single-molecule junction. Together, our work demonstrates how the concept of antiaromaticity can be exploited to create single-molecule devices that are highly conducting.« less

A reversible single-molecule switch based on activated antiaromaticity

DOE PAGES

Yin, Xiaodong; Zang, Yaping; Zhu, Liangliang; ...

2017-10-27

Single-molecule electronic devices provide researchers with an unprecedented ability to relate novel physical phenomena to molecular chemical structures. Typically, conjugated aromatic molecular backbones are relied upon to create electronic devices, where the aromaticity of the building blocks is used to enhance conductivity. We capitalize on the classical physical organic chemistry concept of Hückel antiaromaticity by demonstrating a single-molecule switch that exhibits low conductance in the neutral state and, upon electrochemical oxidation, reversibly switches to an antiaromatic high-conducting structure. We form single-molecule devices using the scanning tunneling microscope–based break-junction technique and observe an on/off ratio of ~70 for a thiophenylidene derivativemore » that switches to an antiaromatic state with 6-4-6-p electrons. Through supporting nuclear magnetic resonance measurements, we show that the doubly oxidized core has antiaromatic character and we use density functional theory calculations to rationalize the origin of the high-conductance state for the oxidized single-molecule junction. Together, our work demonstrates how the concept of antiaromaticity can be exploited to create single-molecule devices that are highly conducting.« less

Image-based multi-scale simulation and experimental validation of thermal conductivity of lanthanum zirconate

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

Guo, Xingye; Hu, Bin; Wei, Changdong

Lanthanum zirconate (La2Zr2O7) is a promising candidate material for thermal barrier coating (TBC) applications due to its low thermal conductivity and high-temperature phase stability. In this work, a novel image-based multi-scale simulation framework combining molecular dynamics (MD) and finite element (FE) calculations is proposed to study the thermal conductivity of La2Zr2O7 coatings. Since there is no experimental data of single crystal La2Zr2O7 thermal conductivity, a reverse non-equilibrium molecular dynamics (reverse NEMD) approach is first employed to compute the temperature-dependent thermal conductivity of single crystal La2Zr2O7. The single crystal data is then passed to a FE model which takes into accountmore » of realistic thermal barrier coating microstructures. The predicted thermal conductivities from the FE model are in good agreement with experimental validations using both flash laser technique and pulsed thermal imaging-multilayer analysis. The framework proposed in this work provides a powerful tool for future design of advanced coating systems. (C) 2016 Elsevier Ltd. All rights reserved.« less

Spacer type mediated tunable spin crossover (SCO) characteristics of pyrene decorated 2,6-bis(pyrazol-1-yl)pyridine (bpp) based Fe(ii) molecular spintronic modules.

PubMed

Kumar, Kuppusamy Senthil; Šalitroš, Ivan; Moreno-Pineda, Eufemio; Ruben, Mario

2017-08-14

A simple "isomer-like" variation of the spacer group in a set of Fe(ii) spin crossover (SCO) complexes designed to probe spin state dependence of electrical conductivity in graphene-based molecular spintronic junctions led to the observation of remarkable variations in the thermal- and light-induced magnetic characteristics, paving a simple route for the design of functional SCO complexes with different temperature switching regimes based on a 2,6-bis(pyrazol-1-yl)pyridine ligand skeleton.

Thermal Conductivity of Single-Walled Carbon Nanotube with Internal Heat Source Studied by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Li, Yuan-Wei; Cao, Bing-Yang

2013-12-01

The thermal conductivity of (5, 5) single-walled carbon nanotubes (SWNTs) with an internal heat source is investigated by using nonequilibrium molecular dynamics (NEMD) simulation incorporating uniform heat source and heat source-and-sink schemes. Compared with SWNTs without an internal heat source, i.e., by a fixed-temperature difference scheme, the thermal conductivity of SWNTs with an internal heat source is much lower, by as much as half in some cases, though it still increases with an increase of the tube length. Based on the theory of phonon dynamics, a function called the phonon free path distribution is defined to develop a simple one-dimensional heat conduction model considering an internal heat source, which can explain diffusive-ballistic heat transport in carbon nanotubes well.

A Research Project-Based and Self-Determined Teaching System of Molecular Biology Techniques for Undergraduates

ERIC Educational Resources Information Center

Zhang, Shuping

2008-01-01

Molecular biology techniques play a very important role in understanding the biological activity. Students who major in biology should know not only how to perform experiments, but also the reasons for performing them. Having the concept of conducting research by integrating various techniques is especially important. This paper introduces a…

Effects of molecular structure on microscopic heat transport in chain polymer liquids

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

Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku

2015-04-28

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the newmore » concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.« less

Effects of molecular structure on microscopic heat transport in chain polymer liquids.

PubMed

Matsubara, Hiroki; Kikugawa, Gota; Bessho, Takeshi; Yamashita, Seiji; Ohara, Taku

2015-04-28

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7Tc) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

Computational design of intrinsic molecular rectifiers based on asymmetric functionalization of N-phenylbenzamide

DOE PAGES

Ding, Wendu; Koepf, Matthieu; Koenigsmann, Christopher; ...

2015-11-03

Here, we report a systematic computational search of molecular frameworks for intrinsic rectification of electron transport. The screening of molecular rectifiers includes 52 molecules and conformers spanning over 9 series of structural motifs. N-Phenylbenzamide is found to be a promising framework with both suitable conductance and rectification properties. A targeted screening performed on 30 additional derivatives and conformers of N-phenylbenzamide yielded enhanced rectification based on asymmetric functionalization. We demonstrate that electron-donating substituent groups that maintain an asymmetric distribution of charge in the dominant transport channel (e.g., HOMO) enhance rectification by raising the channel closer to the Fermi level. These findingsmore » are particularly valuable for the design of molecular assemblies that could ensure directionality of electron transport in a wide range of applications, from molecular electronics to catalytic reactions.« less

Synthesis of Long-Chain-Branched (LCB) Polysulfones for Multifunctional Transport Membranes

DTIC Science & Technology

2010-09-01

R.; Dutta, N. K. Interfacial Interactions in Aprotic Ionic Liquid Based Protonic Membrane and Its Correlation with High Temperature Conductivity...rigidity. The series of novel polymers was characterized for chemical structure, thermal transitions, and molecular weight. Ionic conductivity was tested...Although much progress exists based on perfluorosulfonated platforms ( Nafion , σ ≈ 10-1 – 10-2 S/cm) new and more complicated parameters arise as

Temperature gating and competing temperature-dependent effects in DNA molecular wires

NASA Astrophysics Data System (ADS)

Wibowo, Denni; Narenji, Alaleh; Kassegne, Sam

2017-02-01

While recent research in electron-transport mechanism on a double strands DNA seems to converge into a consensus, experiments in direct electrical measurements on a long DNA molecules still lead to a conflicting result This study is the continuation of our previous research in electrical characterization of DNA molecular wires, where we furtherly investigate the effects of temperature on the electrical conductivity of DNA molecular wires by measuring its impedance response. We found that at higher temperatures, the expected increase in charge hopping mechanism may account for the decrease in impedance (and hence increase in conductivity) supporting the 'charge hopping mechanism' theory. UV light exposure, on the other hand, causes damage to GC base pairs reducing the path available for hopping mechanism and hence resulting in increased impedance - this again supporting the 'charge hopping mechanism' theory. We also report that λ-DNA molecular wires have differing impedance responses at two temperature regimes: impedance increases between 4 °C - 40 °C and then decreases between 40 °C - melting point (˜110 °C), after which λ-DNA denatures resulting in no current transduction. We submit that the low impedance of λ-DNA molecular wires observed at moderate to high frequencies may have significant implications to the field of DNA-based bionanoelectronics.

Polyaniline particles: Material properties when synthesized with aqueous nonionic micelles and environmental stability

NASA Astrophysics Data System (ADS)

Hobaica, Stephen Charles

Polyaniline is a member of the class of electrically conducting polymers, which have possible commercial applications as anticorrosive or static charge removal coatings. Aqueous-based polyaniline coatings are preferred over organic solvent or strong acid based coatings because the water used in these coatings does not pollute the environment. The overall goal of this dissertation was to further the development of useful water-based polyaniline coatings by studying new methods of synthesizing polyaniline particles for water-based coatings, to investigate the material properties of these particles such as molecular weight, electrical conductivity, particle size distribution, and stability of polyaniline in air and water. One method of polymerizing polyaniline for aqueous-based coatings uses micelles, which are composed of a cluster of amphiphile surfactants. Micelles can change the local environment by aligning and absorbing the monomer, and may yield polymers with improved material properties and reaction rates. Nonionic micelles have not been extensively investigated. Therefore the first specific goal of this work was to use an aqueous nonionic micelle solution of nonylphenoxypoly(ethyleneoxy) ethanol surfactant (NP-30 surfactant) to comprehensively investigate a one step chemical polymerization of polyaniline conducted at -3°C, in 1.25 M HCl, with ammonium peroxydisulfate oxidizer. The results show that increasing surfactant concentrations caused a decrease in molecular weight, electrical conductivity and sharper particle size distribution of the polymer. The second specific objective of this dissertation was to determine the effect of water and air on polyaniline. The results showed no degradation of molecular weight, a decrease in chloride and hydrogen composition, and decrease in electrical conductivity for polyaniline immersed in water for extended periods. A chloride ion diffusion coefficient of 2.5 to 74 x 10-9 cm2/hour was measured. The aging of polyaniline powders in a desiccator for 5 years showed no effect on the molecular structure as indicated by the FTIR spectrum. The third specific goal of the research was to measure the real and imaginary refractive index of polyaniline saturated with 1.25 M HCl, which was found to be 1.345 to 1.355 and 0.025 to 0.027, respectively. This information is crucial to measuring the distribution of polyaniline colloids by light scattering.

A Computational and Theoretical Study of Conductance in Hydrogen-bonded Molecular Junctions

NASA Astrophysics Data System (ADS)

Wimmer, Michael

This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano-junctions between molecular electronic devices and biological systems. This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junction significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction. In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH˙˙˙O, OH˙˙˙O, and NH˙˙˙N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has focused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance descriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular description of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions. A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.

Reduction in thermal conductivity and tunable heat capacity of inorganic/organic hybrid superlattices

NASA Astrophysics Data System (ADS)

Giri, Ashutosh; Niemelä, Janne-Petteri; Szwejkowski, Chester J.; Karppinen, Maarit; Hopkins, Patrick E.

2016-01-01

We study the influence of molecular monolayers on the thermal conductivities and heat capacities of hybrid inorganic/organic superlattice thin films fabricated via atomic/molecular layer deposition. We measure the cross plane thermal conductivities and volumetric heat capacities of TiO2- and ZnO-based superlattices with periodic inclusion of hydroquinone layers via time domain thermoreflectance. In comparison to their homogeneous counterparts, the thermal conductivities in these superlattice films are considerably reduced. We attribute this reduction in the thermal conductivity mainly due to incoherent phonon boundary scattering at the inorganic/organic interface. Increasing the inorganic/organic interface density reduces the thermal conductivity and heat capacity of these films. High-temperature annealing treatment of the superlattices results in a change in the orientation of the hydroquinone molecules to a 2D graphitic layer along with a change in the overall density of the hybrid superlattice. The thermal conductivity of the hybrid superlattice increases after annealing, which we attribute to an increase in crystallinity.

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

Lawrence R. Sita

Ferrocene-based molecular components for nanoelectronics offer a number of distinct advantages relative to all carbon frameworks due to metal-centered molecular states that should be closer in energy to the Fermi levels of the metal electrodes in metal / molecule / metal heterojunctions. Given this, the overall goal of the project was to investigate the conduction physics of a variety of proposed ferrocene diode / transistor designs in order to address the fundamental question; can electron transport within nm-length scale structures be modulated in a controlled fashion? During the funded period, substantial progress towards achieving this goal was made by surmountingmore » a number of scientific and technical obstacles. More specifically, a concise and general synthetic route to several mono- and diferrocene dithiols and monothiols was achieved that now allows for the directed and controlled assembly of a variety of metal / molecule /metal test structures for the single molecule conductance measurements and the fabrication of self-assembled monolayers (SAMs) on Au(111) that are amenable to quantitative electrochemical characterization of electron-transfer rates. Most importantly, by using an electromigrated test structure, reproducible I/V data for one of the ferrocene dithiol molecules have been collected which exhibit surprisingly high conductance. Exceptional agreement of this result with theory serves to substantiate the original hypothesis that metal-centered states within a molecular bridge can indeed serve to establish higher conductance relative to all-organic molecular bridges. Overall, the successful demonstration of the ability of ferrocene-molecular frameworks to serve as exceptional molecular conductors will play an important role in the continued evolution in design of molecular components for nanoelectronic devices, which in turn, will have a positive impact on the science and potential technologies associated with these systems.« less

Defined-size DNA triple crossover construct for molecular electronics: modification, positioning and conductance properties.

PubMed

Linko, Veikko; Leppiniemi, Jenni; Paasonen, Seppo-Tapio; Hytönen, Vesa P; Toppari, J Jussi

2011-07-08

We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.

Ion Channel Conductance Measurements on a Silicon-Based Platform

DTIC Science & Technology

2006-01-01

calculated using the molecular dynamics code, GROMACS . Reasonable agreement is obtained in the simulated versus measured conductance over the range of...measurements of the lipid giga-seal characteristics have been performed, including AC conductance measurements and statistical analysis in order to...Dynamics kernel self-consistently coupled to Poisson equations using a P3M force field scheme and the GROMACS description of protein structure and

Molecular engineering and measurements to test hypothesized mechanisms in single molecule conductance switching.

PubMed

Moore, Amanda M; Dameron, Arrelaine A; Mantooth, Brent A; Smith, Rachel K; Fuchs, Daniel J; Ciszek, Jacob W; Maya, Francisco; Yao, Yuxing; Tour, James M; Weiss, Paul S

2006-02-15

Six customized phenylene-ethynylene-based oligomers have been studied for their electronic properties using scanning tunneling microscopy to test hypothesized mechanisms of stochastic conductance switching. Previously suggested mechanisms include functional group reduction, functional group rotation, backbone ring rotation, neighboring molecule interactions, bond fluctuations, and hybridization changes. Here, we test these hypotheses experimentally by varying the molecular designs of the switches; the ability of the molecules to switch via each hypothetical mechanism is selectively engineered into or out of each molecule. We conclude that hybridization changes at the molecule-surface interface are responsible for the switching we observe.

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.

Quantitative scanning thermal microscopy of ErAs/GaAs superlattice structures grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Park, K. W.; Nair, H. P.; Crook, A. M.; Bank, S. R.; Yu, E. T.

2013-02-01

A proximal probe-based quantitative measurement of thermal conductivity with ˜100-150 nm lateral and vertical spatial resolution has been implemented. Measurements on an ErAs/GaAs superlattice structure grown by molecular beam epitaxy with 3% volumetric ErAs content yielded thermal conductivity at room temperature of 9 ± 2 W/m K, approximately five times lower than that for GaAs. Numerical modeling of phonon scattering by ErAs nanoparticles yielded thermal conductivities in reasonable agreement with those measured experimentally and provides insight into the potential influence of nanoparticle shape on phonon scattering. Measurements of wedge-shaped samples created by focused ion beam milling provide direct confirmation of depth resolution achieved.

Evidence for a first-order liquid-liquid transition in high-pressure hydrogen from ab initio simulations.

PubMed

Morales, Miguel A; Pierleoni, Carlo; Schwegler, Eric; Ceperley, D M

2010-07-20

Using quantum simulation techniques based on either density functional theory or quantum Monte Carlo, we find clear evidence of a first-order transition in liquid hydrogen, between a low conductivity molecular state and a high conductivity atomic state. Using the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures near 2,000 K and pressures near 120 GPa. Furthermore, we have determined the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line. The melting line crosses the metalization line at 700 K and 220 GPa using density functional energetics and at 550 K and 290 GPa using quantum Monte Carlo energetics.

Feasibility study of molecular memory device based on DNA using methylation to store information

NASA Astrophysics Data System (ADS)

Jiang, Liming; Qiu, Wanzhi; Al-Dirini, Feras; Hossain, Faruque M.; Evans, Robin; Skafidas, Efstratios

2016-07-01

DNA, because of its robustness and dense information storage capability, has been proposed as a potential candidate for next-generation storage media. However, encoding information into the DNA sequence requires molecular synthesis technology, which to date is costly and prone to synthesis errors. Reading the DNA strand information is also complex. Ideally, DNA storage will provide methods for modifying stored information. Here, we conduct a feasibility study investigating the use of the DNA 5-methylcytosine (5mC) methylation state as a molecular memory to store information. We propose a new 1-bit memory device and study, based on the density functional theory and non-equilibrium Green's function method, the feasibility of electrically reading the information. Our results show that changes to methylation states lead to changes in the peak of negative differential resistance which can be used to interrogate memory state. Our work demonstrates a new memory concept based on methylation state which can be beneficial in the design of next generation DNA based molecular electronic memory devices.

Conductance based characterization of structure and hopping site density in 2D molecule-nanoparticle arrays

NASA Astrophysics Data System (ADS)

McCold, Cliff E.; Fu, Qiang; Howe, Jane Y.; Hihath, Joshua

2015-09-01

Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems.Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems. Electronic supplementary information (ESI) available: Temperature dependent measurements, activation energies, particle size distributions, void density-polydispersity relation, and DLS data. See DOI: 10.1039/c5nr04460j

Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology.

PubMed

Sepulveda, Antonia R; Hamilton, Stanley R; Allegra, Carmen J; Grody, Wayne; Cushman-Vokoun, Allison M; Funkhouser, William K; Kopetz, Scott E; Lieu, Christopher; Lindor, Noralane M; Minsky, Bruce D; Monzon, Federico A; Sargent, Daniel J; Singh, Veena M; Willis, Joseph; Clark, Jennifer; Colasacco, Carol; Bryan Rumble, R; Temple-Smolkin, Robyn; B Ventura, Christina; Nowak, Jan A

2017-05-01

- To develop evidence-based guideline recommendations through a systematic review of the literature to establish standard molecular biomarker testing of colorectal cancer (CRC) tissues to guide epidermal growth factor receptor (EGFR) therapies and conventional chemotherapy regimens. - The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology convened an expert panel to develop an evidence-based guideline to establish standard molecular biomarker testing and guide therapies for patients with CRC. A comprehensive literature search that included more than 4,000 articles was conducted. - Twenty-one guideline statements were established. - Evidence supports mutational testing for EGFR signaling pathway genes, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize CRC molecular testing are presented.

The diffusion and conduction of lithium in poly(ethylene oxide)-based sulfonate ionomers

NASA Astrophysics Data System (ADS)

LaFemina, Nikki H.; Chen, Quan; Colby, Ralph H.; Mueller, Karl T.

2016-09-01

Pulsed field gradient nuclear magnetic resonance spectroscopy and dielectric relaxation spectroscopy have been utilized to investigate lithium dynamics within poly(ethylene oxide) (PEO)-based lithium sulfonate ionomers of varying ion content. The ion content is set by the fraction of sulfonated phthalates and the molecular weight of the PEO spacer, both of which can be varied independently. The molecular level dynamics of the ionomers are dominated by either Vogel-Fulcher-Tammann or Arrhenius behavior depending on ion content, spacer length, temperature, and degree of ionic aggregation. In these ionomers the main determinants of the self-diffusion of lithium and the observed conductivities are the ion content and ionic states of the lithium ion, which are profoundly affected by the interactions of the lithium ions with the ether oxygens of the polymer. Since many lithium ions move by segmental polymer motion in the ion pair state, their diffusion is significantly larger than that estimated from conductivity using the Nernst-Einstein equation.

Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders

Treesearch

Kentaro Hosaka; Scott T. Bates; Ross E. Beever; Michael A. Castellano; Wesley Colgan; Laura S. Dominguez; Eduardo R. Nouhra; Jozsef Geml; Admir J. Giachini; S. Ray Kenney; Nicholas B. Simpson; Joseph W. Spatafora; James M. Trappe

2006-01-01

Molecular phylogenetic analyses for the gomphoid-phalloid fungi were conducted based on the five gene dataset with extensive taxon sampling. The monophyly of the gomphoid-phalloid clade was strongly supported, and four well supported major subclades were recognized. Three of the four subclades were represented entirely by gastroid taxa, and only Gomphales contained...

The merger of electrochemistry and molecular electronics.

PubMed

McCreery, Richard L

2012-02-01

Molecular Electronics has the potential to greatly enhance existing silicon-based microelectronics to realize new functions, higher device density, lower power consumption, and lower cost. Although the investigation of electron transport through single molecules and molecular monolayers in "molecular junctions" is a recent development, many of the relevant concepts and phenomena are derived from electrochemistry, as practiced for the past several decades. The past 10+ years have seen an explosion of research activity directed toward how the structure of molecules affects electron transport in molecular junctions, with the ultimate objective of "rational design" of molecular components with new electronic functions, such as chemical sensing, interactions with light, and low-cost, low-power consumer electronics. In order to achieve these scientifically and commercially important objectives, the factors controlling charge transport in molecules "connected" to conducting contacts must be understood, and methods for massively parallel manufacturing of molecular circuits must be developed. This Personal Account describes the development of reproducible and robust molecular electronic devices, starting with modified electrodes used in electrochemistry and progressing to manufacturable molecular junctions. Although the field faced some early difficulties in reliability and characterization, the pieces are now in place for rapid advances in understanding charge transport at the molecular level. Inherent in the field of Molecular Electronics are many electrochemical concepts, including tunneling, redox exchange, activated electron transfer, and electron coupling between molecules and conducting contacts. Copyright © 2012 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

First-principles studies of electrical transport in nanoscale molecular junctions

NASA Astrophysics Data System (ADS)

Neaton, J. B.

2008-03-01

Understanding the conductance of individual molecular junctions is a forefront topic in theoretical nanoscience. The development of a general, efficient atomistic approach for treating an open system out of equilibrium with good accuracy, and then using it to inform experiment, is a significant open challenge in the field. Here I will describe studies where first-principles techniques, based on density functional theory (DFT) and beyond, are used to investigate some of the fundamental issues associated with single-molecule transport measurements. After a brief summary of previous work, a DFT-based scattering-state approach is presented and applied to H2 and amine-Au linked molecular junctions [1], two systems for which there exist reliable data [2]. Similar to most ab initio studies, we rely on a Landauer approach within DFT for junction conductance. Using this framework, which has proven relatively accurate for metallic point contacts, good agreement with experiment is obtained for the H2 conductance. For amine-Au linked junctions, however, the computed conductance is significantly larger than that measured,although structural trends are reproduced by the calculations. To explore this further, we draw on GW calculations of a prototypical metal-molecule contact, benzene on graphite, where interfacial polarization effects are found to drastically modify frontier orbital energies [3]. A physically motivated model self-energy correction is developed from our GW calculations,applied to the amine case, and shown to quantitatively explain the discrepancy with experiment. The importance of many-electron corrections beyond DFT for accurately computing molecular conductance and understanding experiments is thoroughly discussed. [1] S. Y. Quek et al., Nano Lett 7, 3482 (2007); K. H. Khoo et al., submitted (2007). [2] R. Smit et al., Nature 419, 906 (2002); L. Venkataraman et al., Nature 442 ,904 (2006). [3] J. B. Neaton et al., Phys. Rev. Lett. 97, 216405 (2006).

Ion Conduction through the hERG Potassium Channel

PubMed Central

Cavalli, Andrea; Recanatini, Maurizio

2012-01-01

The inward rectifier voltage-gated potassium channel hERG is of primary importance for the regulation of the membrane potential of cardiomyocytes. Unlike most voltage-gated K+-channels, hERG shows a low elementary conductance at physiological voltage and potassium concentration. To investigate the molecular features underlying this unusual behavior, we simulated the ion conduction through the selectivity filter at a fully atomistic level by means of molecular dynamics-based methods, using a homology-derived model. According to our calculations, permeation of potassium ions can occur along two pathways, one involving site vacancies inside the filter (showing an energy barrier of about 6 kcal mol−1), and the other characterized by the presence of a knock-on intermediate (about 8 kcal mol−1). These barriers are indeed in accordance with a low conductance behavior, and can be explained in terms of a series of distinctive structural features displayed by the hERG ion permeation pathway. PMID:23133669

Evidence for a first-order liquid-liquid transition in high-pressure hydrogen from ab initio simulations

PubMed Central

Morales, Miguel A.; Pierleoni, Carlo; Schwegler, Eric; Ceperley, D. M.

2010-01-01

Using quantum simulation techniques based on either density functional theory or quantum Monte Carlo, we find clear evidence of a first-order transition in liquid hydrogen, between a low conductivity molecular state and a high conductivity atomic state. Using the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures near 2,000 K and pressures near 120 GPa. Furthermore, we have determined the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line. The melting line crosses the metalization line at 700 K and 220 GPa using density functional energetics and at 550 K and 290 GPa using quantum Monte Carlo energetics. PMID:20566888

Negative differential resistance by molecular resonant tunneling between neutral tribenzosubporphine anchored to a Au(111) surface and tribenzosubporphine cation adsorbed on to a tungsten tip.

PubMed

Majima, Yutaka; Ogawa, Daisuke; Iwamoto, Masachika; Azuma, Yasuo; Tsurumaki, Eiji; Osuka, Atsuhiro

2013-09-25

Tribenzosubporphyrins are boron(III)-chelated triangular bowl-shaped ring-contracted porphyrins that possess a 14π-aromatic circuit. Their flat molecular shapes and discrete molecular orbital diagrams make them ideal for observation by scanning tunneling microscopy (STM). Expanding their applications toward single molecule-based devices requires a fundamental knowledge of single molecular conductance between tribenzosubporphines and the STM metal tip. We utilized a tungsten (W) STM tip to investigate the electronic properties of B-(5-mercaptopentoxy)tribenzosubporphine 1 at the single molecular level. B-(5-mercaptopentoxy)-tribenzosubporphine 1 was anchored to the Au(111) surface via reaction with 1-heptanethiol linkers that were preorganized as a self-assembled monolayer (C7S SAM) on the Au(111) substrate. This arrangement ensured that 1 was electronically decoupled from the metal surface. Differential conductance (dI/dV - V) measurements with the bare W tip exhibited a broad gap region of low conductance and three distinct responses at 2.4,-1.3, and -2.1 V. Bias-voltage-dependent STM imaging of 1 at 65 K displayed a triangle shape at -2.1 < V < -1.3 V and a circle shape at V < -2.1 V, reflecting its HOMO and HOMO-1, respectively. In addition, different conductance behaviors were reproducibly observed, which has been ascribed to the adsorption of a tribenzosubporphine-cation on the W tip. When using a W tip doped with preadsorbed tribenzosubporphine-cation, negative differential resistance (NDR) phenomena were clearly observed in a reproducible manner with a peak-to-valley ratio of 2.6, a value confirmed by spatial mapping conductance measurements. Collectively, the observed NDR phenomena have been attributed to effective molecular resonant tunneling between a neutral tribenzosubporphine anchored to the metal surface and a tribenzosubporphine cation adsorbed on a W tip.

Computational Nanotechnology of Materials, Devices, and Machines: Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Kwak, Dolhan (Technical Monitor)

2000-01-01

The mechanics and chemistry of carbon nanotubes have relevance for their numerous electronic applications. Mechanical deformations such as bending and twisting affect the nanotube's conductive properties, and at the same time they possess high strength and elasticity. Two principal techniques were utilized including the analysis of large scale classical molecular dynamics on a shared memory architecture machine and a quantum molecular dynamics methodology. In carbon based electronics, nanotubes are used as molecular wires with topological defects which are mediated through various means. Nanotubes can be connected to form junctions.

Electronic tunneling through a fullerene-like molecular bridge

NASA Astrophysics Data System (ADS)

Vanaie, H.; Yaghobi, M.

2018-04-01

This study was conducted to consider the electronic transport properties of the N_{36} B_{36} molecule, using the Green's function method based on the GW model. The number, width, height and position of density of state peaks are dramatically dependent on the correlation effect, the contact type and symmetric properties of the molecule. Also, negative differential resistance behavior was observed for all modes in voltages 4.4 V (- 4.5 V) to 4.7 V (- 4.7 V). The N_{36} B_{36} molecule behaves as an insulator where the total current becomes zero for the same values of the gate voltages but acts as a metal at other values. Therefore, the physical picture of electron conduction may change in N_{36} B_{36}—based molecular devices and it could behave as a semiconductor.

Finite Element and Molecular Dynamics Modeling and Simulation of Thermal Properties

DTIC Science & Technology

2007-06-01

dots represent the experimental results of the normalized conductivity data ke/kf (ke is κ of the composite, kf is κ of the fluid) CNT in oil ...individual Single Walled Nanotube to four centimeters in length. [4] 6 Carbon based materials, in-plane pyrolytic graphite and diamonds, have the...conductivity of nanocomposites has not yet been achieved. A 2001 experiment studied the thermal conductivity of oil with CNT in suspension. The results

A self-consistent transport model for molecular conduction based on extended Hückel theory with full three-dimensional electrostatics

NASA Astrophysics Data System (ADS)

Zahid, F.; Paulsson, M.; Polizzi, E.; Ghosh, A. W.; Siddiqui, L.; Datta, S.

2005-08-01

We present a transport model for molecular conduction involving an extended Hückel theoretical treatment of the molecular chemistry combined with a nonequilibrium Green's function treatment of quantum transport. The self-consistent potential is approximated by CNDO (complete neglect of differential overlap) method and the electrostatic effects of metallic leads (bias and image charges) are included through a three-dimensional finite element method. This allows us to capture spatial details of the electrostatic potential profile, including effects of charging, screening, and complicated electrode configurations employing only a single adjustable parameter to locate the Fermi energy. As this model is based on semiempirical methods it is computationally inexpensive and flexible compared to ab initio models, yet at the same time it is able to capture salient qualitative features as well as several relevant quantitative details of transport. We apply our model to investigate recent experimental data on alkane dithiol molecules obtained in a nanopore setup. We also present a comparison study of single molecule transistors and identify electronic properties that control their performance.

Controlling destructive quantum interference in tunneling junctions comprising self-assembled monolayers via bond topology and functional groups† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00165k

PubMed Central

Zhang, Yanxi; Ye, Gang; Soni, Saurabh; Qiu, Xinkai; Krijger, Theodorus L.; Jonkman, Harry T.; Carlotti, Marco; Sauter, Eric; Zharnikov, Michael

2018-01-01

Quantum interference effects (QI) are of interest in nano-scale devices based on molecular tunneling junctions because they can affect conductance exponentially through minor structural changes. However, their utilization requires the prediction and deterministic control over the position and magnitude of QI features, which remains a significant challenge. In this context, we designed and synthesized three benzodithiophenes based molecular wires; one linearly-conjugated, one cross-conjugated and one cross-conjugated quinone. Using eutectic Ga–In (EGaIn) and CP-AFM, we compared them to a well-known anthraquinone in molecular junctions comprising self-assembled monolayers (SAMs). By combining density functional theory and transition voltage spectroscopy, we show that the presence of an interference feature and its position can be controlled independently by manipulating bond topology and electronegativity. This is the first study to separate these two parameters experimentally, demonstrating that the conductance of a tunneling junction depends on the position and depth of a QI feature, both of which can be controlled synthetically. PMID:29896382

Inorganic and Organometallic Molecular Wires for Single-Molecule Devices.

PubMed

Tanaka, Yuya; Kiguchi, Manabu; Akita, Munetaka

2017-04-06

Recent developments of single-molecule conductance measurements allow us to understand fundamental conducting properties of molecular wires. While a wide variety of organic molecular wires have been studied so far, inorganic and organometallic molecular wires have received much less attention. However, molecular wires with transition-metal atoms show interesting features and functions distinct from those of organic wires. These properties originate mainly from metal-ligand dπ-pπ interactions and metal-metal d-d interactions. Thanks to the rich combination of metal atoms and supporting ligands, frontier orbital energies of the molecular wires can be finely tuned to lead to highly conducting molecular wires. Moreover, the unique electronic structures of metal complexes are susceptible to subtle environmental changes, leading to potential functional molecular devices. This article reviews recent advances in the single-molecule conductance study of inorganic and organometallic molecular wires. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Device considerations for development of conductance-based biosensors

PubMed Central

Lee, Kangho; Nair, Pradeep R.; Scott, Adina; Alam, Muhammad A.; Janes, David B.

2009-01-01

Design and fabrication of electronic biosensors based on field-effect-transistor (FET) devices require understanding of interactions between semiconductor surfaces and organic biomolecules. From this perspective, we review practical considerations for electronic biosensors with emphasis on molecular passivation effects on FET device characteristics upon immobilization of organic molecules and an electrostatic model for FET-based biosensors. PMID:24753627

Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition.

PubMed

Korshoj, Lee E; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant

2017-11-01

Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

Establishment of a Molecular Serotyping Scheme and a Multiplexed Luminex-Based Array for Enterobacter aerogenes

PubMed Central

Guo, Xi; Wang, Min; Wang, Lu; Wang, Yao; Chen, Tingting; Wu, Pan; Chen, Min; Liu, Bin; Feng, Lu

2018-01-01

Serotyping based on surface polysaccharide antigens is important for the clinical detection and epidemiological surveillance of pathogens. Polysaccharide gene clusters (PSgcs) are typically responsible for the diversity of bacterial surface polysaccharides. Through whole-genome sequencing and analysis, eight putative PSgc types were identified in 23 Enterobacter aerogenes strains from several geographic areas, allowing us to present the first molecular serotyping system for E. aerogenes. A conventional antigenic scheme was also established and correlated well with the molecular serotyping system that was based on PSgc genetic variation, indicating that PSgc-based molecular typing and immunological serology provide equally valid results. Further, a multiplex Luminex-based array was developed, and a double-blind test was conducted with 97 clinical specimens from Shanghai, China, to validate our array. The results of these analyses indicated that strains containing PSgc4 and PSgc7 comprised the predominant groups. We then examined 86 publicly available E. aerogenes strain genomes and identified an additional seven novel PSgc types, with PSgc10 being the most abundant type. In total, our study identified 15 PSgc types in E. aerogenes, providing the basis for a molecular serotyping scheme. From these results, differing epidemic patterns were identified between strains that were predominant in different regions. Our study highlights the feasibility and reliability of a serotyping system based on PSgc diversity, and for the first time, presents a molecular serotyping system, as well as an antigenic scheme for E. aerogenes, providing the basis for molecular diagnostics and epidemiological surveillance of this important emerging pathogen. PMID:29616012

Establishment of a Molecular Serotyping Scheme and a Multiplexed Luminex-Based Array for Enterobacter aerogenes.

PubMed

Guo, Xi; Wang, Min; Wang, Lu; Wang, Yao; Chen, Tingting; Wu, Pan; Chen, Min; Liu, Bin; Feng, Lu

2018-01-01

Serotyping based on surface polysaccharide antigens is important for the clinical detection and epidemiological surveillance of pathogens. Polysaccharide gene clusters (PSgcs) are typically responsible for the diversity of bacterial surface polysaccharides. Through whole-genome sequencing and analysis, eight putative PSgc types were identified in 23 Enterobacter aerogenes strains from several geographic areas, allowing us to present the first molecular serotyping system for E. aerogenes . A conventional antigenic scheme was also established and correlated well with the molecular serotyping system that was based on PSgc genetic variation, indicating that PSgc-based molecular typing and immunological serology provide equally valid results. Further, a multiplex Luminex-based array was developed, and a double-blind test was conducted with 97 clinical specimens from Shanghai, China, to validate our array. The results of these analyses indicated that strains containing PSgc4 and PSgc7 comprised the predominant groups. We then examined 86 publicly available E. aerogenes strain genomes and identified an additional seven novel PSgc types, with PSgc10 being the most abundant type. In total, our study identified 15 PSgc types in E. aerogenes , providing the basis for a molecular serotyping scheme. From these results, differing epidemic patterns were identified between strains that were predominant in different regions. Our study highlights the feasibility and reliability of a serotyping system based on PSgc diversity, and for the first time, presents a molecular serotyping system, as well as an antigenic scheme for E. aerogenes , providing the basis for molecular diagnostics and epidemiological surveillance of this important emerging pathogen.

Possibility designing half-wave and full-wave molecular rectifiers by using single benzene molecule

NASA Astrophysics Data System (ADS)

Abbas, Mohammed A.; Hanoon, Falah H.; Al-Badry, Lafy F.

2018-02-01

This work focused on possibility designing half-wave and full-wave molecular rectifiers by using single and two benzene rings, respectively. The benzene rings were threaded by a magnetic flux that changes over time. The quantum interference effect was considered as the basic idea in the rectification action, the para and meta configurations were investigated. All the calculations are performed by using steady-state theoretical model, which is based on the time-dependent Hamiltonian model. The electrical conductance and the electric current are considered as DC output signals of half-wave and full-wave molecular rectifiers. The finding in this work opens up the exciting potential to use these molecular rectifiers in molecular electronics.

Feasibility study of molecular memory device based on DNA using methylation to store information

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

Jiang, Liming; Al-Dirini, Feras; Center for Neural Engineering

DNA, because of its robustness and dense information storage capability, has been proposed as a potential candidate for next-generation storage media. However, encoding information into the DNA sequence requires molecular synthesis technology, which to date is costly and prone to synthesis errors. Reading the DNA strand information is also complex. Ideally, DNA storage will provide methods for modifying stored information. Here, we conduct a feasibility study investigating the use of the DNA 5-methylcytosine (5mC) methylation state as a molecular memory to store information. We propose a new 1-bit memory device and study, based on the density functional theory and non-equilibriummore » Green's function method, the feasibility of electrically reading the information. Our results show that changes to methylation states lead to changes in the peak of negative differential resistance which can be used to interrogate memory state. Our work demonstrates a new memory concept based on methylation state which can be beneficial in the design of next generation DNA based molecular electronic memory devices.« less

A research project-based and self-determined teaching system of molecular biology techniques for undergraduates.

PubMed

Zhang, Shuping

2008-05-01

Molecular biology techniques play a very important role in understanding the biological activity. Students who major in biology should know not only how to perform experiments, but also the reasons for performing them. Having the concept of conducting research by integrating various techniques is especially important. This paper introduces a research project-based and self-determined teaching system of molecular biology techniques for undergraduates. Its aim is to create an environment mimicking real research programs and to help students build up confidence in their research skills. The students are allowed to explore a set of commonly used molecular biology techniques to solve some fundamental problems about genes on their own. They find a gene of interest, write a mini-proposal, and give an oral presentation. This course provides students a foundation before entering the research laboratory and allows them to adapt easily to real research programs. Copyright © 2008 International Union of Biochemistry and Molecular Biology, Inc.

Effect of Ring Strain on the Charge Transport of a Robust Norbornadiene–Quadricyclane-Based Molecular Photoswitch

PubMed Central

2017-01-01

Integrating functional molecules into single-molecule devices is a key step toward the realization of future computing machines based on the smallest possible components. In this context, photoswitching molecules that can make a transition between high and low conductivity in response to light are attractive candidates. Here we present the synthesis and conductance properties of a new type of robust molecular photothermal switch based on the norbornadiene (NB)–quadricyclane (QC) system. The transport through the molecule in the ON state is dominated by a pathway through the π-conjugated system, which is no longer available when the system is switched to the OFF state. Interestingly, in the OFF state we find that the same pathway contributes only 12% to the transport properties. We attribute this observation to the strained tetrahedral geometry of the QC. These results challenge the prevailing assumption that current will simply flow through the shortest through-bond path in a molecule. PMID:28408968

Developing ultrasensitive pressure sensor based on graphene nanoribbon: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Kwon, Oh Kuen; Lee, Jun Ha; Kim, Ki-Sub; Kang, Jeong Won

2013-01-01

We propose schematics for an ultra-sensitive pressure sensor based on graphene-nanoribbon (GNR) and investigate its electromechanical properties using classical molecular dynamics simulations and piezo-electricity theory. Since the top plate applied to the actual pressure is large whereas the contact area on the GNR is very small, both the sensitivity and the sensing range can be adjusted by controlling the aspect ratio between the top plate and the contact point areas. Our calculation shows that the electrical conductivity of GNRs can be tuned by the applied pressure and the electric conductance of the deflected GNR linearly increases with increasing applied pressure for the linear elastic region in low pressure below the cut-off point. In the curves for both the deflection and potential energy, the linear elastic regime in low pressure was explicitly separated with the non-linear elastic regime in high pressure. The proposed GNR-based nanoelectromechanical devices have great potential for application as electromechanical memory, relay or switching devices.

ProbeZT: Simulation of transport coefficients of molecular electronic junctions under environmental effects using Büttiker's probes

NASA Astrophysics Data System (ADS)

Korol, Roman; Kilgour, Michael; Segal, Dvira

2018-03-01

We present our in-house quantum transport package, ProbeZT. This program provides linear response coefficients: electrical and electronic thermal conductances, as well as the thermopower of molecular junctions in which electrons interact with the surrounding thermal environment. Calculations are performed based on the Büttiker probe method, which introduces decoherence, energy exchange and dissipation effects phenomenologically using virtual electrode terminals called probes. The program can realize different types of probes, each introducing various environmental effects, including elastic and inelastic scattering of electrons. The molecular system is described by an arbitrary tight-binding Hamiltonian, allowing the study of different geometries beyond simple one-dimensional wires. Applications of the program to study the thermoelectric performance of molecular junctions are illustrated. The program also has a built-in functionality to simulate electron transport in double-stranded DNA molecules based on a tight-binding (ladder) description of the junction.

Smallest fullerene-like clusters in two-probe device junctions: first principle study

NASA Astrophysics Data System (ADS)

Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

2017-07-01

First principle calculations based on density functional theory are realised to investigate the electron transport of the smallest fullerene-like clusters as two-probe junction devices. The junction devices are constructed by mechanically controlled break junction techniques to ensure the maximum stability of the Be20, B20 and N20 cluster molecular junctions. We investigate the density of states, transmission spectrum, molecular orbitals, current and differential conductance characteristics at discrete bias voltages to gain insight about the various transport phenomena occurring in these nano-junctions. The results show that B20 molecule when stringed to gold electrodes works as an ideal nano-device similar to the pure C20 device and is more symmetric in its characteristic nature. However, in N20 molecular device, the conduction is negligible due to the higher atomic interactions within N20 molecule, despite the fact that it is constructed with penta-valent atoms.

Polymer-Oxide Nanolayer/Al Composite Cathode for Efficient Polymer Light-Emitting Diodes

DTIC Science & Technology

2007-06-30

4. Influence of polymer gate dielectrics on n-channel conduction of pentacene -based organic field-effect transistors J. Appl. Phys. 101, 124505...molecular materials, including rubrene, 1,3,5-tris(2-N-phenyl-benzimidzolyl)benzene (TPBI), pentacene , and 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline...BCP, and pentacene . The inset in Fig. 3 presents the molecular structures. TPBI is often utilized as an effective electron injection and hole-blocking

Characterization of polymer, DNA-based, and silk thin film resistivities and of DNA-based films prepared for enhanced electrical conductivity

NASA Astrophysics Data System (ADS)

Yaney, Perry P.; Ouchen, Fahima; Grote, James G.

2009-08-01

DC resistivity studies were carried out on biopolymer films of DNA-CTMA and silk fibroin, and on selected traditional polymer films, including PMMA and APC. Films of DNA-CTMA versus molecular weight and with conductive dopants PCBM, BAYTRON P and ammonium tetrachloroplatinate are reported. The films were spin coated on glass slides configured for measurements of volume dc resistance. The measurements used the alternating polarity method to record the applied voltage-dependent current independent of charging and background currents. The Arrhenius equation plus a constant was fitted to the conductivity versus temperature data of the polymers and the non-doped DNA-based biopolymers with activation energies ranging from 0.8 to 1.4 eV.

Azobenzenes as light-controlled molecular electronic switches in nanoscale metal-molecule-metal junctions.

PubMed

Mativetsky, Jeffrey M; Pace, Giuseppina; Elbing, Mark; Rampi, Maria A; Mayor, Marcel; Samorì, Paolo

2008-07-23

Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal-molecule-metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach, where a metallic AFM tip was used to electrically contact a gold-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule.

First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

DOE PAGES

Hu, S. X.; Collins, Lee A.; Goncharov, V. N.; ...

2016-04-14

Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations on the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm 3 and T = 15,625 to 500,000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a “Saha-type” model as a function of the CH plasma density and temperature, which exhibits the correct behaviors of continuum lowering and pressure ionization. The thermal conductivities (κ QMD) of CH, derived directly from the Kohn–Sham molecular-dynamics calculations, are then analytically fitted withmore » a generalized Coulomb logarithm [(lnΛ) QMD] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation–hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Furthermore, hydrodynamic simulations of cryogenic deuterium–tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted –20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.« less

Recent advances in targeted endoscopic imaging: Early detection of gastrointestinal neoplasms

PubMed Central

Kwon, Yong-Soo; Cho, Young-Seok; Yoon, Tae-Jong; Kim, Ho-Shik; Choi, Myung-Gyu

2012-01-01

Molecular imaging has emerged as a new discipline in gastrointestinal endoscopy. This technology encompasses modalities that can visualize disease-specific morphological or functional tissue changes based on the molecular signature of individual cells. Molecular imaging has several advantages including minimal damage to tissues, repetitive visualization, and utility for conducting quantitative analyses. Advancements in basic science coupled with endoscopy have made early detection of gastrointestinal cancer possible. Molecular imaging during gastrointestinal endoscopy requires the development of safe biomarkers and exogenous probes to detect molecular changes in cells with high specificity anda high signal-to-background ratio. Additionally, a high-resolution endoscope with an accurate wide-field viewing capability must be developed. Targeted endoscopic imaging is expected to improve early diagnosis and individual therapy of gastrointestinal cancer. PMID:22442742

Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

PubMed Central

Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

2017-01-01

Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

Structure Controlled Long-Range Sequential Tunneling in Carbon-Based Molecular Junctions.

PubMed

Morteza Najarian, Amin; McCreery, Richard L

2017-04-25

Carbon-based molecular junctions consisting of aromatic oligomers between conducting sp 2 hybridized carbon electrodes exhibit structure-dependent current densities (J) when the molecular layer thickness (d) exceeds ∼5 nm. All four of the molecular structures examined exhibit an unusual, nonlinear ln J vs bias voltage (V) dependence which is not expected for conventional coherent tunneling or activated hopping mechanisms. All molecules exhibit a weak temperature dependence, with J increasing typically by a factor of 2 over the range of 200-440 K. Fluorene and anthraquinone show linear plots of ln J vs d with nearly identical J values for the range d = 3-10 nm, despite significant differences in their free-molecule orbital energy levels. The observed current densities for anthraquinone, fluorene, nitroazobenzene, and bis-thienyl benzene for d = 7-10 nm show no correlation with occupied (HOMO) or unoccupied (LUMO) molecular orbital energies, contrary to expectations for transport mechanisms based on the offset between orbital energies and the electrode Fermi level. UV-vis absorption spectroscopy of molecular layers bonded to carbon electrodes revealed internal energy levels of the chemisorbed films and also indicated limited delocalization in the film interior. The observed current densities correlate well with the observed UV-vis absorption maxima for the molecular layers, implying a transport mechanism determined by the HOMO-LUMO energy gap. We conclude that transport in carbon-based aromatic molecular junctions is consistent with multistep tunneling through a barrier defined by the HOMO-LUMO gap, and not by charge transport at the electrode interfaces. In effect, interfacial "injection" at the molecule/electrode interfaces is not rate limiting due to relatively strong electronic coupling, and transport is controlled by the "bulk" properties of the molecular layer interior.

Tuning the thermal conductivity of solar cell polymers through side chain engineering.

PubMed

Guo, Zhi; Lee, Doyun; Liu, Yi; Sun, Fangyuan; Sliwinski, Anna; Gao, Haifeng; Burns, Peter C; Huang, Libai; Luo, Tengfei

2014-05-07

Thermal transport is critical to the performance and reliability of polymer-based energy devices, ranging from solar cells to thermoelectrics. This work shows that the thermal conductivity of a low band gap conjugated polymer, poly(4,8-bis-alkyloxybenzo[1,2-b:4,5-b']dithiophene-2,6-diyl-alt-(alkylthieno[3,4-b]thiophene-2-carboxylate)-2,6-diyl) (PBDTTT), for photovoltaic applications can be actively tuned through side chain engineering. Compared to the original polymer modified with short branched side chains, the engineered polymer using all linear and long side chains shows a 160% increase in thermal conductivity. The thermal conductivity of the polymer exhibits a good correlation with the side chain lengths as well as the crystallinity of the polymer characterized using small-angle X-ray scattering (SAXS) experiments. Molecular dynamics simulations and atomic force microscopy are used to further probe the molecular level local order of different polymers. It is found that the linear side chain modified polymer can facilitate the formation of more ordered structures, as compared to the branched side chain modified ones. The effective medium theory modelling also reveals that the long linear side chain enables a larger heat carrier propagation length and the crystalline phase in the bulk polymer increases the overall thermal conductivity. It is concluded that both the length of the side chains and the induced polymer crystallization are important for thermal transport. These results offer important guidance for actively tuning the thermal conductivity of conjugated polymers through molecular level design.

Research Update: Molecular electronics: The single-molecule switch and transistor

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

Sotthewes, Kai; Heimbuch, René, E-mail: r.heimbuch@utwente.nl; Kumar, Avijit

2014-01-01

In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage dropmore » across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.« less

Electric conductance of a mechanically strained molecular junction from first principles: Crucial role of structural relaxation and conformation sampling

NASA Astrophysics Data System (ADS)

Nguyen, Huu Chuong; Szyja, Bartłomiej M.; Doltsinis, Nikos L.

2014-09-01

Density functional theory (DFT) based molecular dynamics simulations have been performed of a 1,4-benzenedithiol molecule attached to two gold electrodes. To model the mechanical manipulation in typical break junction and atomic force microscopy experiments, the distance between two electrodes was incrementally increased up to the rupture point. For each pulling distance, the electric conductance was calculated using the DFT nonequilibrium Green's-function approach for a statistically relevant sample of configurations extracted from the simulation. With increasing mechanical strain, the formation of monoatomic gold wires is observed. The conductance decreases by three orders of magnitude as the initial twofold coordination of the thiol sulfur to the gold is reduced to a single S-Au bond at each electrode and the order in the electrodes is destroyed. Independent of the pulling distance, the conductance was found to fluctuate by at least two orders of magnitude depending on the instantaneous junction geometry.

Tuning the thermal conductance of molecular junctions with interference effects

NASA Astrophysics Data System (ADS)

Klöckner, J. C.; Cuevas, J. C.; Pauly, F.

2017-12-01

We present an ab initio study of the role of interference effects in the thermal conductance of single-molecule junctions. To be precise, using a first-principles transport method based on density functional theory, we analyze the coherent phonon transport in single-molecule junctions made of several benzene and oligo(phenylene ethynylene) derivatives. We show that the thermal conductance of these junctions can be tuned via the inclusion of substituents, which induces destructive interference effects and results in a decrease of the thermal conductance with respect to the unmodified molecules. In particular, we demonstrate that these interference effects manifest as antiresonances in the phonon transmission, whose energy positions can be tuned by varying the mass of the substituents. Our work provides clear strategies for the heat management in molecular junctions and, more generally, in nanostructured metal-organic hybrid systems, which are important to determine how these systems can function as efficient energy-conversion devices such as thermoelectric generators and refrigerators.

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.

Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology.

PubMed

Sepulveda, Antonia R; Hamilton, Stanley R; Allegra, Carmen J; Grody, Wayne; Cushman-Vokoun, Allison M; Funkhouser, William K; Kopetz, Scott E; Lieu, Christopher; Lindor, Noralane M; Minsky, Bruce D; Monzon, Federico A; Sargent, Daniel J; Singh, Veena M; Willis, Joseph; Clark, Jennifer; Colasacco, Carol; Rumble, R Bryan; Temple-Smolkin, Robyn; Ventura, Christina B; Nowak, Jan A

2017-03-01

To develop evidence-based guideline recommendations through a systematic review of the literature to establish standard molecular biomarker testing of colorectal cancer (CRC) tissues to guide epidermal growth factor receptor (EGFR) therapies and conventional chemotherapy regimens. The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology convened an expert panel to develop an evidence-based guideline to establish standard molecular biomarker testing and guide therapies for patients with CRC. A comprehensive literature search that included more than 4,000 articles was conducted. Twenty-one guideline statements were established. Evidence supports mutational testing for EGFR signaling pathway genes, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize CRC molecular testing are presented. Key Words: Molecular diagnostics; Gastrointestinal; Histology; Genetics; Oncology. Copyright © 2017 American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, American Society for Clinical Oncology, and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Dynamic and Structure of Polymer-Cellulose Composite Electrolyte for Li-ion Battery

NASA Astrophysics Data System (ADS)

Zhan, Pengfei; Maranas, Janna

Crystalline PEO6LiX complex is a tunnel-like polymer/salt structure that promotes fast Li motion. The application is limited because high ion conductivity is only observed with short molecular weight PEO, as the molecular weight increase, tunnels are misaligned and the conductivity is decreased. High aspect ratio nanofillers based on cellulose nanowhiskers are hypothesized to promote the formation of tunnel structures. Compared with unfilled electrolyte, the room temperature ion conductivity increased as much as 1100% in filled electrolyte. With wide angle x-ray scattering (WAXS), we observe that the structure transitions from amorphous phase to crystalline phase as we add cellulose nanowhiskers and this is because the interaction between cellulose surface and polymer chain enhances the crystallization. From the temperature dependence of conductivity, the calculated Li+ hopping activation energy is shown to be lower in acidic cellulose nanowhisker filled samples. Our quasi-elastic neutron scattering (QENS) indicates with acidic surface, the rotation of PEO6 channels are more stabilized and this could be the origin of the low activation energy and high conductivity

High conductance values in π-folded molecular junctions

NASA Astrophysics Data System (ADS)

Carini, Marco; Ruiz, Marta P.; Usabiaga, Imanol; Fernández, José A.; Cocinero, Emilio J.; Melle-Franco, Manuel; Diez-Perez, Ismael; Mateo-Alonso, Aurelio

2017-05-01

Folding processes play a crucial role in the development of function in biomacromolecules. Recreating this feature on synthetic systems would not only allow understanding and reproducing biological functions but also developing new functions. This has inspired the development of conformationally ordered synthetic oligomers known as foldamers. Herein, a new family of foldamers, consisting of an increasing number of anthracene units that adopt a folded sigmoidal conformation by a combination of intramolecular hydrogen bonds and aromatic interactions, is reported. Such folding process opens up an efficient through-space charge transport channel across the interacting anthracene moieties. In fact, single-molecule conductance measurements carried out on this series of foldamers, using the scanning tunnelling microscopy-based break-junction technique, reveal exceptionally high conductance values in the order of 10-1 G0 and a low length decay constant of 0.02 Å-1 that exceed the values observed in molecular junctions that make use of through-space charge transport pathways.

First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

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

Hu, S. X., E-mail: shu@lle.rochester.edu; Goncharov, V. N.; McCrory, R. L.

2016-04-15

Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations of the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm{sup 3} and T = 15 625 to 500 000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a “Saha-type” model as a function of the CH plasma density and temperature, which gives an increasing ionization as the CH density increases even at low temperatures (T < 50 eV). The orbital-free molecular dynamics method is only used to gauge the average ionization behavior of CH under the average-atommore » model in conjunction with the pressure-matching mixing rule. The thermal conductivities (κ{sub QMD}) of CH, derived directly from the Kohn–Sham molecular-dynamics calculations, are then analytically fitted with a generalized Coulomb logarithm [(lnΛ){sub QMD}] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation–hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Hydrodynamic simulations of cryogenic deuterium–tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted ∼20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.« less

A comprehensive study of extended tetrathiafulvalene cruciform molecules for molecular electronics: synthesis and electrical transport measurements.

PubMed

Parker, Christian R; Leary, Edmund; Frisenda, Riccardo; Wei, Zhongming; Jennum, Karsten S; Glibstrup, Emil; Abrahamsen, Peter Bæch; Santella, Marco; Christensen, Mikkel A; Della Pia, Eduardo Antonio; Li, Tao; Gonzalez, Maria Teresa; Jiang, Xingbin; Morsing, Thorbjørn J; Rubio-Bollinger, Gabino; Laursen, Bo W; Nørgaard, Kasper; van der Zant, Herre; Agrait, Nicolas; Nielsen, Mogens Brøndsted

2014-11-26

Cruciform-like molecules with two orthogonally placed π-conjugated systems have in recent years attracted significant interest for their potential use as molecular wires in molecular electronics. Here we present synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene) (OPE) and tetrathiafulvalene (TTF) scaffolds, end-capped with acetyl-protected thiolates as electrode anchoring groups. The molecules were subjected to a comprehensive study of their conducting properties as well as their photophysical and electrochemical properties in solution. The complex nature of the molecules and their possible binding in different configurations in junctions called for different techniques of conductance measurements: (1) conducting-probe atomic force microscopy (CP-AFM) measurements on self-assembled monolayers (SAMs), (2) mechanically controlled break-junction (MCBJ) measurements, and (3) scanning tunneling microscopy break-junction (STM-BJ) measurements. The CP-AFM measurements showed structure-property relationships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increased with the number of dithiafulvene (DTF) units (0, 1, 2) along the wire, and it increased when substituting two arylethynyl end groups of the OPE3 backbone with two DTF units. The MCBJ and STM-BJ studies on single molecules both showed that DTFs decreased the junction formation probability, but, in contrast, no significant influence on the single-molecule conductance was observed. We suggest that the origins of the difference between SAM and single-molecule measurements lie in the nature of the molecule-electrode interface as well as in effects arising from molecular packing in the SAMs. This comprehensive study shows that for complex molecules care should be taken when directly comparing single-molecule measurements and measurements of SAMs and solid-state devices thereof.

Understanding ionic conductivity trends in polyborane solid electrolytes from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Varley, Joel; Kweon, Kyoung; Mehta, Prateek; Shea, Patrick; Heo, Tae Wook; Stavila, Vitalie; Udovic, Terrence; Wood, Brandon

Polyborane salts based on B12H122- , B10H102- , and their carboborane counterparts CB11H12- and CB9H10- demonstrate extraordinary Li and Na superionic conductivity that make them attractive as electrolytes in all-solid-state batteries. Their rich chemical and structural diversity creates a versatile design space that could be used to optimize materials with even higher conductivity at lower temperatures; however, many mechanistic details remain enigmatic, including reasons why certain modifications lead to improved performance. Here, we use extensive ab initio molecular dynamics simulations to broadly explore the dependence of ionic conductivity on cation/anion pair combinations for Li and Na polyborane salts. Further simulations based on Li2B12H12 as a model system are used to probe the additional influence of local perturbations, including modifications to chemistry, stoichiometry, and composition. Carbon doping, anion alloying, and cation off-stoichiometry are found to be favorable because they introduce intrinsic disorder, which facilitates local deviations from the expected cation population. Anion reorientations are also discovered to be critical for conduction, with benefits associated with lattice expansion traceable to the facilitation of anion rotation at larger volumes. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

MICROFLORA INVOLVED IN PHYTOREMEDIATION OF POLYAROMATIC HYDROCARBONS

EPA Science Inventory

This research was accomplished by conducting a series of integrated studies starting with field work at contaminated sites, followed by laboratory studies based on the field work, and concluded with development of preliminary molecular monitoring methods tested on field sam...

Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

PubMed Central

Tambunan, Usman Sumo Friend; Nasution, Mochammad Arfin Fardiansyah; Azhima, Fauziah; Parikesit, Arli Aditya; Toepak, Erwin Prasetya; Idrus, Syarifuddin; Kerami, Djati

2017-01-01

Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔGbinding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever. PMID:28469408

Composite Solid Electrolyte Containing Li+- Conducting Fibers

NASA Technical Reports Server (NTRS)

Appleby, A. John; Wang, Chunsheng; Zhang, Xiangwu

2006-01-01

Improved composite solid polymer electrolytes (CSPEs) are being developed for use in lithium-ion power cells. The matrix components of these composites, like those of some prior CSPEs, are high-molecular-weight dielectric polymers [generally based on polyethylene oxide (PEO)]. The filler components of these composites are continuous, highly-Li(+)-conductive, inorganic fibers. PEO-based polymers alone would be suitable for use as solid electrolytes, were it not for the fact that their room-temperature Li(+)-ion conductivities lie in the range between 10(exp -6) and 10(exp -8) S/cm, too low for practical applications. In a prior approach to formulating a CSPE, one utilizes nonconductive nanoscale inorganic filler particles to increase the interfacial stability of the conductive phase. The filler particles also trap some electrolyte impurities. The achievable increase in conductivity is limited by the nonconductive nature of the filler particles.

Calculating lattice thermal conductivity: a synopsis

NASA Astrophysics Data System (ADS)

Fugallo, Giorgia; Colombo, Luciano

2018-04-01

We provide a tutorial introduction to the modern theoretical and computational schemes available to calculate the lattice thermal conductivity in a crystalline dielectric material. While some important topics in thermal transport will not be covered (including thermal boundary resistance, electronic thermal conduction, and thermal rectification), we aim at: (i) framing the calculation of thermal conductivity within the general non-equilibrium thermodynamics theory of transport coefficients, (ii) presenting the microscopic theory of thermal conduction based on the phonon picture and the Boltzmann transport equation, and (iii) outlining the molecular dynamics schemes to calculate heat transport. A comparative and critical addressing of the merits and drawbacks of each approach will be discussed as well.

Morphometric and molecular analyses of the sand fly species Lutzomyia shannoni (Diptera: Psychodidae: Phlebotominae) collected from seven different geographical areas in the southeastern United States.

PubMed

Florin, David A; Davies, Stephen J; Olsen, Cara; Lawyer, Phillip; Lipnick, Robert; Schultz, George; Rowton, Edgar; Wilkerson, Richard; Keep, Lisa

2011-03-01

A morphometric and molecular study of adult male and female Lutzomyia shannoni (Dyar 1929) collected at seven different locations within the southeastern United States was conducted to assess the degree of divergence between the grouped specimens from each location. The collection locations were as follows: Fort Bragg, NC; Fort Campbell, KY; Fort Rucker, AL; Ossabaw Island, GA; Patuxent National Wildlife Research Refuge, MD; Suwannee National Wildlife Refuge, FL; and Baton Rouge, LA. Forty males and forty females from each location were analyzed morphometrically from 54 and 49 character measurements, respectively. In addition, the molecular markers consisting of the partial cytochrome c oxidase subunit I (from 105 sand flies: 15 specimens/collection site) and the partial internal transcribed spacer 2 (from 42 sand flies: six specimens/collection site) were compared. Multivariate analyses indicate that the low degree of variation between the grouped specimens from each collection site prevents the separation of any collection site into an entity that could be interpreted as a distinct population. The molecular analyses were in concordance with the morphometric study as no collection location grouped into a separate population based on the two partial markers. The grouped specimens from each collection site appear to be within the normal variance of the species, indicating a single population in the southeast United States. It is recommended that additional character analyses of L. shannoni based on more molecular markers, behavioral, ecological, and physiological characteristics, be conducted before ruling out the possibility of populations or a cryptic species complex within the southeastern United States.

Multielectron donors based on TTF-phosphine and ferrocene-phosphine hybrid complexes of a hexarhenium(III) octahedral cluster core.

PubMed

Perruchas, Sandrine; Avarvari, Narcis; Rondeau, David; Levillain, Eric; Batail, Patrick

2005-05-16

Electroactive molecular materials precursors are obtained through coordination chemistry of the hexarhenium cluster core [Re(6)Se(8)](2+) on the six available apical positions with redox-active phosphines bearing tetrathiafulvalene- or ferrocene-based moieties. Single-crystal X-ray diffraction study and electrospray mass spectrometry ascertain the synthesis of these hexasubstituted electroactive clusters, containing up to 12 redox active sites. Cyclic voltammetry experiments demonstrate that these compounds can be reversibly oxidized at rather low potentials, thus allowing an easy access to the corresponding radical species which should provide new conducting and/or magnetic molecular materials.

MIDG-Emerging grid technologies for multi-site preclinical molecular imaging research communities.

PubMed

Lee, Jasper; Documet, Jorge; Liu, Brent; Park, Ryan; Tank, Archana; Huang, H K

2011-03-01

Molecular imaging is the visualization and identification of specific molecules in anatomy for insight into metabolic pathways, tissue consistency, and tracing of solute transport mechanisms. This paper presents the Molecular Imaging Data Grid (MIDG) which utilizes emerging grid technologies in preclinical molecular imaging to facilitate data sharing and discovery between preclinical molecular imaging facilities and their collaborating investigator institutions to expedite translational sciences research. Grid-enabled archiving, management, and distribution of animal-model imaging datasets help preclinical investigators to monitor, access and share their imaging data remotely, and promote preclinical imaging facilities to share published imaging datasets as resources for new investigators. The system architecture of the Molecular Imaging Data Grid is described in a four layer diagram. A data model for preclinical molecular imaging datasets is also presented based on imaging modalities currently used in a molecular imaging center. The MIDG system components and connectivity are presented. And finally, the workflow steps for grid-based archiving, management, and retrieval of preclincial molecular imaging data are described. Initial performance tests of the Molecular Imaging Data Grid system have been conducted at the USC IPILab using dedicated VMware servers. System connectivity, evaluated datasets, and preliminary results are presented. The results show the system's feasibility, limitations, direction of future research. Translational and interdisciplinary research in medicine is increasingly interested in cellular and molecular biology activity at the preclinical levels, utilizing molecular imaging methods on animal models. The task of integrated archiving, management, and distribution of these preclinical molecular imaging datasets at preclinical molecular imaging facilities is challenging due to disparate imaging systems and multiple off-site investigators. A Molecular Imaging Data Grid design, implementation, and initial evaluation is presented to demonstrate the secure and novel data grid solution for sharing preclinical molecular imaging data across the wide-area-network (WAN).

The symmetry of single-molecule conduction.

PubMed

Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

2006-11-14

We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.

[Development of indel markers for molecular authentication of Panax ginseng and P. quinquefolius].

PubMed

Wang, Rong-Bo; Tian, Hui-Li; Wang, Hong-Tao; Li, Gui-Sheng

2018-04-01

Panax ginseng and P. quinquefolius are two kinds of important medicinal herbs. They are morphologically similar but have different pharmacological effects. Therefore, botanical origin authentication of these two ginsengs is of great importance for ensuring pharmaceutical efficacy and food safety. Based on the fact that intron position in orthologous genes is highly conserved across plant species, intron length polymorphisms were exploited from unigenes of ginseng. Specific primers were respectively designed for these two species based on their insertion/deletion sequences of cytochrome P450 and glyceraldehyde 3-phosphate dehydrogenase, and multiplex PCR was conducted for molecular authentication of P.ginseng and P. quinquefolius. The results showed that the developed multiplex PCR assay was effective for molecular authentication of P.ginseng and P. quinquefolius without strict PCR condition and the optimization of reaction system.This study provides a preferred ideal marker system for molecular authentication of ginseng,and the presented method can be employed in origin authentication of other herbal preparations. Copyright© by the Chinese Pharmaceutical Association.

A composite molecular phylogeny of living lemuroid primates.

PubMed

DelPero, Massimiliano; Pozzi, Luca; Masters, Judith C

2006-01-01

Lemuroid phylogeny is a source of lively debate among primatologists. Reconstructions based on morphological, physiological, behavioural and molecular data have yielded a diverse array of tree topologies with few nodes in common. In the last decade, molecular phylogenetic studies have grown in popularity, and a wide range of sequences has been brought to bear on the problem, but consensus has remained elusive. We present an analysis based on a composite molecular data set of approx. 6,400 bp assembled from the National Center for Biotechnology Information (NCBI) database, including both mitochondrial and nuclear genes, and diverse analytical methods. Our analysis consolidates some of the nodes that were insecure in previous reconstructions, but is still equivocal on the placement of some taxa. We conducted a similar analysis of a composite data set of approx. 3,600 bp to investigate the controversial relationships within the family Lemuridae. Here our analysis was more successful; only the position of Eulemur coronatus remained uncertain. Copyright 2006 S. Karger AG, Basel.

Fullerenes, carbon nanotubes, and graphene for molecular electronics.

PubMed

Pinzón, Julio R; Villalta-Cerdas, Adrián; Echegoyen, Luis

2012-01-01

With the constant growing complexity of electronic devices, the top-down approach used with silicon based technology is facing both technological and physical challenges. Carbon based nanomaterials are good candidates to be used in the construction of electronic circuitry using a bottom-up approach, because they have semiconductor properties and dimensions within the required physical limit to establish electrical connections. The unique electronic properties of fullerenes for example, have allowed the construction of molecular rectifiers and transistors that can operate with more than two logical states. Carbon nanotubes have shown their potential to be used in the construction of molecular wires and FET transistors that can operate in the THz frequency range. On the other hand, graphene is not only the most promising material for replacing ITO in the construction of transparent electrodes but it has also shown quantum Hall effect and conductance properties that depend on the edges or chemical doping. The purpose of this review is to present recent developments on the utilization carbon nanomaterials in molecular electronics.

PH Sensitive WO3-Based Microelectrochemical Transistors.

DTIC Science & Technology

1986-09-22

molecular electronics, microelectrochemistr microelectrodes, sur ace modtfication, molecule-based transistors, .... " polyaniline , poly-3-methylthiophene...polypyrrole,8 poly(N-methyl pyrrole),8b polyaniline , 9 or poly(3-methylthiophene),1 0 the polymer- ’-p2 ’ -p " ; , Q ’ , : ’ ’ ’ ... , , ’ i connected...VD. Polypyrrole, 8 polyaniline , 9 and poly(3-methylthiophene)1 0 are similar in that they are conducting when oxidized, and transistors based on these

Length dependence of electron transport through molecular wires--a first principles perspective.

PubMed

Khoo, Khoong Hong; Chen, Yifeng; Li, Suchun; Quek, Su Ying

2015-01-07

One-dimensional wires constitute a fundamental building block in nanoscale electronics. However, truly one-dimensional metallic wires do not exist due to Peierls distortion. Molecular wires come close to being stable one-dimensional wires, but are typically semiconductors, with charge transport occurring via tunneling or thermally-activated hopping. In this review, we discuss electron transport through molecular wires, from a theoretical, quantum mechanical perspective based on first principles. We focus specifically on the off-resonant tunneling regime, applicable to shorter molecular wires (<∼4-5 nm) where quantum mechanics dictates electron transport. Here, conductance decays exponentially with the wire length, with an exponential decay constant, beta, that is independent of temperature. Different levels of first principles theory are discussed, starting with the computational workhorse - density functional theory (DFT), and moving on to many-electron GW methods as well as GW-inspired DFT + Sigma calculations. These different levels of theory are applied in two major computational frameworks - complex band structure (CBS) calculations to estimate the tunneling decay constant, beta, and Landauer-Buttiker transport calculations that consider explicitly the effects of contact geometry, and compute the transmission spectra directly. In general, for the same level of theory, the Landauer-Buttiker calculations give more quantitative values of beta than the CBS calculations. However, the CBS calculations have a long history and are particularly useful for quick estimates of beta. Comparing different levels of theory, it is clear that GW and DFT + Sigma calculations give significantly improved agreement with experiment compared to DFT, especially for the conductance values. Quantitative agreement can also be obtained for the Seebeck coefficient - another independent probe of electron transport. This excellent agreement provides confirmative evidence of off-resonant tunneling in the systems under investigation. Calculations show that the tunneling decay constant beta is a robust quantity that does not depend on details of the contact geometry, provided that the same contact geometry is used for all molecular lengths considered. However, because conductance is sensitive to contact geometry, values of beta obtained by considering conductance values where the contact geometry is changing with the molecular junction length can be quite different. Experimentally measured values of beta in general compare well with beta obtained using DFT + Sigma and GW transport calculations, while discrepancies can be attributed to changes in the experimental contact geometries with molecular length. This review also summarizes experimental and theoretical efforts towards finding perfect molecular wires with high conductance and small beta values.

Molecular origins of conduction channels observed in shot-noise measurements.

PubMed

Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

2006-11-01

Measurements of shot noise from single molecules have indicated the presence of various conduction channels. We present three descriptions of these channels in molecular terms showing that the number of conduction channels is limited by bottlenecks in the molecule and that the channels can be linked to transmission through different junction states. We introduce molecular-conductance orbitals, which allow the transmission to be separated into contributions from individual orbitals and contributions from interference between pairs of orbitals.

Molecular electronics: some views on transport junctions and beyond.

PubMed

Joachim, Christian; Ratner, Mark A

2005-06-21

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of "conduction as scattering" generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions.

Molecular electronics: Some views on transport junctions and beyond

PubMed Central

Joachim, Christian; Ratner, Mark A.

2005-01-01

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of “conduction as scattering” generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions. PMID:15956192

Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

NASA Astrophysics Data System (ADS)

Korol, Roman; Kilgour, Michael; Segal, Dvira

2016-12-01

We study the electrical conductance G and the thermopower S of single-molecule junctions and reveal signatures of different transport mechanisms: off-resonant tunneling, on-resonant coherent (ballistic) motion, and multi-step hopping. These mechanisms are identified by studying the behavior of G and S while varying molecular length and temperature. Based on a simple one-dimensional model for molecular junctions, we derive approximate expressions for the thermopower in these different regimes. Analytical results are compared to numerical simulations, performed using a variant of Büttiker's probe technique, the so-called voltage-temperature probe, which allows us to phenomenologically introduce environmentally induced elastic and inelastic electron scattering effects, while applying both voltage and temperature biases across the junction. We further simulate the thermopower of GC-rich DNA sequences with mediating A:T blocks and manifest the tunneling-to-hopping crossover in both the electrical conductance and the thermopower, in accord with measurements by Li et al. [Nat. Commun. 7, 11294 (2016)].

Molecular dynamics simulation of the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide.

PubMed

Siqueira, Leonardo J A; Ribeiro, Mauro C C

2007-10-11

Thermodynamics, structure, and dynamics of an ionic liquid based on a quaternary ammonium salt with ether side chain, namely, N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide, MOENM2E TFSI, are investigated by molecular dynamics (MD) simulations. Average density and configurational energy of simulated MOENM2E TFSI are interpreted with models that take into account empirical ionic volumes. A throughout comparison of the equilibrium structure of MOENM2E TFSI with previous results for the more common ionic liquids based on imidazolium cations is provided. Several time correlation functions are used to reveal the microscopic dynamics of MOENM2E TFSI. Structural relaxation is discussed by the calculation of simultaneous space-time correlation functions. Temperature effects on transport coefficients (diffusion, conductivity, and viscosity) are investigated. The ratio between the actual conductivity and the estimate from ionic diffusion by the Nernst-Einstein equation indicates that correlated motion of neighboring ions in MOENM2E TFSI is similar to imidazolium ionic liquids. In line with experiment, Walden plot of conductivity and viscosity indicates that simulated MOENM2E TFSI should be classified as a poor ionic liquid.

Pre-examination factors affecting molecular diagnostic test results and interpretation: A case-based approach.

PubMed

Payne, Deborah A; Baluchova, Katarina; Peoc'h, Katell H; van Schaik, Ron H N; Chan, K C Allen; Maekawa, Masato; Mamotte, Cyril; Russomando, Graciela; Rousseau, François; Ahmad-Nejad, Parviz

2017-04-01

Multiple organizations produce guidance documents that provide opportunities to harmonize quality practices for diagnostic testing. The International Organization for Standardization ISO 15189 standard addresses requirements for quality in management and technical aspects of the clinical laboratory. One technical aspect addresses the complexities of the pre-examination phase prior to diagnostic testing. The Committee for Molecular Diagnostics of the International Federation for Clinical Chemistry and Laboratory Medicine (also known as, IFCC C-MD) conducted a survey of international molecular laboratories and determined ISO 15189 to be the most referenced guidance document. In this review, the IFCC C-MD provides case-based examples illustrating the value of select pre-examination processes as these processes relate to molecular diagnostic testing. Case-based examples in infectious disease, oncology, inherited disease and pharmacogenomics address the utility of: 1) providing information to patients and users, 2) designing requisition forms, 3) obtaining informed consent and 4) maintaining sample integrity prior to testing. The pre-examination phase requires extensive and consistent communication between the laboratory, the healthcare provider and the end user. The clinical vignettes presented in this paper illustrate the value of applying select ISO 15189 recommendations for general laboratory to the more specialized area of Molecular Diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.

Negative differential conductance and super-Poissonian shot noise in single-molecule magnet junctions

PubMed Central

Xue, Hai-Bin; Liang, Jiu-Qing; Liu, Wu-Ming

2015-01-01

Molecular spintroinic device based on a single-molecule magnet is one of the ultimate goals of semiconductor nanofabrication technologies. It is thus necessary to understand the electron transport properties of a single-molecule magnet junction. Here we study the negative differential conductance and super-Poissonian shot noise properties of electron transport through a single-molecule magnet weakly coupled to two electrodes with either one or both of them being ferromagnetic. We predict that the negative differential conductance and super-Poissonian shot noise, which can be tuned by a gate voltage, depend sensitively on the spin polarization of the source and drain electrodes. In particular, the shot noise in the negative differential conductance region can be enhanced or decreased originating from the different formation mechanisms of negative differential conductance. The effective competition between fast and slow transport channels is responsible for the observed negative differential conductance and super-Poissonian shot noise. In addition, we further discuss the skewness and kurtosis properties of transport current in the super-Poissonian shot noise regions. Our findings suggest a tunable negative differential conductance molecular device, and the predicted properties of high-order current cumulants are very interesting for a better understanding of electron transport through single-molecule magnet junctions. PMID:25736094

Negative differential conductance and super-Poissonian shot noise in single-molecule magnet junctions.

PubMed

Xue, Hai-Bin; Liang, Jiu-Qing; Liu, Wu-Ming

2015-03-04

Molecular spintroinic device based on a single-molecule magnet is one of the ultimate goals of semiconductor nanofabrication technologies. It is thus necessary to understand the electron transport properties of a single-molecule magnet junction. Here we study the negative differential conductance and super-Poissonian shot noise properties of electron transport through a single-molecule magnet weakly coupled to two electrodes with either one or both of them being ferromagnetic. We predict that the negative differential conductance and super-Poissonian shot noise, which can be tuned by a gate voltage, depend sensitively on the spin polarization of the source and drain electrodes. In particular, the shot noise in the negative differential conductance region can be enhanced or decreased originating from the different formation mechanisms of negative differential conductance. The effective competition between fast and slow transport channels is responsible for the observed negative differential conductance and super-Poissonian shot noise. In addition, we further discuss the skewness and kurtosis properties of transport current in the super-Poissonian shot noise regions. Our findings suggest a tunable negative differential conductance molecular device, and the predicted properties of high-order current cumulants are very interesting for a better understanding of electron transport through single-molecule magnet junctions.

Molecular imprinted polymer functionalized carbon nanotube sensors for detection of saccharides

NASA Astrophysics Data System (ADS)

Badhulika, Sushmee; Mulchandani, Ashok

2015-08-01

In this work, we report the synthesis and fabrication of an enzyme-free sugar sensor based on molecularly imprinted polymer (MIP) on the surface of single walled carbon nanotubes (SWNTs). Electropolymerization of 3-aminophenylboronic acid (3-APBA) in the presence of 10 M d-fructose and fluoride at neutral pH conditions resulted in the formation of a self-doped, molecularly imprinted conducting polymer (MICP) via the formation of a stable anionic boronic ester complex between poly(aniline boronic acid) and d-fructose. Template removal generated binding sites on the polymer matrix that were complementary to d-fructose both in structure, i.e., shape, size, and positioning of functional groups, thus enabling sensing of d-fructose with enhanced affinity and specificity over non-MIP based sensors. Using carbon nanotubes along with MICPs helped to develop an efficient electrochemical sensor by enhancing analyte recognition and signal generation. These sensors could be regenerated and used multiple times unlike conventional affinity based biosensors which suffer from physical and chemical stability.

Conformational gating of DNA conductance

PubMed Central

Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M. P.; Hihath, Joshua

2015-01-01

DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature. PMID:26648400

Conformational gating of DNA conductance.

PubMed

Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M P; Hihath, Joshua

2015-12-09

DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature.

Multiplicity At Early Stages Of Star Formation, Small Clusters. Observations Overview

NASA Astrophysics Data System (ADS)

Saito, Masao

2017-07-01

The SOLA (Soul of Lupus with ALMA) project is conducting comprehensive studies of the Lupus Molecular Clouds and their star formation processes covering 10-10^4 AU scale. Our goal is to exploit ALMA and other facilities over a wide wavelength range to establish a prototypical low-mass star forming scenario based on the Lupus region. In the presentation, we will focus on angular momentum in dense cores in a filament, molecular outflows from young stars, and Class 0/I binary survey in Lupus as well as overview of our projects. Our binary survey was conducted in ALMA cycle 2 and achieved at 0.2-0.3 arcsec resolution discovering new binary systems in Lupus. At the same time, we obtained EX Lup, EXor type burst source, data in ALMA Cycle 3.

Multiplicity at Early Stages of Star Formation, Small Clusters. Observations Overview

NASA Astrophysics Data System (ADS)

Saito, Masao

2017-06-01

The SOLA (Soul of Lupus with ALMA) project is conducting comprehensive studies of the Lupus Molecular Clouds and their star formation processes covering 10-10^4 AU scale. Our goal is to exploit ALMA and other facilities over a wide wavelength range to establish a prototypical low-mass star forming scenario based on the Lupus region. In the presentation, we will focus on angular momentum in dense cores in a filament, molecular outflows from young stars, and Class 0/I binary survey in Lupus as well as overview of our projects. Our binary survey was conducted in ALMA cycle 2 and achieved at 0.2-0.3 arcsec resolution discovering new binary systems in Lupus. At the same time, we obtained EX Lup, EXor type burst source, data in ALMA Cycle 3.

Conducting Polymeric Hydrogel Electrolyte Based on Carboxymethylcellulose and Polyacrylamide/Polyaniline for Supercapacitor Applications

NASA Astrophysics Data System (ADS)

Suganya, N.; Jaisankar, V.; Sivakumar, E. K. T.

Conducting polymer hydrogels represent a unique class of materials that possess enormous application in flexible electronic devices. In the present work, conducting carboxymethylcellulose (CMC)-co-polyacrylamide (PAAm)/polyaniline was synthesized by a two-step interpenetrating network solution polymerization technique. The synthesized CMC-co-PAAm/polyaniline with interpenetrating network structure was prepared by in situ polymerization of aniline to enhance conductivity. The molecular structure and morphology of the copolymer hydrogels were characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. The novel conducting polymer hydrogels show good electrical and electrochemical behavior, which makes them potentially useful in electronic devices such as supercapacitors, biosensors, bioelectronics, solar cells and memory devices.

Current Trends in Sensors Based on Conducting Polymer Nanomaterials

PubMed Central

Yoon, Hyeonseok

2013-01-01

Conducting polymers represent an important class of functional organic materials for next-generation electronic and optical devices. Advances in nanotechnology allow for the fabrication of various conducting polymer nanomaterials through synthesis methods such as solid-phase template synthesis, molecular template synthesis, and template-free synthesis. Nanostructured conducting polymers featuring high surface area, small dimensions, and unique physical properties have been widely used to build various sensor devices. Many remarkable examples have been reported over the past decade. The enhanced sensitivity of conducting polymer nanomaterials toward various chemical/biological species and external stimuli has made them ideal candidates for incorporation into the design of sensors. However, the selectivity and stability still leave room for improvement. PMID:28348348

An all-electric single-molecule motor.

PubMed

Seldenthuis, Johannes S; Prins, Ferry; Thijssen, Joseph M; van der Zant, Herre S J

2010-11-23

Many types of molecular motors have been proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chemical reactions. We propose a new type of molecular motor based on electric field actuation and electric current detection of the rotational motion of a molecular dipole embedded in a three-terminal single-molecule device. The key aspect of this all-electronic design is the conjugated backbone of the molecule, which simultaneously provides the potential landscape of the rotor orientation and a real-time measure of that orientation through the modulation of the conductivity. Using quantum chemistry calculations, we show that this approach provides full control over the speed and continuity of motion, thereby combining electrical and mechanical control at the molecular level over a wide range of temperatures. Moreover, chemistry can be used to change all key parameters of the device, enabling a variety of new experiments on molecular motors.

A nanoscale study of charge extraction in organic solar cells: the impact of interfacial molecular configurations.

PubMed

Tang, Fu-Ching; Wu, Fu-Chiao; Yen, Chia-Te; Chang, Jay; Chou, Wei-Yang; Gilbert Chang, Shih-Hui; Cheng, Horng-Long

2015-01-07

In the optimization of organic solar cells (OSCs), a key problem lies in the maximization of charge carriers from the active layer to the electrodes. Hence, this study focused on the interfacial molecular configurations in efficient OSC charge extraction by theoretical investigations and experiments, including small molecule-based bilayer-heterojunction (sm-BLHJ) and polymer-based bulk-heterojunction (p-BHJ) OSCs. We first examined a well-defined sm-BLHJ model system of OSC composed of p-type pentacene, an n-type perylene derivative, and a nanogroove-structured poly(3,4-ethylenedioxythiophene) (NS-PEDOT) hole extraction layer. The OSC with NS-PEDOT shows a 230% increment in the short circuit current density compared with that of the conventional planar PEDOT layer. Our theoretical calculations indicated that small variations in the microscopic intermolecular interaction among these interfacial configurations could induce significant differences in charge extraction efficiency. Experimentally, different interfacial configurations were generated between the photo-active layer and the nanostructured charge extraction layer with periodic nanogroove structures. In addition to pentacene, poly(3-hexylthiophene), the most commonly used electron-donor material system in p-BHJ OSCs was also explored in terms of its possible use as a photo-active layer. Local conductive atomic force microscopy was used to measure the nanoscale charge extraction efficiency at different locations within the nanogroove, thus highlighting the importance of interfacial molecular configurations in efficient charge extraction. This study enriches understanding regarding the optimization of the photovoltaic properties of several types of OSCs by conducting appropriate interfacial engineering based on organic/polymer molecular orientations. The ultimate power conversion efficiency beyond at least 15% is highly expected when the best state-of-the-art p-BHJ OSCs are combined with present arguments.

Syntheses, spectroscopic characterization, thermal study, molecular modeling, and biological evaluation of novel Schiff's base benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) with Ni(II), and Cu(II) metal complexes

NASA Astrophysics Data System (ADS)

Chandra, Sulekh; Gautam, Seema; Rajor, Hament Kumar; Bhatia, Rohit

2015-02-01

Novel Schiff's base ligand, benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) was synthesized by the condensation of benzil and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio. The structure of ligand was determined on the basis of elemental analyses, IR, 1H NMR, mass, and molecular modeling studies. Synthesized ligand behaved as tetradentate and coordinated to metal ion through sulfur atoms of thiol ring and nitrogen atoms of imine group. Ni(II), and Cu(II) complexes were synthesized with this nitrogen-sulfur donor (N2S2) ligand. Metal complexes were characterized by elemental analyses, molar conductance, magnetic susceptibility measurements, IR, electronic spectra, EPR, thermal, and molecular modeling studies. All the complexes showed molar conductance corresponding to non-electrolytic nature, expect [Ni(L)](NO3)2 complex, which was 1:2 electrolyte in nature. [Cu(L)(SO4)] complex may possessed square pyramidal geometry, [Ni(L)](NO3)2 complex tetrahedral and rest of the complexes six coordinated octahedral/tetragonal geometry. Newly synthesized ligand and its metal complexes were examined against the opportunistic pathogens. Results suggested that metal complexes were more biological sensitive than free ligand.

Lattice thermal conductivity of monolayer AsP from first-principles molecular dynamics.

PubMed

Sun, Yajing; Shuai, Zhigang; Wang, Dong

2018-05-23

Few-layered arsenic-phosphorus alloys, AsxP(1-x), with a puckered structure have been recently synthesized and demonstrated with fully tunable band gaps and optical properties. It is predicted that the carrier mobility of monolayer AsP compounds is even higher than that of black phosphorene (b-P). The anisotropic and orthogonal electrical and thermal transport properties of the puckered group VA elements make them intriguing materials for thermoelectric applications. Herein, we investigated the thermal transport properties of AsP based on first-principles molecular dynamics and the Boltzmann transport equation. We reveal that monolayer AsP with three different chemical structures possesses thermal conductivities lower than b-P, but with increased anisotropy. Further, these structures behave profoundly different on heat conduction. This can be attributed to the distinct low-frequency optical modes associated with their bonding nature. Our results highlight the impact of atomic arrangement on the thermal conductivity of AsP, and the structure-property relationship established may guide the fabrication of thermoelectric materials via the engineered alloying method.

Anomalous length dependence of conductance of aromatic nanoribbons with amine anchoring groups

NASA Astrophysics Data System (ADS)

Bilić, Ante; Sanvito, Stefano

2012-09-01

Two sets of aromatic nanoribbons, based around a common hexagonal scaffolding, with single and dual terminal amine groups have been considered as potential molecular wires in a junction formed by gold leads. Charge transport through the two-terminal device has been modeled using density functional theory (with and without self-interaction correction) and the nonequilibrium Green's function method. The effects of wire length, multiple terminal contacts, and pathways across the junction have been investigated. For nanoribbons with the oligopyrene motif and conventional single amine terminal groups, an increase in the wire length causes an exponential drop in the conductance. In contrast, for the nanoribbons with the oligoperylene motif and dual amine anchoring groups the predicted conductance rises with the wire length over the whole range of investigated lengths. Only when the effects of self-interaction correction are taken into account, the conductance of the oligoperylene ribbons exhibits saturation for longer members of the series. The oligoperylene nanoribbons, with dual amine groups at both terminals, show the potential to fully harness the highly conjugated system of π molecular orbitals across the junction.

Hybrid Organic-Inorganic Films Grown Using Molecular Layer Deposition

DTIC Science & Technology

2011-03-01

shown that zincone films based on DEZ and hydroquinone (HQ) have displayed some conductivity when alloyed with ZnO ALD films [35]. The schematic...11 Schematic showing the two-step reaction sequence for AB zincone MLD growth using diethylzinc (DEZ) and hydroquinone (HQ). The hybrid organic

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

A single molecule rectifier with strong push-pull coupling

NASA Astrophysics Data System (ADS)

Saraiva-Souza, Aldilene; Macedo de Souza, Fabricio; Aleixo, Vicente F. P.; Girão, Eduardo Costa; Filho, Josué Mendes; Meunier, Vincent; Sumpter, Bobby G.; Souza Filho, Antônio Gomes; Del Nero, Jordan

2008-11-01

We theoretically investigate the electronic charge transport in a molecular system composed of a donor group (dinitrobenzene) coupled to an acceptor group (dihydrophenazine) via a polyenic chain (unsaturated carbon bridge). Ab initio calculations based on the Hartree-Fock approximations are performed to investigate the distribution of electron states over the molecule in the presence of an external electric field. For small bridge lengths (n =0-3) we find a homogeneous distribution of the frontier molecular orbitals, while for n >3 a strong localization of the lowest unoccupied molecular orbital is found. The localized orbitals in between the donor and acceptor groups act as conduction channels when an external electric field is applied. We also calculate the rectification behavior of this system by evaluating the charge accumulated in the donor and acceptor groups as a function of the external electric field. Finally, we propose a phenomenological model based on nonequilibrium Green's function to rationalize the ab initio findings.

Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

PubMed

Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

2017-07-21

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

Geological dates and molecular rates: rapid divergence of rivers and their biotas.

PubMed

Waters, Jonathan M; Rowe, Diane L; Apte, Smita; King, Tania M; Wallis, Graham P; Anderson, Leigh; Norris, Richard J; Craw, Dave; Burridge, Christopher P

2007-04-01

We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.

Enhancing electron transport in molecular wires by insertion of a ferrocene center.

PubMed

Sun, Yan-Yan; Peng, Zheng-Lian; Hou, Rong; Liang, Jing-Hong; Zheng, Ju-Fang; Zhou, Xiao-Yi; Zhou, Xiao-Shun; Jin, Shan; Niu, Zhen-Jiang; Mao, Bing-Wei

2014-02-14

We have determined the conductance of alkane-linked ferrocene molecules with carboxylic acid anchoring groups using the STM break junction technique, and three sets of conductance values were found, i.e. high conductance (HC), medium conductance (MC) and low conductance (LC) values. The enhancing effect of the incorporated ferrocene on the electron transport in saturated alkane molecular wires is demonstrated by the increased conductance of the ferrocene molecules, attributed to the reduction of the tunneling barrier and the HOMO-LUMO gap induced by the insertion of ferrocene. Furthermore, the electron-withdrawing carbonyl group on the unconjugated backbone has little or no influence on single-molecule conductance. The current work provides a feasible approach for the design of high-performance molecular wires.

Thermal conductivity of tungsten: Effects of plasma-related structural defects from molecular-dynamics simulations

NASA Astrophysics Data System (ADS)

Hu, Lin; Wirth, Brian D.; Maroudas, Dimitrios

2017-08-01

We report results on the lattice thermal conductivities of tungsten single crystals containing nanoscale-sized pores or voids and helium (He) nanobubbles as a function of void/bubble size and gas pressure in the He bubbles based on molecular-dynamics simulations. For reference, we calculated lattice thermal conductivities of perfect tungsten single crystals along different crystallographic directions at room temperature and found them to be about 10% of the overall thermal conductivity of tungsten with a weak dependence on the heat flux direction. The presence of nanoscale voids in the crystal causes a significant reduction in its lattice thermal conductivity, which decreases with increasing void size. Filling the voids with He to form He nanobubbles and increasing the bubble pressure leads to further significant reduction of the tungsten lattice thermal conductivity, down to ˜20% of that of the perfect crystal. The anisotropy in heat conduction remains weak for tungsten single crystals containing nanoscale-sized voids and He nanobubbles throughout the pressure range examined. Analysis of the pressure and atomic displacement fields in the crystalline region that surrounds the He nanobubbles reveals that the significant reduction of tungsten lattice thermal conductivity in this region is due to phonon scattering from the nanobubbles, as well as lattice deformation around the nanobubbles and formation of lattice imperfections at higher bubble pressure.

Tuning the conductance of H2O@C60 by position of the encapsulated H2O

PubMed Central

Zhu, Chengbo; Wang, Xiaolin

2015-01-01

The change of conductance of single-molecule junction in response to various external stimuli is the fundamental mechanism for the single-molecule electronic devices with multiple functionalities. We propose the concept that the conductance of molecular systems can be tuned from inside. The conductance is varied in C60 with encapsulated H2O, H2O@C60. The transport properties of the H2O@C60-based nanostructure sandwiched between electrodes are studied using first-principles calculations combined with the non-equilibrium Green’s function formalism. Our results show that the conductance of the H2O@C60 is sensitive to the position of the H2O and its dipole direction inside the cage with changes in conductance up to 20%. Our study paves a way for the H2O@C60 molecule to be a new platform for novel molecule-based electronics and sensors. PMID:26643873

Thermal conductance at atomically clean and disordered silicon/aluminum interfaces: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Ih Choi, Woon; Kim, Kwiseon; Narumanchi, Sreekant

2012-09-01

Thermal resistance between layers impedes effective heat dissipation in electronics packaging applications. Thermal conductance for clean and disordered interfaces between silicon (Si) and aluminum (Al) was computed using realistic Si/Al interfaces and classical molecular dynamics with the modified embedded atom method potential. These realistic interfaces, which include atomically clean as well as disordered interfaces, were obtained using density functional theory. At 300 K, the magnitude of interfacial conductance due to phonon-phonon scattering obtained from the classical molecular dynamics simulations was approximately five times higher than the conductance obtained using analytical elastic diffuse mismatch models. Interfacial disorder reduced the thermal conductance due to increased phonon scattering with respect to the atomically clean interface. Also, the interfacial conductance, due to electron-phonon scattering at the interface, was greater than the conductance due to phonon-phonon scattering. This indicates that phonon-phonon scattering is the bottleneck for interfacial transport at the semiconductor/metal interfaces. The molecular dynamics modeling predictions for interfacial thermal conductance for a 5-nm disordered interface between Si/Al were in-line with recent experimental data in the literature.

Conducting non-commercial international clinical trials: the ICR-CTSU experience.

PubMed

Fox, Lisa; Toms, Christy; Kernaghan, Sarah; Snowdon, Claire; Bliss, Judith M

2017-09-26

Academic clinical trials play a fundamental role in the development of new treatments, the repurposing of existing treatments and in addressing areas of unmet clinical need. With cancer treatments increasingly targeted at molecular subtypes, and with priority placed on developing new treatments for rare tumour types, the need for international trial participation to access sufficient patient numbers for successful trial conduct is growing. However, lack of harmonisation of international legal, ethical and financial systems can make this challenging and the cost and effort of conducting trials internationally can be considered prohibitive, particularly where the sample size is comparatively small. The Institute of Cancer Research - Clinical Trials and Statistics Unit (ICR-CTSU) is a UK-based academic clinical trials unit that specialises in the design, conduct and analysis of clinical trials of cancer treatments with an expanding portfolio of trials in molecular subtypes of breast and urological cancers and in other rare cancer types. Implementing appropriate mechanisms to enable international participation has therefore been imperative. In this article, we explain how we have approached the challenges involved and describe examples of successful international trial conduct, achieved through robust collaborations with academic and industry partners. Conducting academic trials internationally is challenging but can and should be achieved through appropriate governance mechanisms and strong collaborations.

On the transport coefficients of hydrogen in the inertial confinement fusion regime

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

Lambert, Flavien; Recoules, Vanina; Decoster, Alain

2011-05-15

Ab initio molecular dynamics is used to compute the thermal and electrical conductivities of hydrogen from 10 to 160 g cm{sup -3} and temperatures up to 800 eV, i.e., thermodynamical conditions relevant to inertial confinement fusion (ICF). The ionic structure is obtained using molecular dynamics simulations based on an orbital-free treatment for the electrons. The transport properties were computed using ab initio simulations in the DFT/LDA approximation. The thermal and electrical conductivities are evaluated using Kubo-Greenwood formulation. Particular attention is paid to the convergence of electronic transport properties with respect to the number of bands and atoms. These calculations aremore » then used to check various analytical models (Hubbard's, Lee-More's and Ichimaru's) widely used in hydrodynamics simulations of ICF capsule implosions. The Lorenz number, which is the ratio between thermal and electrical conductivities, is also computed and compared to the well-known Wiedemann-Franz law in different regimes ranging from the highly degenerate to the kinetic one. This allows us to deduce electrical conductivity from thermal conductivity for analytical model. We find that the coupling of Hubbard and Spitzer models gives a correct description of the behavior of electrical and thermal conductivities in the whole thermodynamic regime.« less

[Researches on virology at the Tohoku University Research Center in the Philippines].

PubMed

Oshitani, Hitoshi; Saito, Mariko; Okamoto, Michiko; Tamaki, Raita; Kamigaki, Taro; Suzuki, Akira

2013-01-01

Tohoku University Graduate School of Medicine has established the Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Diseases at Research Institute for Tropical Medicine (RITM) in the Philippines in 2008. Our aim of the center is to conduct operational researches, which can contribute to control of infectious diseases in the Philippines. Therefore most of our researches in the Philippines are being conducted in the fields. Main research themes include severe acute respiratory infections in children, influenza disease burden study, molecular epidemiology of rabies, and viral etiology of acute diarrhea. The study on severe acute respiratory infections in children in Leyte Island has recruited hospitalized cases with severe pneumonia. We showed that enterovirus 68 was one of important causative agents in severe pneumonia cases. We also conducted other analyses including molecular epidemiology of respiratory syncytial virus (RSV) and pathogenesis of human rhinoviruses (HRV). Based on these studies, we initiated more comprehensive researches in the Philippines since 2010.

Tunnel current across linear homocatenated germanium chains

NASA Astrophysics Data System (ADS)

Matsuura, Yukihito

2014-01-01

The electronic transport properties of germanium oligomers catenating into linear chains (linear Ge chains) have been theoretically studied using first principle methods. The conduction mechanism of a Ge chain sandwiched between gold electrodes was analyzed based on the density of states and the eigenstates of the molecule in a two-probe environment. Like that of silicon chains (Si chains), the highest occupied molecular orbital of Ge chains contains the extended σ-conjugation of Ge 4p orbitals at energy levels close to the Fermi level; this is in contrast to the electronic properties of linear carbon chains. Furthermore, the conductance of a Ge chain is expected to decrease exponentially with molecular length L. The decay constant β, which is defined as e-βL, of a Ge chain is similar to that of a Si chain, whereas the conductance of the Ge chains is higher than that of Si chains even though the Ge-Ge bond length is longer than the Si-Si bond length.

Photoluminescence of Ta2O5 films formed by the molecular layer deposition method

NASA Astrophysics Data System (ADS)

Baraban, A. P.; Dmitriev, V. A.; Prokof'ev, V. A.; Drozd, V. E.; Filatova, E. O.

2016-04-01

Ta2O5 films of different thicknesses (20-100 nm) synthesized by the molecular layer deposition method on p-type silicon substrates and thermally oxidized silicon substrates have been studied by the methods of high-frequency capacitance-voltage characteristics and photoluminescence. A hole-conduction channel is found to form in the Si-Ta2O5-field electrode system. A model of the electronic structure of Ta2O5 films is proposed based on an analysis of the measured PL spectra and performed electrical investigations.

First-principles molecular transport calculation for the benzenedithiolate molecule

NASA Astrophysics Data System (ADS)

Rumetshofer, M.; Dorn, G.; Boeri, L.; Arrigoni, E.; von der Linden, W.

2017-10-01

A first-principles approach based on density functional theory and non-equilibrium Green’s functions is used to study the molecular transport system consisting of benzenedithiolate connected with monoatomic gold and platinum electrodes. Using symmetry arguments we explain why the conductance mechanism is different for gold and platinum electrodes. We present the charge stability diagram for the benzenedithiolate connected with monoatomic platinum electrodes including many-body effects in terms of an extended Hubbard Hamiltonian and discuss how the electrodes and the many-body effects influence the transport properties of the system.

Notre Dame Geothermal Ionic Liquids Research: Ionic Liquids for Utilization of Geothermal Energy

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

Brennecke, Joan F.

The goal of this project was to develop ionic liquids for two geothermal energy related applications. The first goal was to design ionic liquids as high temperature heat transfer fluids. We identified appropriate compounds based on both experiments and molecular simulations. We synthesized the new ILs, and measured their thermal stability, measured storage density, viscosity, and thermal conductivity. We found that the most promising compounds for this application are aminopyridinium bis(trifluoromethylsulfonyl)imide based ILs. We also performed some measurements of thermal stability of IL mixtures and used molecular simulations to better understand the thermal conductivity of nanofluids (i.e., mixtures of ILsmore » and nanoparticles). We found that the mixtures do not follow ideal mixture theories and that the addition of nanoparticles to ILs may well have a beneficial influence on the thermal and transport properties of IL-based heat transfer fluids. The second goal was to use ionic liquids in geothermally driven absorption refrigeration systems. We performed copious thermodynamic measurements and modeling of ionic liquid/water systems, including modeling of the absorption refrigeration systems and the resulting coefficients of performance. We explored some IL/organic solvent mixtures as candidates for this application, both with experimentation and molecular simulations. We found that the COPs of all of the IL/water systems were higher than the conventional system – LiBr/H2O. Thus, IL/water systems appear very attractive for absorption refrigeration applications.« less

Length-Dependent Nanotransport and Charge Hopping Bottlenecks in Long Thiophene-Containing π-Conjugated Molecular Wires.

PubMed

Smith, Christopher E; Odoh, Samuel O; Ghosh, Soumen; Gagliardi, Laura; Cramer, Christopher J; Frisbie, C Daniel

2015-12-23

Self-assembled conjugated molecular wires containing thiophene up to 6 nm in length were grown layer-by-layer using click chemistry. Reflection-absorption infrared spectroscopy, ellipsometry and X-ray photoelectron spectroscopy were used to follow the stepwise growth. The electronic structure of the conjugated wires was studied with cyclic voltammetry and UV-vis spectroscopy as well as computationally with density functional theory (DFT). The current-voltage curves (±1 V) of the conjugated molecular wires were measured with conducting probe atomic force microscopy (CP-AFM) in which the molecular wire film bound to a gold substrate was contacted with a conductive AFM probe. By systematically measuring the low bias junction resistance as a function of length for molecules 1-4 nm long, we extracted the structure dependent tunneling attenuation factor (β) of 3.4 nm(-1) and a contact resistance of 220 kΩ. The crossover from tunneling to hopping transport was observed at a molecular length of 4-5 nm with an activation energy of 0.35 eV extracted from Arrhenius plots of resistance versus temperature. DFT calculations revealed localizations of spin densities (polarons) on molecular wire radical cations. The calculations were employed to gauge transition state energies for hopping of polarons along wire segments. Individual estimated transition state energies were 0.2-0.4 eV, in good agreement with the experimental activation energy. The transition states correspond to flattening of dihedral angles about specific imine bonds. These results open up possibilities to further explore the influence of molecular architecture on hopping transport in molecular junctions, and highlight the utility of DFT to understand charge localization and associated hopping-based transport.

Molecular transistors based on BDT-type molecular bridges.

PubMed

Wheeler, W D; Dahnovsky, Yu

2008-10-21

In this work we study the effect of electron correlations in molecular transistors with molecular bridges based on 1,4-benzene-dithiol (BDT) and 2-nitro-1,4-benzene-dithiol (nitro-BDT) by using ab initio electron propagator calculations. We find that there is no gate field effect for the BDT based transistor in accordance with the experimental data. After verifying the computational method on the BDT molecule, we consider a transistor with a nitro-BDT molecular bridge. From the electron propagator calculations, we predict strong negative differential resistance at small positive and negative values of source-drain voltages. The explanation of the peak and the minimum in the current is given in terms of the molecular orbital picture and switch-on (-off) properties due to the voltage dependencies of the Dyson poles (ionization potentials). When the current is off, the electronic states on both electrodes are populated resulting in the vanishing tunneling probability due to the Pauli principle. Besides the minimum and the maximum in the I-V characteristics, we find a strong gate field effect in the conductance where the peak at V(sd) = 0.15 eV and E(g) = 4x10(-3) a.u. switches to the minimum at E(g) = -4x10(-3) a.u. A similar behavior is discovered at the negative V(sd). Such a feature can be used for fast current modulation by changing the polarity of a gate field.

High Electrical Conductivity of Single Metal-Organic Chains.

PubMed

Ares, Pablo; Amo-Ochoa, Pilar; Soler, José M; Palacios, Juan José; Gómez-Herrero, Julio; Zamora, Félix

2018-05-01

Molecular wires are essential components for future nanoscale electronics. However, the preparation of individual long conductive molecules is still a challenge. MMX metal-organic polymers are quasi-1D sequences of single halide atoms (X) bridging subunits with two metal ions (MM) connected by organic ligands. They are excellent electrical conductors as bulk macroscopic crystals and as nanoribbons. However, according to theoretical calculations, the electrical conductance found in the experiments should be even higher. Here, a novel and simple drop-casting procedure to isolate bundles of few to single MMX chains is demonstrated. Furthermore, an exponential dependence of the electrical resistance of one or two MMX chains as a function of their length that does not agree with predictions based on their theoretical band structure is reported. This dependence is attributed to strong Anderson localization originated by structural defects. Theoretical modeling confirms that the current is limited by structural defects, mainly vacancies of iodine atoms, through which the current is constrained to flow. Nevertheless, measurable electrical transport along distances beyond 250 nm surpasses that of all other molecular wires reported so far. This work places in perspective the role of defects in 1D wires and their importance for molecular electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Peltier cooling in molecular junctions

NASA Astrophysics Data System (ADS)

Cui, Longji; Miao, Ruijiao; Wang, Kun; Thompson, Dakotah; Zotti, Linda Angela; Cuevas, Juan Carlos; Meyhofer, Edgar; Reddy, Pramod

2018-02-01

The study of thermoelectricity in molecular junctions is of fundamental interest for the development of various technologies including cooling (refrigeration) and heat-to-electricity conversion1-4. Recent experimental progress in probing the thermopower (Seebeck effect) of molecular junctions5-9 has enabled studies of the relationship between thermoelectricity and molecular structure10,11. However, observations of Peltier cooling in molecular junctions—a critical step for establishing molecular-based refrigeration—have remained inaccessible. Here, we report direct experimental observations of Peltier cooling in molecular junctions. By integrating conducting-probe atomic force microscopy12,13 with custom-fabricated picowatt-resolution calorimetric microdevices, we created an experimental platform that enables the unified characterization of electrical, thermoelectric and energy dissipation characteristics of molecular junctions. Using this platform, we studied gold junctions with prototypical molecules (Au-biphenyl-4,4'-dithiol-Au, Au-terphenyl-4,4''-dithiol-Au and Au-4,4'-bipyridine-Au) and revealed the relationship between heating or cooling and charge transmission characteristics. Our experimental conclusions are supported by self-energy-corrected density functional theory calculations. We expect these advances to stimulate studies of both thermal and thermoelectric transport in molecular junctions where the possibility of extraordinarily efficient energy conversion has been theoretically predicted2-4,14.

Molecular adsorption on graphene

NASA Astrophysics Data System (ADS)

Kong, Lingmei; Enders, Axel; Rahman, Talat S.; Dowben, Peter A.

2014-11-01

Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H2O, H2, O2, CO, NO2, NO, and NH3), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH2, An-CH3, An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene’s electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity.

The influence of ion content on mobility and ion aggregation in PEO-based single-ion conductors

NASA Astrophysics Data System (ADS)

Caldwell, David; Maranas, Janna

2013-03-01

PEO-based ionomers reduce concentration polarization in solid polymer electrolytes by binding the anion to the polymer backbone. Ionomers have significant ion aggregation compared to PEO/salt systems, and the influence of these aggregates is unclear. When ion transport is coupled to the segmental dynamics of the polymer, aggregation will always reduce ion motion and conductivity. However, the conductivity of PEO ionomers is not sensitive to the degree of aggregation. We present results of molecular dynamics simulations where ion content is systematically varied. We consider the influence of ion content on ion aggregation, polymer mobility and cation motion.

Atomistic simulation of the thermal conductivity in amorphous SiO2 matrix/Ge nanocrystal composites

NASA Astrophysics Data System (ADS)

Kuryliuk, Vasyl V.; Korotchenkov, Oleg A.

2017-04-01

We use nonequilibrium molecular dynamics computer simulations with the Tersoff potential aiming to provide a comprehensive picture of the thermal conductivity of amorphous SiO2 (a-SiO2) matrix with embedded Ge nanocrystals (nc-Ge). The modelling predicts the a-SiO2 matrix thermal conductivity in a temperature range of 50 < T < 500 K yielding a fair agreement with experiment at around room temperature. It is worth noticing that the predicted room-temperature thermal conductivity in a-SiO2 is in very good agreement with the experimental result, which is in marked contrast with the thermal conductivity calculated employing the widely used van Beest-Kramer-van Santen (BKS) potential. We show that the thermal conductivity of composite nc-Ge/a-SiO2 systems decreases steadily with increasing the volume fraction of Ge inclusions, indicative of enhanced interface scattering of phonons imposed by embedded Ge nanocrystals. We also observe that increasing the volume fractions above a certain threshold value results in a progressively increased thermal conductivity of the nanocomposite, which can be explained by increasing volume fraction of a better thermally conducting Ge. Finally, non-equilibrium molecular dynamics simulations with the Tersoff potential are promising for computing the thermal conductivity of nanocomposites based on amorphous SiO2 and can be readily scaled to more complex composite structures with embedded nanoparticles, which thus help design nanocomposites with desired thermal properties.

Molecular detection of Staphylococcus aureus resistant to temperature in milk and its products

NASA Astrophysics Data System (ADS)

Sutejo, Stephani Valentina Harda; Amarantini, Charis; Budiarso, Tri Yahya

2017-11-01

Contamination of Staphylococcus aureus on milk can cause intoxication and infection by Staphylococcal enterotoxin. It has nuc gene, coding thermonuclease enzyme (TNase) that is responsible for nature of resistance in the heating process. This study was conducted to identify nuc gene of as S. aureus isolated from milk and its products like ultra-high temperature, sterile milk, sweetened condensed milk, formula milk, café/milk street traders and fresh milk. Biochemical identification was conducted by using carbohydrate fermentation tests and confirmed by API Staph. Molecular confirmation by amplification of nuc gene using PCR. Based on the results of confirmation using API Staph, all isolates were confirmed as S. aureus with index determinant percentage of 97%. An amplicon product of 270 bp was gained in all isolates. It is concluded that isolate of S. aureus has nuc gene.

Approaching the alloy limit of thermal conductivity in single-crystalline Si-based thermoelectric nanocomposites: A molecular dynamics investigation

PubMed Central

Guo, Ruiqiang; Huang, Baoling

2015-01-01

Single-crystalline Si-based nanocomposites have become promising candidates for thermoelectric applications due to their prominent merits. Reducing the thermal conductivity κ without deteriorating the electrical properties is the key to improve their performance. Through non-equilibrium molecular dynamics simulations, we show that κ of single-crystalline Si-based nanocomposites can be reduced to the alloy limit by embedding various nanoinclusions of similar lattice constants but different lattice orientations or space symmetries with respect to the matrix. The surprisingly low κ is mainly due to the large acoustic phonon density of states mismatch caused by the destruction of lattice periodicity at the interfaces between the nanoinclusions and matrix, which leads to the substantial reduction of phonon group velocity and relaxation time, as well as the enhancement of phonon localization. The resulting κ is also temperature-insensitive due to the dominance of boundary scattering. The increase in thermal resistance induced by lattice structure mismatch mainly comes from the nanoinclusions and the channels between them and is caused by the enhanced boundary scattering at the interfaces parallel to the heat flux. Approaching the alloy limit of κ with potentially improved electrical properties by fillers will remarkably improve ZT of single-crystalline Si-based nanocomposites and extend their application. PMID:25851401

A novel conductivity mechanism of highly disordered carbon systems based on an investigation of graph zeta function

NASA Astrophysics Data System (ADS)

Matsutani, Shigeki; Sato, Iwao

2017-09-01

In the previous report (Matsutani and Suzuki, 2000 [21]), by proposing the mechanism under which electric conductivity is caused by the activational hopping conduction with the Wigner surmise of the level statistics, the temperature-dependent of electronic conductivity of a highly disordered carbon system was evaluated including apparent metal-insulator transition. Since the system consists of small pieces of graphite, it was assumed that the reason why the level statistics appears is due to the behavior of the quantum chaos in each granular graphite. In this article, we revise the assumption and show another origin of the Wigner surmise, which is more natural for the carbon system based on a recent investigation of graph zeta function in graph theory. Our method can be applied to the statistical treatment of the electronic properties of the randomized molecular system in general.

SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance.

PubMed

Jeong, Hyundoo; Yoon, Byung-Jun

2017-03-14

Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular complexes. Two main challenges for network querying algorithms are the high computational complexity of detecting potential isomorphism between the query and the target graphs and ensuring the biological significance of the query results. In this paper, we propose SEQUOIA, a novel network querying algorithm that effectively addresses these issues by utilizing a context-sensitive random walk (CSRW) model for network comparison and minimizing the network conductance of potential matches in the target network. The CSRW model, inspired by the pair hidden Markov model (pair-HMM) that has been widely used for sequence comparison and alignment, can accurately assess the node-to-node correspondence between different graphs by accounting for node insertions and deletions. The proposed algorithm identifies high-scoring network regions based on the CSRW scores, which are subsequently extended by maximally reducing the network conductance of the identified subnetworks. Performance assessment based on real PPI networks and known molecular complexes show that SEQUOIA outperforms existing methods and clearly enhances the biological significance of the query results. The source code and datasets can be downloaded from http://www.ece.tamu.edu/~bjyoon/SEQUOIA .

Molecular imaging assessment of periodontitis lesions in an experimental mouse model.

PubMed

Ideguchi, Hidetaka; Yamashiro, Keisuke; Yamamoto, Tadashi; Shimoe, Masayuki; Hongo, Shoichi; Kochi, Shinsuke; Yoshihara-Hirata, Chiaki; Aoyagi, Hiroaki; Kawamura, Mari; Takashiba, Shogo

2018-06-06

We aimed to evaluate molecular imaging as a novel diagnostic tool for mice periodontitis model induced by ligature and Porphyromonas gingivalis (Pg) inoculation. Twelve female mice were assigned to the following groups: no treatment as control group (n = 4); periodontitis group induced by ligature and Pg as Pg group (n = 4); and Pg group treated with glycyrrhizinic acid (GA) as Pg + GA group (n = 4). All mice were administered a myeloperoxidase (MPO) activity-specific luminescent probe and observed using a charge-coupled device camera on day 14. Image analysis on all mice was conducted using software to determine the signal intensity of inflammation. Additionally, histological and radiographic evaluation for periodontal inflammation and bone resorption at the site of periodontitis, and quantitative enzyme-linked immunosorbent assay (ELISA) were conducted on three mice for each group. Each experiment was performed three times. Levels of serum IgG antibody against P. gingivalis were significantly higher in the Pg than in the Pg + GA group. Histological analyses indicated that the number of osteoclasts and neutrophils were significantly lower in the Pg + GA than in the Pg group. Micro-CT image analysis indicated no difference in bone resorption between the Pg and Pg + GA groups. The signal intensity of MPO activity was detected on the complete craniofacial image; moreover, strong signal intensity was localized specifically at the periodontitis site in the ex vivo palate, with group-wise differences. Molecular imaging analysis based on MPO activity showed high sensitivity of detection of periodontal inflammation in mice. Molecular imaging analysis based on MPO activity has potential as a diagnostic tool for periodontitis.

Synthesis, spectroscopic, thermal and molecular modeling studies of Zn2+, Cd2+ and UO22+ complexes of Schiff bases containing triazole moiety. Antimicrobial, anticancer, antioxidant and DNA binding studies.

PubMed

Gaber, Mohamed; El-Ghamry, Hoda A; Fathalla, Shaimaa K; Mansour, Mohammed A

2018-02-01

A novel series of Zn 2+ , Cd 2+ and UO 2 2+ complexes of ligands namely 1-[(5-mercapto-1H-1,2,4-triazole-3-ylimino) methyl]naphthalene-2-ol (HL 1 ) and [(1H-1,2,4-triazole-3-ylimino) methyl] naphthalene-2-ol (HL 2 ) have been prepared and characterized by different analytical and spectral techniques. The stoichiometry, stereochemistry, conductivity measurements and mode of bonding of the complexes have been elucidated. Accurate comparison of the IR spectra of the ligands with their metal chelates proved the involvement of nitrogen atoms of the azomethine group and/or triazole ring in chelation in addition to the deprotonated hydroxyl oxygen. The UV-Vis and molar conductance data supported the octahedral geometry for the metal complexes. TGA technique has been used to study the thermal decomposition way of the metal complexes and the thermo kinetic parameters were estimated. Valuable information is obtained from calculations of molecular parameters using the molecular modeling techniques. The interaction between the metal complexes and CT-DNA has been studied from which the binding constants (k b ) were calculated. The Schiff bases and their metal chelates have shown potent antimicrobial, antioxidant and antitumor activities. The antitumor activities of the compounds have been tested in vitro against HEPG2 cell line and in silico by the molecular docking analysis with the VEGFR-2 receptor responsible for angiogenesis. Copyright © 2017 Elsevier B.V. All rights reserved.

Controlling ion aggregation and conduction in PEO-based ionomers.

NASA Astrophysics Data System (ADS)

Caldwell, David, II; Maranas, Janna

2015-03-01

PEO-based ionomers are ideal for reducing concentration polarization found in typical solid polymer electrolytes. This is achieved by binding the anion to the polymer backbone, significantly reducing the anions mobility. Ion aggregation is prevalent in these systems, but their influence on SPE performance is difficult to study experimentally. We present results of molecular dynamics simulations that explore the relationship between ion content and temperature on ion aggregation, polymer motion, and ion conduction. An unforeseen result of ionomers is the creation of string like aggregates that form conduction pathways in the amorphous region. These conduction pathways allow for a partial decoupling of ion conduction with polymer dynamics. The improvement in conductivity through the use of ion aggregates can be quantified by calculating the inverse of the Haven Ratio, dubbed f-value. Typical SPEs have an f-value less than 0.2, while the ionomers of study exhibit f-values near unity or higher. Understanding what properties influence the development and use of these conduction pathways will provide insight for further development of solid polymer electrolytes.

Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

Atomistic Detailed Mechanism and Weak Cation-Conducting Activity of HIV-1 Vpu Revealed by Free Energy Calculations

PubMed Central

Padhi, Siladitya; Burri, Raghunadha Reddy; Jameel, Shahid; Priyakumar, U. Deva

2014-01-01

The viral protein U (Vpu) encoded by HIV-1 has been shown to assist in the detachment of virion particles from infected cells. Vpu forms cation-specific ion channels in host cells, and has been proposed as a potential drug target. An understanding of the mechanism of ion transport through Vpu is desirable, but remains limited because of the unavailability of an experimental structure of the channel. Using a structure of the pentameric form of Vpu – modeled and validated based on available experimental data – umbrella sampling molecular dynamics simulations (cumulative simulation time of more than 0.4 µs) were employed to elucidate the energetics and the molecular mechanism of ion transport in Vpu. Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies. The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments. A two-dimensional free energy landscape has been computed to model multiple ion permeation, based on which a mechanism for ion conduction is proposed. It is shown that only one ion can pass through the channel at a time. This, along with a stretch of hydrophobic residues in the transmembrane domain of Vpu, explains the slow kinetics of ion conduction. The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel. PMID:25392993

Three-dimensional protonic conductivity in porous organic cage solids.

PubMed

Liu, Ming; Chen, Linjiang; Lewis, Scott; Chong, Samantha Y; Little, Marc A; Hasell, Tom; Aldous, Iain M; Brown, Craig M; Smith, Martin W; Morrison, Carole A; Hardwick, Laurence J; Cooper, Andrew I

2016-09-13

Proton conduction is a fundamental process in biology and in devices such as proton exchange membrane fuel cells. To maximize proton conduction, three-dimensional conduction pathways are preferred over one-dimensional pathways, which prevent conduction in two dimensions. Many crystalline porous solids to date show one-dimensional proton conduction. Here we report porous molecular cages with proton conductivities (up to 10(-3) S cm(-1) at high relative humidity) that compete with extended metal-organic frameworks. The structure of the organic cage imposes a conduction pathway that is necessarily three-dimensional. The cage molecules also promote proton transfer by confining the water molecules while being sufficiently flexible to allow hydrogen bond reorganization. The proton conduction is explained at the molecular level through a combination of proton conductivity measurements, crystallography, molecular simulations and quasi-elastic neutron scattering. These results provide a starting point for high-temperature, anhydrous proton conductors through inclusion of guests other than water in the cage pores.

Three-dimensional protonic conductivity in porous organic cage solids

NASA Astrophysics Data System (ADS)

Liu, Ming; Chen, Linjiang; Lewis, Scott; Chong, Samantha Y.; Little, Marc A.; Hasell, Tom; Aldous, Iain M.; Brown, Craig M.; Smith, Martin W.; Morrison, Carole A.; Hardwick, Laurence J.; Cooper, Andrew I.

2016-09-01

Proton conduction is a fundamental process in biology and in devices such as proton exchange membrane fuel cells. To maximize proton conduction, three-dimensional conduction pathways are preferred over one-dimensional pathways, which prevent conduction in two dimensions. Many crystalline porous solids to date show one-dimensional proton conduction. Here we report porous molecular cages with proton conductivities (up to 10-3 S cm-1 at high relative humidity) that compete with extended metal-organic frameworks. The structure of the organic cage imposes a conduction pathway that is necessarily three-dimensional. The cage molecules also promote proton transfer by confining the water molecules while being sufficiently flexible to allow hydrogen bond reorganization. The proton conduction is explained at the molecular level through a combination of proton conductivity measurements, crystallography, molecular simulations and quasi-elastic neutron scattering. These results provide a starting point for high-temperature, anhydrous proton conductors through inclusion of guests other than water in the cage pores.

North American isolates of Fusarium graminearum produce a novel type A trichothecene

USDA-ARS?s Scientific Manuscript database

Deoxynivalenol (DON) is a virulence factor of Fusarium graminearum on wheat and most likely on other host plants. A large scale survey of F. graminearum (sensu strictu) conducted in the northern United States revealed the existence of strains which - based on molecular markers - belong to the 3-acet...

Flexible, Carbon-Based Ohmic Contacts for Organic Transistors

NASA Technical Reports Server (NTRS)

Brandon, Erik

2005-01-01

A low-temperature process for fabricating flexible, ohmic contacts for use in organic thin-film transistors (OTFTs) has been developed. Typical drainsource contact materials used previously for OTFTs include (1) vacuum-deposited noble-metal contacts and (2) solution-deposited intrinsically conducting molecular or polymeric contacts. Both of these approaches, however, have serious drawbacks.

Nano-sized, quaternary titanium(IV) metal-organic frameworks with multidentate ligands.

PubMed

Baranwal, Balram Prasad; Singh, Alok Kumar

2010-12-01

Some mononuclear nano-sized, quaternary titanium(IV) complexes having the general formula [Ti(acac)(OOCR)2(SB)] (where Hacac=acetylacetone, R=C15H31 or C17H35, HSB=Schiff bases) have been synthesized using different multidentate ligands. These were characterized by elemental analyses, molecular weight determinations and spectral (FTIR, 1H NMR and powder XRD) studies. Conductance measurement indicated their non-conducting nature which may behave like insulators. Structural parameters like the values of limiting indices h, k, l, cell constants a, b, c, angles α, β, γ and particle size are calculated from powder XRD data for complex 1 which indicated nano-sized triclinic system in them. Bidentate chelating nature of acetylacetone, carboxylate and Schiff base anions in the complexes was established by their infrared spectra. Molecular weight determinations confirmed mononuclear nature of the complexes. On the basis of physico-chemical studies, coordination number 8 was assigned for titanium(IV) in the complexes. Transmission electron microscopy (TEM) and the selected area electron diffraction (SAED) studies indicated spherical particles with poor crystallinity. Copyright © 2010 Elsevier B.V. All rights reserved.

PEG 400-Based Phase Change Materials Nano-Enhanced with Functionalized Graphene Nanoplatelets.

PubMed

Marcos, Marco A; Cabaleiro, David; Guimarey, María J G; Comuñas, María J P; Fedele, Laura; Fernández, Josefa; Lugo, Luis

2017-12-29

This study presents new Nano-enhanced Phase Change Materials, NePCMs, formulated as dispersions of functionalized graphene nanoplatelets in a poly(ethylene glycol) with a mass-average molecular mass of 400 g·mol -1 for possible use in Thermal Energy Storage. Morphology, functionalization, purity, molecular mass and thermal stability of the graphene nanomaterial and/or the poly(ethylene glycol) were characterized. Design parameters of NePCMs were defined on the basis of a temporal stability study of nanoplatelet dispersions using dynamic light scattering. Influence of graphene loading on solid-liquid phase change transition temperature, latent heat of fusion, isobaric heat capacity, thermal conductivity, density, isobaric thermal expansivity, thermal diffusivity and dynamic viscosity were also investigated for designed dispersions. Graphene nanoplatelet loading leads to thermal conductivity enhancements up to 23% while the crystallization temperature reduces up to in 4 K. Finally, the heat storage capacities of base fluid and new designed NePCMs were examined by means of the thermophysical properties through Stefan and Rayleigh numbers. Functionalized graphene nanoplatelets leads to a slight increase in the Stefan number.

PEG 400-Based Phase Change Materials Nano-Enhanced with Functionalized Graphene Nanoplatelets

PubMed Central

Marcos, Marco A.; Guimarey, María J. G.; Comuñas, María J. P.

2017-01-01

This study presents new Nano-enhanced Phase Change Materials, NePCMs, formulated as dispersions of functionalized graphene nanoplatelets in a poly(ethylene glycol) with a mass-average molecular mass of 400 g·mol−1 for possible use in Thermal Energy Storage. Morphology, functionalization, purity, molecular mass and thermal stability of the graphene nanomaterial and/or the poly(ethylene glycol) were characterized. Design parameters of NePCMs were defined on the basis of a temporal stability study of nanoplatelet dispersions using dynamic light scattering. Influence of graphene loading on solid-liquid phase change transition temperature, latent heat of fusion, isobaric heat capacity, thermal conductivity, density, isobaric thermal expansivity, thermal diffusivity and dynamic viscosity were also investigated for designed dispersions. Graphene nanoplatelet loading leads to thermal conductivity enhancements up to 23% while the crystallization temperature reduces up to in 4 K. Finally, the heat storage capacities of base fluid and new designed NePCMs were examined by means of the thermophysical properties through Stefan and Rayleigh numbers. Functionalized graphene nanoplatelets leads to a slight increase in the Stefan number. PMID:29286324

Tuning Interfacial Thermal Conductance of Graphene Embedded in Soft Materials by Vacancy Defects

DOE PAGES

Liu, Ying; Hu, Chongze; Huang, Jingsong; ...

2015-06-23

Nanocomposites based on graphene dispersed in matrices of soft materials are promising thermal management materials. Their effective thermal conductivity depends on both the thermal conductivity of graphene and the conductance of the thermal transport across graphene-matrix interfaces. Here we report on molecular dynamics simulations of the thermal transport across the interfaces between defected graphene and soft materials in two different modes: in the across mode, heat enters graphene from one side of its basal plane and leaves through the other side; in the non-across mode, heat enters or leaves a graphene simultaneously from both sides of its basal plane. Wemore » show that, as the density of vacancy defects in graphene increases from 0 to 8%, the conductance of the interfacial thermal transport in the across mode increases from 160.4 16 to 207.8 11 MW/m2K, while that in the non-across mode increases from 7.2 0.1 to 17.8 0.6 MW/m2K. The molecular mechanisms for these variations of thermal conductance are clarified by using the phonon density of states and structural characteristics of defected graphenes. On the basis of these results and effective medium theory, we show that it is possible to enhance the effective thermal conductivity of thermal nanocomposites by tuning the density of vacancy defects in graphene despite the fact that graphene s thermal conductivity always decreases as vacancy defects are introduced.« less

Conducting single-molecule magnet materials.

PubMed

Cosquer, Goulven; Shen, Yongbing; Almeida, Manuel; Yamashita, Masahiro

2018-05-11

Multifunctional molecular materials exhibiting electrical conductivity and single-molecule magnet (SMM) behaviour are particularly attractive for electronic devices and related applications owing to the interaction between electronic conduction and magnetization of unimolecular units. The preparation of such materials remains a challenge that has been pursued by a bi-component approach of combination of SMM cationic (or anionic) units with conducting networks made of partially oxidized (or reduced) donor (or acceptor) molecules. The present status of the research concerning the preparation of molecular materials exhibiting SMM behaviour and electrical conductivity is reviewed, describing the few molecular compounds where both SMM properties and electrical conductivity have been observed. The evolution of this research field through the years is discussed. The first reported compounds are semiconductors in spite being able to present relatively high electrical conductivity, and the SMM behaviour is observed at low temperatures where the electrical conductivity of the materials is similar to that of an insulator. During the recent years, a breakthrough has been achieved with the coexistence of high electrical conductivity and SMM behaviour in a molecular compound at the same temperature range, but so far without evidence of a synergy between these properties. The combination of high electrical conductivity with SMM behaviour requires not only SMM units but also the regular and as far as possible uniform packing of partially oxidized molecules, which are able to provide a conducting network.

Carbon Nanotube Based Molecular Electronics

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1998-01-01

Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

Syntheses, spectroscopic characterization, thermal study, molecular modeling, and biological evaluation of novel Schiff's base benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) with Ni(II), and Cu(II) metal complexes.

PubMed

Chandra, Sulekh; Gautam, Seema; Rajor, Hament Kumar; Bhatia, Rohit

2015-02-25

Novel Schiff's base ligand, benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) was synthesized by the condensation of benzil and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio. The structure of ligand was determined on the basis of elemental analyses, IR, (1)H NMR, mass, and molecular modeling studies. Synthesized ligand behaved as tetradentate and coordinated to metal ion through sulfur atoms of thiol ring and nitrogen atoms of imine group. Ni(II), and Cu(II) complexes were synthesized with this nitrogen-sulfur donor (N2S2) ligand. Metal complexes were characterized by elemental analyses, molar conductance, magnetic susceptibility measurements, IR, electronic spectra, EPR, thermal, and molecular modeling studies. All the complexes showed molar conductance corresponding to non-electrolytic nature, expect [Ni(L)](NO3)2 complex, which was 1:2 electrolyte in nature. [Cu(L)(SO4)] complex may possessed square pyramidal geometry, [Ni(L)](NO3)2 complex tetrahedral and rest of the complexes six coordinated octahedral/tetragonal geometry. Newly synthesized ligand and its metal complexes were examined against the opportunistic pathogens. Results suggested that metal complexes were more biological sensitive than free ligand. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Press-Printed Conductive Carbon Black Nanoparticle Films for Molecular Detection at the Microscale.

PubMed

Della Pelle, Flavio; Vázquez, Luis; Del Carlo, Michele; Sergi, Manuel; Compagnone, Dario; Escarpa, Alberto

2016-08-26

Carbon black nanoparticle (CBNP) press-transferred film-based transducers for the molecular detection at the microscale level were proposed for the first time. Current-sensing atomic force microscopy (CS-AFM) revealed that the CBNP films were effectively press-transferred, retaining their good conductivity. A significant correlation between the morphology and the resistance was observed. The highest resistance was localized at the top of the press-transferred film protrusions, whereas low values are usually obtained at the deep crevices or grooves. The amount of press-transferred CBNPs is the key parameter to obtain films with improved conductivity, which is in good agreement with the electrochemical response. In addition, the conductivity of such optimum films was not only Ohmic; in fact, tunneling/hopping contributions were observed, as assessed by CS-AFM. The CBNP films acted as exclusive electrochemical transducers as evidenced by using two classes of molecules, that is, neurotransmitters and environmental organic contaminants. These results revealed the potential of these CBNP press-transferred films for providing new options in microfluidics and other related micro- and nanochemistry applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance

NASA Astrophysics Data System (ADS)

Wilson, Michael A.; Nguyen, Thuy Hien; Pohorille, Andrew

2014-12-01

Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation.

The gelation influence on diffusion and conductivity enhancement effect in renewable ionic gels based on a LMWG.

PubMed

Bielejewski, M; Rachocki, A; Kaszyńska, J; Tritt-Goc, J

2018-02-21

This paper reports the interdisciplinary study on molecular dynamics, ionic interactions and electrical conductivity in a quaternary ammonium salt (TMABr) ionogel based on a low molecular weight gelator (LMWG) in a wide range of electrolyte molar concentrations. The thermal scanning conductometry (TSC) was used to investigate the electric properties of the ionogels. The prepared TMABr/H 2 O/LMWG ionogel exhibits better ion transport properties than the dissociated TMA + cation in solution. The enhanced ionic conductivity effect (EICE) was observed in the concentration range of the TMABr salt up to 1 M. To investigate the transport properties of the TMA + cation and solvent molecules in the gel and sol phase, the NMR diffusiometry method was used. The field-cycling relaxometry method (FFC NMR) was applied to study the local motions of the electrolyte at the surface of the gelator matrix. On the basis of the obtained data, the higher ionic conductivity observed in the gel phase has been related to the microstructure of the gel matrix. The possible explanation for the origin of this effect has been given. The investigated system is a thermally reversible physical gel, all registered data were reproducible upon transforming the sample from gel to sol and back to the gel state, confirming the enhancement effect as a permanent property of the investigated ionogels. Therefore, the EICE has been proposed to be used as an internal sensor to monitor the condition of the ionogel phase, thus making them smart materials.

Zellweger Syndrome

MedlinePlus

... Institutes of Health (NIH), conduct research exploring the molecular and genetic basis of Zellweger syndrome and the other PBDs, ... Institutes of Health (NIH), conduct research exploring the molecular and genetic basis of Zellweger syndrome and the other PBDs, ...

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

Controlling single-molecule junction conductance by molecular interactions

NASA Astrophysics Data System (ADS)

Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

2015-07-01

For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment.

Development and validation of risk models and molecular diagnostics to permit personalized management of cancer.

PubMed

Pu, Xia; Ye, Yuanqing; Wu, Xifeng

2014-01-01

Despite the advances made in cancer management over the past few decades, improvements in cancer diagnosis and prognosis are still poor, highlighting the need for individualized strategies. Toward this goal, risk prediction models and molecular diagnostic tools have been developed, tailoring each step of risk assessment from diagnosis to treatment and clinical outcomes based on the individual's clinical, epidemiological, and molecular profiles. These approaches hold increasing promise for delivering a new paradigm to maximize the efficiency of cancer surveillance and efficacy of treatment. However, they require stringent study design, methodology development, comprehensive assessment of biomarkers and risk factors, and extensive validation to ensure their overall usefulness for clinical translation. In the current study, the authors conducted a systematic review using breast cancer as an example and provide general guidelines for risk prediction models and molecular diagnostic tools, including development, assessment, and validation. © 2013 American Cancer Society.

Charge transport with single molecules--an electrochemical approach.

PubMed

Li, Chen; Mishchenko, Artem; Pobelov, Ilya; Wandlowski, Thomas

2010-01-01

After an introduction and brief review of charge transport in nanoscale molecular systems we report on experimental studies in gold / (single) molecule / gold junctions at solid / liquid interfaces employing a scanning tunneling microscopy (STM)-based 'break junction' technique. We demonstrate attempts in developing basic relationships between molecular structure, conductance properties and nanoscale electrochemical concepts based on four case studies from our own work. In experiments with alpha, omega-alkanedithiol and biphenyldithiol molecular junctions we address the role of sulfur-gold couplings and molecular conformation, such as gauche defects in the alkyl chains and the torsion angle between two phenyl rings. Combination with quantum chemistry calculations enabled a detailed molecular-level understanding of the electronic structure and transport characteristics of both systems. Employing the concept of 'electrolyte gating' with redox-active molecules, such as thiol-terminated derivatives of viologens (HS-6V6-SH or (HS-6V6)) we demonstrate the construction of symmetric and asymmetric active molecular junctions with transistor- or diode-like behavior upon polarization in an electrochemical environment. The experimental data could be represented quantitatively by the Kutznetsov/Ulstrup model assuming a two-step electron transfer with partial vibration relaxation. Finally, we show that surface-immobilized gold nanoparticles with a diameter of (2.4 +/- 0.5) nm exhibit features of locally addressable multi-state electronic switching upon electrolyte gating, which appears to be reminiscent of a sequential charging through several 'oxidation/reduction states'.

Molecular fingerprint-region spectroscopy from 5 to 12  μm using an orientation-patterned gallium phosphide optical parametric oscillator.

PubMed

Maidment, Luke; Schunemann, Peter G; Reid, Derryck T

2016-09-15

We report a femtosecond optical parametric oscillator (OPO) based on the new semiconductor gain material orientation-patterned gallium phosphide (OP-GaP), which enables the production of high-repetition-rate femtosecond pulses spanning 5-12 μm with average powers in the few to tens of milliwatts range. This is the first example of a broadband OPO operating across the molecular fingerprint region, and we demonstrate its potential by conducting broadband Fourier-transform spectroscopy using water vapor and a polystyrene reference standard.

DFT-based ab initio MD simulation of the ionic conduction in doped ZrO₂ systems under epitaxial strain.

PubMed

Oka, M; Kamisaka, H; Fukumura, T; Hasegawa, T

2015-11-21

The oxygen ionic conduction in ZrO2 systems under tensile epitaxial strain was investigated by performing ab initio molecular dynamics (MD) calculations based on density functional theory (DFT) to elucidate the essential factors in the colossal ionic conductivity observed in the yttria stabilized ZrO2 (YSZ)/SrTiO3 heterostructure. Three factors were evaluated: lattice strain, oxygen vacancies, and dopants. Phonon calculations based on density functional perturbation theory (DFPT) were used to obtain the most stable structure for nondoped ZrO2 under 7% tensile strain along the a- and b-axes. This structure has the space group Pbcn, which is entirely different from that of cubic ZrO2, suggesting that previous ab initio MD calculations assuming cubic ZrO2 may have overestimated the ionic conductivity due to relaxation from the initial structure to the stable structure (Pbcn). Our MD calculations revealed that the ionic conductivity is enhanced only when tensile strain and oxygen vacancies are incorporated, although the presently obtained diffusion constant is far below the range for the colossal ionic conduction experimentally observed. The enhanced ionic conductivity is due to the combined effects of oxygen sublattice formation induced by strain and deformation of this sublattice by oxygen vacancies.

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

Nakayama, T.; Kubo, O.; Shingaya, Y.

the research of advanced materials based on nanoscience and nanotechnology, it is often desirable to measure nanoscale local electrical conductivity at a designated position of a given sample. For this purpose, multiple-probe scanning probe microscopes (MP-SPMs), in which two, three or four scanning tunneling microscope (STM) or atomic force microscope (AFM) probes are operated independently, have been developed. Each probe in an MP-SPM is used not only for observing high-resolution STM or AFM images but also for forming an electrical contact enabling nanoscale local electrical conductivity measurement. The world's first double-probe STM (DP-STM) developed by the authors, which was subsequentlymore » modified to a triple-probe STM (TP-STM), has been used to measure the conductivities of one-dimensional metal nanowires and carbon nanotubes and also two-dimensional molecular films. A quadruple-probe STM (QP-STM) has also been developed and used to measure the conductivity of two-dimensional molecular films without the ambiguity of contact resistance between the probe and sample. Moreover, a quadruple-probe AFM (QP-AFM) with four conductive tuning-fork-type self-detection force sensing probes has been developed to measure the conductivity of a nanostructure on an insulating substrate. A general-purpose computer software to control four probes at the same time has also been developed and used in the operation of the QP-AFM. These developments and applications of MP-SPMs are reviewed in this paper.« less

Li conduction pathways in solid-state electrolytes: Insights from dynamics and polarizability

NASA Astrophysics Data System (ADS)

Takahashi, Tsukasa; Nagagiri, Koki; Iwadate, Yasuhiko; Utsuno, Futoshi; Yamaguchi, Hiroshi; Ohkubo, Takahiro

2018-04-01

We investigated the dynamical and polarizable properties of Li7P3S11, which is a fast Li-conducting material, by performing ab initio molecular dynamics simulations. A zone analysis based on Li migration highlighted the effective path along which Li diffuses in the crystal. The effective Li diffusion was analyzed in terms of the dynamics and polarizability of the sulfur surrounding the Li migration path. High flexibility and large anisotropic polarizability were the characteristics identified as necessary for the formation of an effective Li migration path. These findings provide principles for understanding Li conduction in solid-state electrolytes.

Binding affinity toward human prion protein of some anti-prion compounds - Assessment based on QSAR modeling, molecular docking and non-parametric ranking.

PubMed

Kovačević, Strahinja; Karadžić, Milica; Podunavac-Kuzmanović, Sanja; Jevrić, Lidija

2018-01-01

The present study is based on the quantitative structure-activity relationship (QSAR) analysis of binding affinity toward human prion protein (huPrP C ) of quinacrine, pyridine dicarbonitrile, diphenylthiazole and diphenyloxazole analogs applying different linear and non-linear chemometric regression techniques, including univariate linear regression, multiple linear regression, partial least squares regression and artificial neural networks. The QSAR analysis distinguished molecular lipophilicity as an important factor that contributes to the binding affinity. Principal component analysis was used in order to reveal similarities or dissimilarities among the studied compounds. The analysis of in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) parameters was conducted. The ranking of the studied analogs on the basis of their ADMET parameters was done applying the sum of ranking differences, as a relatively new chemometric method. The main aim of the study was to reveal the most important molecular features whose changes lead to the changes in the binding affinities of the studied compounds. Another point of view on the binding affinity of the most promising analogs was established by application of molecular docking analysis. The results of the molecular docking were proven to be in agreement with the experimental outcome. Copyright © 2017 Elsevier B.V. All rights reserved.

Charging-induced asymmetry in molecular conductors

NASA Astrophysics Data System (ADS)

Zahid, F.; Ghosh, A. W.; Paulsson, M.; Polizzi, E.; Datta, S.

2004-12-01

We investigate the origin of asymmetry in various measured current-voltage (I-V) characteristics of molecules with no inherent spatial asymmetry, with particular focus on a recent break junction measurement. We argue that such asymmetry arises due to unequal coupling with the contacts and a consequent difference in charging effects, which can only be captured in a self-consistent model for molecular conduction. The direction of the asymmetry depends on the sign of the majority carriers in the molecule. For conduction through highest occupied molecular orbitals (i.e., HOMO or p -type conduction), the current is smaller for positive voltage on the stronger contact, while for conduction through lowest unoccupied molecular orbitals (i.e., LUMO or n -type conduction), the sense of the asymmetry is reversed. Within an extended Hückel description of the molecular chemistry and the contact microstructure (with two adjustable parameters, the position of the Fermi energy and the sulphur-gold bond length), an appropriate description of Poisson’s equation, and a self-consistently coupled nonequilibrium Green’s function description of transport, we achieve good agreement between theoretical and experimental I-V characteristics, both in shape as well as overall magnitude.

Evaluation of bending modulus of lipid bilayers using undulation and orientation analysis

NASA Astrophysics Data System (ADS)

Chaurasia, Adarsh K.; Rukangu, Andrew M.; Philen, Michael K.; Seidel, Gary D.; Freeman, Eric C.

2018-03-01

In the current paper, phospholipid bilayers are modeled using coarse-grained molecular dynamics simulations with the MARTINI force field. The extracted molecular trajectories are analyzed using Fourier analysis of the undulations and orientation vectors to establish the differences between the two approaches for evaluating the bending modulus. The current work evaluates and extends the implementation of the Fourier analysis for molecular trajectories using a weighted horizon-based averaging approach. The effect of numerical parameters in the analysis of these trajectories is explored by conducting parametric studies. Computational modeling results are validated against experimentally characterized bending modulus of lipid membranes using a shape fluctuation analysis. The computational framework is then used to estimate the bending moduli for different types of lipids (phosphocholine, phosphoethanolamine, and phosphoglycerol). This work provides greater insight into the numerical aspects of evaluating the bilayer bending modulus, provides validation for the orientation analysis technique, and explores differences in bending moduli based on differences in the lipid nanostructures.

Fe-porphyrin-based metal–organic framework films as high-surface concentration, heterogeneous catalysts for electrochemical reduction of CO 2

DOE PAGES

Hod, Idan; Sampson, Matthew D.; Deria, Pravas; ...

2015-09-18

Realization of heterogeneous electrochemical CO 2-to-fuel conversion via molecular catalysis under high-flux conditions requires the assembly of large quantities of reactant-accessible catalysts on conductive surfaces. As a proof of principle, we demonstrate that electrophoretic deposition of thin films of an appropriately chosen metal–organic framework (MOF) material is an effective method for immobilizing the needed quantity of catalyst. For electrocatalytic CO 2 reduction, we used a material that contains functionalized Fe-porphyrins as catalytically competent, redox-conductive linkers. The approach yields a high effective surface coverage of electrochemically addressable catalytic sites (~10 15 sites/cm 2). The chemical products of the reduction, obtained withmore » ~100% Faradaic efficiency, are mixtures of CO and H 2. The results validate the strategy of using MOF chemistry to obtain porous, electrode-immobilized, networks of molecular catalysts having competency for energy-relevant electrochemical reactions.« less

Molecular Dynamical Simulation of Thermal Conductivity in Amorphous Structures

NASA Astrophysics Data System (ADS)

Deangelis, Freddy; Henry, Asegun

While current descriptions of thermal transport exists for well-ordered materials such as crystal latices, new methods are needed to describe thermal transport in disordered materials, including amorphous solids. Because such structures lack periodic, long-range order, a group velocity cannot be defined for thermal modes of vibration; thus, the phonon gas model cannot be applied to these structures. Instead, a new framework must be applied to analyze such materials. Using a combination of density functional theory and molecular dynamics, we have analyzed thermal transport in amorphous structures, chiefly amorphous germanium. The analysis allows us to categorize vibrational modes as propagons, diffusons, or locons, and to determine how they contribute to thermal conductivity within amorphous structures. This method is also being extended to other disordered structures such as amorphous polymers. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1148903.

Phonon thermal properties of graphene on h-BN from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zou, Ji-Hang; Cao, Bing-Yang

2017-03-01

Phonon thermal properties of graphene on hexagonal boron nitride are investigated by the molecular dynamics simulations combined with lattice dynamics theory. It is found that the dispersion curves have minor changes for supported graphene because the interlayer coupling is too weak to shift the harmonic phonon properties. The ZA and ZO phonon lifetimes are significantly reduced in supported graphene due to the breakdown of the symmetry-based selection rule. The dominant mean free path (MFP) of graphene is reduced from 90-800 nm to 60-500 nm at 300 K. The mode thermal conductivities of free and supported graphene are 3517 W/ (m.K) and 2200 W/ (m.K) at 300 K, respectively. The thermal conductivity of supported graphene decreases by about 37.4% due to the large reduction of flexural phonon lifetimes, and the relative contribution of flexural modes decreases from 35.0% to 16.7%.

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.

Substrate-induced reduction of graphene thermal conductivity

NASA Astrophysics Data System (ADS)

Koniakhin, S. V.; Utesov, O. I.; Terterov, I. N.; Nalitov, A. V.

2017-01-01

We develop a theory of heat conductivity in supported graphene, accounting for coherent phonon scattering on disorder induced by an amorphous substrate. We derive spectra for in-plane and out-of-plane phonons in the framework of Green's function approach. The energy parameters of the theory are obtained using molecular dynamics simulations for graphene on a SiO2 substrate. The heat conductivity is calculated by the Boltzmann transport equation. We find that the interaction with the substrate drastically reduces the phonon lifetime and completely suppresses the contribution of flexural (ZA) phonons to the heat conductivity. As a result, the total heat conductivity is reduced by several times, which matches with the tendency observed in the available experimental data. The considered effect is important for managing the thermal properties of graphene-based electronic devices.

Conductivity studies of PEG based polymer electrolyte for applications as electrolyte in ion batteries

NASA Astrophysics Data System (ADS)

Patil, Ravikumar V.; Praveen, D.; Damle, R.

2018-05-01

Development of lithium ion batteries employing solid polymer electrolytes as electrolyte material has led to efficient energy storage and usage in many portable devices. However, due to a few drawbacks like lower ionic conductivity of solid polymer electrolytes (SPEs), studies on SPEs for improvement in conductivity still have a good scope. In the present paper, we report the conductivity studies of a new SPE with low molecular weight poly ethylene glycol (PEG) as host polymer in which a salt with larger anion Lithium trifluro methane sulphonate (LTMS). XRD studies have revealed that the salt completely dissociates in the polymer giving a good stable electrolyte at lower salt concentration. Conductivity of the SPEs has been studied as a function of temperature and we reiterate that the conductivity is a thermally activated process and follows Arrhenius type behavior.

Synthesis, spectral and theoretical studies of Ni(II), Pd(II) and Pt(II) complexes of 5-mercapto-1,2,4-triazole-3-imine-2‧-hydroxynaphyhaline

NASA Astrophysics Data System (ADS)

Gaber, Mohamed; El-Ghamry, Hoda; Atlam, Faten; Fathalla, Shaimaa

2015-02-01

Ni(II), Pd(II) and Pt(II) complexes of 5-mercapto-1,2,4-triazole-3-imine-2‧-hydroxynaphthaline have been isolated and characterized by elemental analysis, IR, 1H NMR, EI-mass, UV-vis, molar conductance, magnetic moment measurements and thermogravimetric analysis. The molar conductance values indicated that the complexes are non-electrolytes. The magnetic moment values of the complexes displayed diamagnetic behavior for Pd(II) and Pt(II) complexes and tetrahedral geometrical structure for Ni(II) complex. From the bioinorganic applications point of view, the interaction of the ligand and its metal complexes with CT-DNA was investigated using absorption and viscosity titration techniques. The Schiff-base ligand and its metal complexes have also been screened for their antimicrobial and antitumor activities. Also, theoretical investigation of molecular and electronic structures of the studied ligand and its metal complexes has been carried out. Molecular orbital calculations were performed using DFT (density functional theory) at B3LYP level with standard 6-31G(d,p) and LANL2DZ basis sets to access reliable results to the experimental values. The calculations were performed to obtain the optimized molecular geometry, charge density distribution, extent of distortion from regular geometry, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), Mulliken atomic charges, reactivity index (ΔE), dipole moment (D), global hardness (η), softness (σ), electrophilicity index (ω), chemical potential and Mulliken electronegativity (χ).

Functional Nanopores: A Solid-state Concept for Artificial Reaction Compartments and Molecular Factories.

PubMed

Puebla-Hellmann, Gabriel; Mayor, Marcel; Lörtscher, Emanuel

2016-01-01

On the road towards the long-term goal of the NCCR Molecular Systems Engineering to create artificial molecular factories, we aim at introducing a compartmentalization strategy based on solid-state silicon technology targeting zeptoliter reaction volumes and simultaneous electrical contact to ensembles of well-oriented molecules. This approach allows the probing of molecular building blocks under a controlled environment prior to their use in a complex molecular factory. Furthermore, these ultra-sensitive electrical conductance measurements allow molecular responses to a variety of external triggers to be used as sensing and feedback mechanisms. So far, we demonstrate the proof-of-concept by electrically contacting self-assembled mono-layers of alkane-dithiols as an established test system. Here, the molecular films are laterally constrained by a circular dielectric confinement, forming a so-called 'nanopore'. Device yields above 85% are consistently achieved down to sub-50 nm nanopore diameters. This generic platform will be extended to create distributed, cascaded reactors with individually addressable reaction sites, including interconnecting micro-fluidic channels for electrochemical communication among nanopores and sensing sites for reaction control and feedback. In this scientific outlook, we will sketch how such a solid-state nanopore concept can be used to study various aspects of molecular compounds tailored for operation in a molecular factory.

Structure and properties of polyaniline nanocomposite coatings containing gold nanoparticles formed by low-energy electron beam deposition

NASA Astrophysics Data System (ADS)

Wang, Surui; Rogachev, A. A.; Yarmolenko, M. A.; Rogachev, A. V.; Xiaohong, Jiang; Gaur, M. S.; Luchnikov, P. A.; Galtseva, O. V.; Chizhik, S. A.

2018-01-01

Highly ordered conductive polyaniline (PANI) coatings containing gold nanoparticles were prepared by low-energy electron beam deposition method, with emeraldine base and chloroauric acid used as target materials. The molecular and chemical structure of the layers was studied by Fourier transform infrared, Raman, UV-vis and X-ray photoelectron spectroscopy. The morphology of the coatings was investigated by atomic force and transmission electron microscopy. Conductive properties were obtained by impedance spectroscopy method and scanning spreading resistance microscopy mode at the micro- and nanoscale. It was found that the emeraldine base layers formed from the products of electron-beam dispersion have extended, non-conductive polymer chains with partially reduced structure, with the ratio of imine and amine groups equal to 0.54. In case of electron-beam dispersion of the emeraldine base and chloroauric acid, a protoemeraldine structure is formed with conductivity 0.1 S/cm. The doping of this structure was carried out due to hydrochloric acid vapor and gold nanoparticles formed by decomposition of chloroauric acid, which have a narrow size distribution, with the most probable diameter about 40 nm. These gold nanoparticles improve the conductivity of the thin layers of PANI + Au composite, promoting intra- and intermolecular charge transfer of the PANI macromolecules aligned along the coating surface both at direct and alternating voltage. The proposed deposition method of highly oriented, conductive nanocomposite PANI-based coatings may be used in the direct formation of functional layers on conductive and non-conductive substrates.

Charge transport in molecular junctions: From tunneling to hopping with the probe technique

NASA Astrophysics Data System (ADS)

Kilgour, Michael; Segal, Dvira

2015-07-01

We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This "Landauer-Büttiker's probe technique" can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, kBT/ɛB > 1/25, with ɛB as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker's probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.

Ab Initio -Based Bond Order Potential to Investigate Low Thermal Conductivity of Stanene Nanostructures

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

Cherukara, Mathew J.; Narayanan, Badri; Kinaci, Alper

2016-08-28

We introduce a bond order potential (BOP) for stanene based on an ab initio derived training data set. The potential is optimized to accurately describe the energetics, as well as thermal and mechanical properties of a free-standing sheet, and used to study diverse nanostructures of stanene, including tubes and ribbons. As a representative case study, using the potential, we perform molecular dynamics simulations to study stanene’s structure and temperature-dependent thermal conductivity. We find that the structure of stanene is highly rippled, far in excess of other 2-D materials (e.g., graphene), owing to its low in-plane stiffness (stanene: ~ 25 N/m;more » graphene: ~ 480 N/ m). The extent of stanene’s rippling also shows stronger temperature dependence compared to that in graphene. Furthermore, we find that stanene based nanostructures have significantly lower thermal conductivity compared to graphene based structures owing to their softness (i.e., low phonon group velocities) and high anharmonic response. Our newly developed BOP will facilitate the exploration of stanene based low dimensional heterostructures for thermoelectric and thermal management applications.« less

Single-molecule conductance through multiple π-π-stacked benzene rings determined with direct electrode-to-benzene ring connections.

PubMed

Schneebeli, Severin T; Kamenetska, Maria; Cheng, Zhanling; Skouta, Rachid; Friesner, Richard A; Venkataraman, Latha; Breslow, Ronald

2011-02-23

Understanding electron transport across π-π-stacked systems will help to answer fundamental questions about biochemical redox processes and benefit the design of new materials and molecular devices. Herein we employed the STM break-junction technique to measure the single-molecule conductance of multiple π-π-stacked aromatic rings. We studied electron transport through up to four stacked benzene rings held together in an eclipsed fashion via a paracyclophane scaffold. We found that the strained hydrocarbons studied herein couple directly to gold electrodes during the measurements; hence, we did not require any heteroatom binding groups as electrical contacts. Density functional theory-based calculations suggest that the gold atoms of the electrodes bind to two neighboring carbon atoms of the outermost cyclophane benzene rings in η(2) fashion. Our measurements show an exponential decay of the conductance with an increasing number of stacked benzene rings, indicating a nonresonant tunneling mechanism. Furthermore, STM tip-substrate displacement data provide additional evidence that the electrodes bind to the outermost benzene rings of the π-π-stacked molecular wires.

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.

Insights into How Students Learn the Difference between a Weak Acid and a Strong Acid from Cartoon Tutorials Employing Visualizations

ERIC Educational Resources Information Center

Kelly, Resa M.; Akaygun, Sevil

2016-01-01

This article summarizes an investigation into how Flash-based cartoon video tutorials featuring molecular visualizations affect students' mental models of acetic acid and hydrochloric acid solutions and how the acids respond when tested for electrical conductance. Variation theory served as the theoretical framework for examining how students…

Inferring ancestral distribution area and survival vegetation of Caragana (Fabaceae) in Tertiary

Treesearch

Mingli Zhang; Juanjuan Xue; Qiang Zhang; Stewart C. Sanderson

2015-01-01

Caragana, a leguminous genus mainly restricted to temperate Central and East Asia, occurs in arid, semiarid, and humid belts, and has forest, grassland, and desert ecotypes. Based on the previous molecular phylogenetic tree and dating, biogeographical analyses of extant species area and ecotype were conducted by means of four ancestral optimization approaches: S-DIVA,...

The use of adverse outcome pathway-based toxicity predictions: A case study evaluating the effects of imazalil on fathead minnow reproduction

EPA Science Inventory

Product Description: As a means to increase the efficiency of chemical safety assessment, there is an interest in using data from molecular and cellular bioassays, conducted in a highly automated fashion using modern robotics, to predict toxicity in humans and wildlife. The prese...

Simulating an Investigative Study of Clinical Cancer Samples: Use of Tissue Slides and PCR-based Promoter-Hypermethylation Analysis

ERIC Educational Resources Information Center

Chew, Yuan Yuan; Chin, Cheen Fei; Yeong, Foong May

2015-01-01

Topics on the molecular basis underlying cancer are quite popular among students. Also, excellent textbooks abound that provide interesting materials for discussion during lectures and tutorials about major events leading to cancer formation and progression. However, much less is available for students to conduct experiments for the analysis of…

Conducting Reflective, Hands-On Research with Advanced Characterization Instruments: A High-Level Undergraduate Practical Exploring Solid-State Polymorphism

ERIC Educational Resources Information Center

Coles, S. J.; Mapp, L. K.

2016-01-01

An undergraduate practical exercise has been designed to provide hands-on, instrument-based experience of advanced characterization techniques. A research experience approach is taken, centered around the concept of solid-state polymorphism, which requires a detailed knowledge of molecular and crystal structure to be gained by advanced analytical…

High temperature proton exchange membranes with enhanced proton conductivities at low humidity and high temperature based on polymer blends and block copolymers of poly(1,3-cyclohexadiene) and poly(ethylene glycol)

DOE PAGES

Deng, Shawn; Hassan, Mohammad K.; Nalawade, Amol; ...

2015-09-16

Hot (at 120 °C) and dry (20% relative humidity) operating conditions benefit fuel cell designs based on proton exchange membranes (PEMs) and hydrogen due to simplified system design and increasing tolerance to fuel impurities. In this paper, presented are preparation, partial characterization, and multi-scale modeling of such PEMs based on cross-linked, sulfonated poly(1,3-cyclohexadiene) (xsPCHD) blends and block copolymers with poly(ethylene glycol) (PEG). These low cost materials have proton conductivities 18 times that of current industry standard Nafion at hot, dry operating conditions. Among the membranes studied, the blend xsPCHD-PEG PEM displayed the highest proton conductivity, which exhibits a morphology withmore » higher connectivity of the hydrophilic domain throughout the membrane. Simulation and modeling provide a molecular level understanding of distribution of PEG within this hydrophilic domain and its relation to proton conductivities. Finally, this study demonstrates enhancement of proton conductivity at high temperature and low relative humidity by incorporation of PEG and optimized sulfonation conditions.« less

Localization of vibrational modes leads to reduced thermal conductivity of amorphous heterostructures

NASA Astrophysics Data System (ADS)

Giri, Ashutosh; Donovan, Brian F.; Hopkins, Patrick E.

2018-05-01

We investigate the vibrational heat transfer mechanisms in amorphous Stillinger-Weber silicon and germanium-based alloys and heterostructures via equilibrium and nonequilibrium molecular dynamics simulations along with lattice dynamics calculations. We find that similar to crystalline alloys, amorphous alloys demonstrate large size effects in thermal conductivity, while layering the constituent materials into superlattice structures leads to length-independent thermal conductivities. The thermal conductivity of an amorphous SixGe1 -x alloy reduces by as much as ˜53 % compared to the thermal conductivity of amorphous silicon; compared to the larger reduction in crystalline phases due to alloying, we show that compositional disorder rather than structural disorder has a larger impact on the thermal conductivity reduction. Our thermal conductivity predictions for a-Si/a-Ge superlattices suggest that the alloy limit in amorphous SiGe-based structures can be surpassed with interface densities above ˜0.35 nm-1 . We attribute the larger reduction in thermal conductivity of layered Si/Ge heterostructures to greater localization of modes at and around the cutoff frequency of the softer layer as demonstrated via lattice dynamics calculations and diffusivities of individual eigenmodes calculated according to the Allen-Feldman theory [P. B. Allen and J. L. Feldman, Phys. Rev. B 48, 12581 (1993), 10.1103/PhysRevB.48.12581] for our amorphous SiGe-based alloys and superlattice structures.

Morphological and molecular features of some freshwater prawn species under genus Macrobrachium Spence Bate, 1868 (Crustacea: Decapoda: Palaemonidae) from Myanmar.

PubMed

Mar, Win; Kang, Peng-Fei; Mao, Bin; Wang, Yu-Feng

2018-02-28

Myanmar is abundant in lakes and rivers, yet only a few investigations on the fauna of shrimps and prawns have been conducted and no molecular characteristics of prawn species have been described. This study reveals the morphologically identification of five freshwater prawn species under the genus Macrobrachium, including M. cavernicola, M. australiense, M. johnsoni, M. josephi and Macrobrachium sp.WMY-2017. As there was no previous record and information concerning with M. australiense, M. johnsoni, M. josephi and Macrobrachium sp. WMY-2017, they were regarded as the first record from Myanmar. A fragment of Mitochondrial Cytochrome Oxidase I Gene (COI) was amplified successfully from three studied species: M. australiense, M. josephi, and Macrobrachium sp.WMY-2017. The interspecific divergences of studied species varied from 0.01 to 0.15. The phylogenetic tree based on COI fragment sequences showed that M. australiense was closely related to M. rosenbergii, while Macrobrachium sp. WMY-2017 was closest to M. josephi. The results of molecular phylogeny has clarified the relationship within the genus Macrobrachium and represents the first step toward understanding the pattern of speciation base on molecular approach in Myanmar.

Students' use of atomic and molecular models in learning chemistry

NASA Astrophysics Data System (ADS)

O'Connor, Eileen Ann

1997-09-01

The objective of this study was to investigate the development of introductory college chemistry students' use of atomic and molecular models to explain physical and chemical phenomena. The study was conducted during the first semester of the course at a University and College II. Public institution (Carnegie Commission of Higher Education, 1973). Students' use of models was observed during one-on-one interviews conducted over the course of the semester. The approach to introductory chemistry emphasized models. Students were exposed to over two-hundred and fifty atomic and molecular models during lectures, were assigned text readings that used over a thousand models, and worked interactively with dozens of models on the computer. These models illustrated various features of the spatial organization of valence electrons and nuclei in atoms and molecules. Despite extensive exposure to models in lectures, in textbook, and in computer-based activities, the students in the study based their explanation in large part on a simple Bohr model (electrons arranged in concentric circles around the nuclei)--a model that had not been introduced in the course. Students used visual information from their models to construct their explanation, while overlooking inter-atomic and intra-molecular forces which are not represented explicitly in the models. In addition, students often explained phenomena by adding separate information about the topic without either integrating or logically relating this information into a cohesive explanation. The results of the study demonstrate that despite the extensive use of models in chemistry instruction, students do not necessarily apply them appropriately in explaining chemical and physical phenomena. The results of this study suggest that for the power of models as aids to learning to be more fully realized, chemistry professors must give more attention to the selection, use, integration, and limitations of models in their instruction.

Alternative types of molecule-decorated atomic chains in Au–CO–Au single-molecule junctions

PubMed Central

Balogh, Zoltán; Makk, Péter

2015-01-01

Summary We investigate the formation and evolution of Au–CO single-molecule break junctions. The conductance histogram exhibits two distinct molecular configurations, which are further investigated by a combined statistical analysis. According to conditional histogram and correlation analysis these molecular configurations show strong anticorrelations with each other and with pure Au monoatomic junctions and atomic chains. We identify molecular precursor configurations with somewhat higher conductance, which are formed prior to single-molecule junctions. According to detailed length analysis two distinct types of molecule-affected chain-formation processes are observed, and we compare these results to former theoretical calculations considering bridge- and atop-type molecular configurations where the latter has reduced conductance due to destructive Fano interference. PMID:26199840

Alternative types of molecule-decorated atomic chains in Au-CO-Au single-molecule junctions.

PubMed

Balogh, Zoltán; Makk, Péter; Halbritter, András

2015-01-01

We investigate the formation and evolution of Au-CO single-molecule break junctions. The conductance histogram exhibits two distinct molecular configurations, which are further investigated by a combined statistical analysis. According to conditional histogram and correlation analysis these molecular configurations show strong anticorrelations with each other and with pure Au monoatomic junctions and atomic chains. We identify molecular precursor configurations with somewhat higher conductance, which are formed prior to single-molecule junctions. According to detailed length analysis two distinct types of molecule-affected chain-formation processes are observed, and we compare these results to former theoretical calculations considering bridge- and atop-type molecular configurations where the latter has reduced conductance due to destructive Fano interference.

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

Lebedev, Oleg V.; N.S. Enikolopov Institute of Synthetic Polymer Materials of RAS, Profsoyuznaya st., Moscow, 117393; Kechek’yan, Alexander S.

Electrically conductive oriented polymer nano-composites of different compositions, based on the reactor powder of ultra-high-molecular-weight polyethylene (UHMWPE) with a special morphology, filled with particles of nanostructured graphite (NG), multi-walled carbon nanotubes (MWCNTs), and electrically conductive carbon black (CB), were investigated. Polymer composites were obtained via compaction of the mechanical mixture of the polymer and filler powder, followed by uniaxial deformation of the material under homogeneous shear (HS) conditions (all of the processing stages were conducted at room temperature). Resulted composites possess a high tensile strength, high level of the electrical conductivity and low percolation threshold, owing it to the formationmore » of the segregated conductive structure, The influence of the type of nanosized carbon filler, degree of the deformation under HS condition, temperature and etc. on the electrical conductivity and mechanical properties of strengthened conductive composites oriented under homogeneous shear conditions was investigated. Changes in the electrical conductivity of oriented composite materials during reversible “tension–shrinkage” cycles along the orientation axis direction were studied. A theoretical approach, describing the process of transformation of the conductive system as a response on polymer phase deformation and volume change, was proposed, based on the data received from the analysis of the conductivity behavior during the uniaxial deformation and thermal treatment of composites.« less

Catching TFSI: A Computational-Experimental Approach to β-Cyclodextrin-Based Host-Guest Systems as electrolytes for Li-Ion Batteries.

PubMed

Jeschke, Steffen; Jankowski, Piotr; Best, Adam S; Johansson, Patrik

2018-03-12

Cyclodextrins (CDs) are pyranoside-based macromolecules with a hydrophobic cavity to encapsulate small molecules. They are used as molecular vehicles, for instance in pharmaceutical drug delivery or as solubility enhancer of monomers for their polymerization in aqueous solution. In this context, it was discovered about 10 years ago that the bis(trifluoromethylsulonyl)imide (TFSI) anion forms host-guest complexes with βCD in aqueous media. This sparked interest in using the TFSI anion in lithium-based battery electrolytes open for its encapsulation by βCD as an attractive approach to increase the contribution of the cation to the total ion conductivity. By using semi-empirical quantum mechanical (SQM) methods and the conductor-like screening model for a real solvent (COSMO-RS), a randomly methylated βCD (RMβCD) is here identified as a suitable host for TFSI when using organic solvents often used in battery technology. By combining molecular dynamics (MD) simulations with different NMR and FTIR experiments, the formation of the corresponding RMβCD-TFSI complex was investigated. Finally, the effects of the addition RMβCD to a set of electrolytes on the ion conductivity are measured and explained using three distinct scenarios. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, characterization and molecular weight monitoring of a novel Schiff base polymer containing phenol group: Thermal stability, conductivity and antimicrobial properties

NASA Astrophysics Data System (ADS)

Yılmaz Baran, Nuray; Saçak, Mehmet

2017-10-01

A novel Schiff base polymer containing phenol group, Poly(3-[[4-(dimethylamino)benzylidene]amino]phenol) P(3-DBAP), was prepared by oxidative polycondensation reaction of 3-[[4-(dimethylamino)benzylidene]amino]phenol (3-DBAP) using NaOCl, H2O2, O2 oxidants in aqueous alkaline medium. Yield and molecular weight distribution of P(3-DBAP) were monitored depending on oxidant types and concentration, monomer concentration and as well as polymerization temperature and time. UV-Vis, FTIR and 1HNMR techniques were used to identify the structures of Schiff base monomer and polymer. Thermal behavior of P(3-DBAP), which was determined to be thermally stable up to 1200 °C via TG-DTG techniques, was illuminated by Thermo-IR spectra recorded in the temperature range of 25-800 °C. It was determined that the electrical conductivity value of the P(3-DBAP) increased 108 fold after doped with iodine for 24 h at 60 °C according to undoped form and it was measured 4.6 × 10-4 S/cm. Also, antibacterial and antifungal activities of the monomer and polymer were assayed against Sarcina lutea, Enterobacter aerogenes, Escherichia coli, Enterococcus Feacalis, Klebsiella pneumoniae, Bacillus subtilis bacteria, and Candida albicans, Saccharomyces cerevisiae fungi.

AFLP-based genetic diversity and its comparison with diversity based on SSR, SAMPL, and phenotypic traits in bread wheat.

PubMed

Roy, J K; Lakshmikumaran, M S; Balyan, H S; Gupta, P K

2004-02-01

Data on AFLP (eight primer pairs) and 14 phenotypic traits, collected on 55 elite and exotic bread wheat genotypes, were utilized for estimations of genetic diversity. We earlier used these 55 genotypes for a similar study using SSRs and SAMPL. As many as 615 scorable AFLP bands visualized included 287 (46.6%) polymorphic bands. The phenotypic traits included yield and its component traits, as well as physiomorphological traits like flag leaf area. Dendrograms were prepared using cluster analysis based on Jaccard's similarity coefficients in case of AFLP and on squared Euclidean distances in case of phenotypic traits. PCA was conducted using AFLP data and a PCA plot was prepared, which was compared with clustering patterns in two dendrograms, one each for AFLP and phenotypic traits. The results were also compared with published results that included studies conducted elsewhere using entirely different wheat germplasm and our own SSR and SAMPL studies based on the same 55 genotypes used in the present study. It was shown that molecular markers are superior to phenotypic traits and that AFLP and SAMPL are superior to other molecular markers for estimation of genetic diversity. On the basis of AFLP analysis and keeping in view the yield performance and stability, a pair of genotypes (E3876 and E677) was recommended for hybridization in order to develop superior cultivars.

Electrically conductive ZnO/GaN distributed Bragg reflectors grown by hybrid plasma-assisted molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Hjort, Filip; Hashemi, Ehsan; Adolph, David; Ive, Tommy; Haglund, Àsa

2017-02-01

III-nitride-based vertical-cavity surface-emitting lasers have so far used intracavity contacting schemes since electrically conductive distributed Bragg reflectors (DBRs) have been difficult to achieve. A promising material combination for conductive DBRs is ZnO/GaN due to the small conduction band offset and ease of n-type doping. In addition, this combination offers a small lattice mismatch and high refractive index contrast, which could yield a mirror with a broad stopband and a high peak reflectivity using less than 20 DBR-pairs. A crack-free ZnO/GaN DBR was grown by hybrid plasma-assisted molecular beam epitaxy. The ZnO layers were approximately 20 nm thick and had an electron concentration of 1×1019 cm-3, while the GaN layers were 80-110 nm thick with an electron concentration of 1.8×1018 cm-3. In order to measure the resistance, mesa structures were formed by dry etching through the top 3 DBR-pairs and depositing non-annealed Al contacts on the GaN-layers at the top and next to the mesas. The measured specific series resistance was dominated by the lateral and contact contributions and gave an upper limit of 10-3Ωcm2 for the vertical resistance. Simulations show that the ZnO electron concentration and the cancellation of piezoelectric and spontaneous polarization in strained ZnO have a large impact on the vertical resistance and that it could be orders of magnitudes lower than what was measured. This is the first report on electrically conductive ZnO/GaN DBRs and the upper limit of the resistance reported here is close to the lowest values reported for III-nitride-based DBRs.

Automated combinatorial method for fast and robust prediction of lattice thermal conductivity

NASA Astrophysics Data System (ADS)

Plata, Jose J.; Nath, Pinku; Usanmaz, Demet; Toher, Cormac; Fornari, Marco; Buongiorno Nardelli, Marco; Curtarolo, Stefano

The lack of computationally inexpensive and accurate ab-initio based methodologies to predict lattice thermal conductivity, κl, without computing the anharmonic force constants or performing time-consuming ab-initio molecular dynamics, is one of the obstacles preventing the accelerated discovery of new high or low thermal conductivity materials. The Slack equation is the best alternative to other more expensive methodologies but is highly dependent on two variables: the acoustic Debye temperature, θa, and the Grüneisen parameter, γ. Furthermore, different definitions can be used for these two quantities depending on the model or approximation. Here, we present a combinatorial approach based on the quasi-harmonic approximation to elucidate which definitions of both variables produce the best predictions of κl. A set of 42 compounds was used to test accuracy and robustness of all possible combinations. This approach is ideal for obtaining more accurate values than fast screening models based on the Debye model, while being significantly less expensive than methodologies that solve the Boltzmann transport equation.

Quantum interference in coherent tunneling through branched molecular junctions containing ferrocene centers

NASA Astrophysics Data System (ADS)

Zhao, Xin; Kastlunger, Georg; Stadler, Robert

2017-08-01

In our theoretical study where we combine a nonequilibrium Green's function approach with density functional theory we investigate branched compounds containing ferrocene moieties in both branches which, due to their metal centers, are designed to allow for asymmetry induced by local charging. In these compounds the ferrocene moieties are connected to pyridyl anchor groups either directly or via acetylenic spacers in a metaconnection, where we also compare our results with those obtained for the respective single-branched molecules with both meta- and paraconnections between the metal center and the anchors. We find a destructive quantum interference (DQI) feature in the transmission function slightly below the lowest unoccupied molecular orbital, which dominates the conductance even for the uncharged branched compound with spacer groups inserted. In an analysis based on mapping the structural characteristics of the range of molecules in our article onto tight-binding models, we identify the structural source of the DQI minimum as the through-space coupling between the pyridyl anchor groups. We also find that local charging in one of the branches changes the conductance only by about one order of magnitude, which we explain in terms of the spatial distributions of the relevant molecular orbitals for the branched compounds.

Systematic computational and experimental investigation of lithium-ion transport mechanisms in polyester-based polymer electrolytes

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

Webb, Michael A.; Jung, Yukyung; Pesko, Danielle M.

Understanding the mechanisms of lithium-ion transport in polymers is crucial for the design of polymer electrolytes. We combine modular synthesis, electrochemical characterization, and molecular simulation to investigate lithium-ion transport in a new family of polyester-based polymers and in poly(ethylene oxide) (PEO). Theoretical predictions of glass-transition temperatures and ionic conductivities in the polymers agree well with experimental measurements. Interestingly, both the experiments and simulations indicate that the ionic conductivity of PEO, relative to the polyesters, is far higher than would be expected from its relative glass-transition temperature. The simulations reveal that diffusion of the lithium cations in the polyesters proceeds viamore » a different mechanism than in PEO, and analysis of the distribution of available cation solvation sites in the various polymers provides a novel and intuitive way to explain the experimentally observed ionic conductivities. This work provides a platform for the evaluation and prediction of ionic conductivities in polymer electrolyte materials.« less

Systematic computational and experimental investigation of lithium-ion transport mechanisms in polyester-based polymer electrolytes

DOE PAGES

Webb, Michael A.; Jung, Yukyung; Pesko, Danielle M.; ...

2015-07-10

Understanding the mechanisms of lithium-ion transport in polymers is crucial for the design of polymer electrolytes. We combine modular synthesis, electrochemical characterization, and molecular simulation to investigate lithium-ion transport in a new family of polyester-based polymers and in poly(ethylene oxide) (PEO). Theoretical predictions of glass-transition temperatures and ionic conductivities in the polymers agree well with experimental measurements. Interestingly, both the experiments and simulations indicate that the ionic conductivity of PEO, relative to the polyesters, is far higher than would be expected from its relative glass-transition temperature. The simulations reveal that diffusion of the lithium cations in the polyesters proceeds viamore » a different mechanism than in PEO, and analysis of the distribution of available cation solvation sites in the various polymers provides a novel and intuitive way to explain the experimentally observed ionic conductivities. This work provides a platform for the evaluation and prediction of ionic conductivities in polymer electrolyte materials.« less

Systematic Computational and Experimental Investigation of Lithium-Ion Transport Mechanisms in Polyester-Based Polymer Electrolytes

PubMed Central

2015-01-01

Understanding the mechanisms of lithium-ion transport in polymers is crucial for the design of polymer electrolytes. We combine modular synthesis, electrochemical characterization, and molecular simulation to investigate lithium-ion transport in a new family of polyester-based polymers and in poly(ethylene oxide) (PEO). Theoretical predictions of glass-transition temperatures and ionic conductivities in the polymers agree well with experimental measurements. Interestingly, both the experiments and simulations indicate that the ionic conductivity of PEO, relative to the polyesters, is far higher than would be expected from its relative glass-transition temperature. The simulations reveal that diffusion of the lithium cations in the polyesters proceeds via a different mechanism than in PEO, and analysis of the distribution of available cation solvation sites in the various polymers provides a novel and intuitive way to explain the experimentally observed ionic conductivities. This work provides a platform for the evaluation and prediction of ionic conductivities in polymer electrolyte materials. PMID:27162971

Complete series of chiral paramagnetic molecular conductors based on tetramethyl-bis(ethylenedithio)-tetrathiafulvalene (TM-BEDT-TTF) and Chloranilate-bridged heterobimetallic honeycomb layers.

PubMed

Atzori, Matteo; Pop, Flavia; Auban-Senzier, Pascale; Clérac, Rodolphe; Canadell, Enric; Mercuri, Maria Laura; Avarvari, Narcis

2015-04-06

Electrocrystallization of enantiopure (S,S,S,S)- and (R,R,R,R)-tetramethyl-bis(ethylenedithio)-tetrathiafulvalene (TM-BEDT-TTF) donors, as well as the racemic mixture, in the presence of potassium cations and the tris(chloranilato)ferrate(III) [Fe(Cl2An)3](3-) paramagnetic anion afforded a complete series of chiral magnetic molecular conductors formulated as β-[(S,S,S,S)-TM-BEDT-TTF]3PPh4[K(I)Fe(III)(Cl2An)3]·3H2O (1), β-[(R,R,R,R)-TM-BEDT-TTF]3PPh4[K(I)Fe(III)(Cl2An)3]·3H2O (2), and β-[(rac)-TM-BEDT-TTF]3PPh4[K(I)Fe(III)(Cl2An)3]·3H2O (3). Compounds 1-3 are isostructural and crystallize in triclinic space groups (P1 for 1 and 2, P-1 for 3) showing a segregated organic-inorganic crystal structure, where anionic honeycomb layers obtained by self-assembling of the Λ and Δ enantiomers of the paramagnetic complex with potassium cations alternate with organic layers where the chiral donors are arranged in the β packing motif. Compounds 1-3 show a molecular packing strongly influenced by the topology of the inorganic layers and behave as molecular semiconductors with room-temperature conductivity values of ca. 3 × 10(-4) S cm(-1). The magnetic properties are dominated by the paramagnetic S = 5/2 [Fe(Cl2An)3](3-) anions whose high-spin character is confirmed by magnetic susceptibility measurements. The correlation between crystal structure and conducting behavior has been studied by means of tight-binding band structure calculations which support the observed conducting properties.

Atomic force microscopy-based characterization and design of biointerfaces

NASA Astrophysics Data System (ADS)

Alsteens, David; Gaub, Hermann E.; Newton, Richard; Pfreundschuh, Moritz; Gerber, Christoph; Müller, Daniel J.

2017-03-01

Atomic force microscopy (AFM)-based methods have matured into a powerful nanoscopic platform, enabling the characterization of a wide range of biological and synthetic biointerfaces ranging from tissues, cells, membranes, proteins, nucleic acids and functional materials. Although the unprecedented signal-to-noise ratio of AFM enables the imaging of biological interfaces from the cellular to the molecular scale, AFM-based force spectroscopy allows their mechanical, chemical, conductive or electrostatic, and biological properties to be probed. The combination of AFM-based imaging and spectroscopy structurally maps these properties and allows their 3D manipulation with molecular precision. In this Review, we survey basic and advanced AFM-related approaches and evaluate their unique advantages and limitations in imaging, sensing, parameterizing and designing biointerfaces. It is anticipated that in the next decade these AFM-related techniques will have a profound influence on the way researchers view, characterize and construct biointerfaces, thereby helping to solve and address fundamental challenges that cannot be addressed with other techniques.

Surface Conduction in III-V Semiconductor Infrared Detector Materials

NASA Astrophysics Data System (ADS)

Sidor, Daniel Evan

III-V semiconductors are increasingly used to produce high performance infrared photodetectors; however a significant challenge inherent to working with these materials is presented by unintended electrical conduction pathways that form along their surfaces. Resulting leakage currents contribute to system noise and are ineffectively mitigated by device cooling, and therefore limit ultimate performance. When the mechanism of surface conduction is understood, the unipolar barrier device architecture offers a potential solution. III-V bulk unipolar barrier detectors that effectively suppress surface leakage have approached the performance of the best II-VI pn-based structures. This thesis begins with a review of empirically determined Schottky barrier heights and uses this information to present a simple model of semiconductor surface conductivity. The model is validated through measurements of degenerate n-type surface conductivity on InAs pn junctions, and non-degenerate surface conductivity on GaSb pn junctions. It is then extended, along with design principles inspired by the InAs-based nBn detector, to create a flat-band pn-based unipolar barrier detector possessing a conductive surface but free of detrimental surface leakage current. Consideration is then given to the relative success of these and related bulk detectors in suppressing surface leakage when compared to analogous superlattice-based designs, and general limitations of unipolar barriers in suppressing surface leakage are proposed. Finally, refinements to the molecular beam epitaxy crystal growth techniques used to produce InAs-based unipolar barrier heterostructure devices are discussed. Improvements leading to III-V device performance well within an order of magnitude of the state-of-the-art are demonstrated.

A surprising way to control the charge transport in molecular electronics: the subtle impact of the coverage of self-assembled monolayers of floppy molecules adsorbed on metallic electrodes.

PubMed

Bâldea, Ioan

2017-10-26

Inspired by earlier attempts in organic electronics aiming at controlling charge injection from metals into organic materials by manipulating the Schottky energy barrier using self-assembled monolayers (SAMs), recent experimental and theoretical work in molecular electronics showed that metal-organic interfaces can be controlled via changes in the metal work function that are induced by SAMs. In this paper we indicate a different route to achieve interface-driven control over the charge transfer/transport at the molecular scale. It is based on the fact that, in floppy molecule based SAMs, the molecular conformation can be tuned by varying the coverage of the adsorbate. We demonstrate this effect with the aid of benchmark molecules that are often used to fabricate nanojunctions and consist of two rings that can easily rotate relative to each other. We show that, by varying the coverage of the SAM, the twisting angle φ of the considered molecular species can be modified by a factor of two. Given the fact that the low bias conductance G scales as cos 2  φ, this results in a change in G of over one order of magnitude for the considered molecular species. Tuning the twisting angle by controlling the SAM coverage may be significant, e.g., for current efforts to fabricate molecular switches. Conversely, the lack of control over the local SAM coverage may be problematic for the reproducibility and interpretation of the STM (scanning tunneling microscope) measurements on repeatedly forming single molecule break junctions.

Gate-controlled conductance switching in DNA

PubMed Central

Xiang, Limin; Palma, Julio L.; Li, Yueqi; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

2017-01-01

Extensive evidence has shown that long-range charge transport can occur along double helical DNA, but active control (switching) of single-DNA conductance with an external field has not yet been demonstrated. Here we demonstrate conductance switching in DNA by replacing a DNA base with a redox group. By applying an electrochemical (EC) gate voltage to the molecule, we switch the redox group between the oxidized and reduced states, leading to reversible switching of the DNA conductance between two discrete levels. We further show that monitoring the individual conductance switching allows the study of redox reaction kinetics and thermodynamics at single molecular level using DNA as a probe. Our theoretical calculations suggest that the switch is due to the change in the energy level alignment of the redox states relative to the Fermi level of the electrodes. PMID:28218275

Patterning of self-assembled monolayers based on differences in molecular conductance.

PubMed

Shen, Cai; Buck, Manfred

2009-06-17

Scanning tunneling microscopy (STM) is used for replacement patterning of self-assembled monolayers (SAMs) of thiols on a sub-10 nm scale. Contrasting other schemes of scanning probe patterning of SAMs, the exchange of molecules relies on differences in conductance and, thus, occurs under tunneling conditions where the resolution of the tip is maintained. Exchange takes place at the boundary between different thiols but only when the tip moves from areas of lower to higher conductance. In combination with SAMs which exhibit excellent structural quality, patterns with a contour definition of +/- 1 molecule, lines as thin as 2.5 nm and islands with an area of less than 20 nm2 are straightforwardly produced. It is suggested that the shear force exerted onto the molecules with the lower conductance triggers displacement of the one with higher conductance.

An all-perovskite p-n junction based on transparent conducting p -La 1-x Sr x CrO 3 epitaxial layers

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

Du, Yingge; Li, Chen; Zhang, Kelvin H. L.

2017-08-07

Transparent, conducting p -La 1-x Sr x CrO 3 epitaxial layers were deposited on Nb-doped SrTiO 3(001) by oxygen-assisted molecular beam epitaxy to form structurally coherent p-n junctions. X-ray photoelectron spectroscopy reveals a type II or “staggered” band alignment, with valence and conduction band offsets of 2.0 eV and 0.9 eV, respectively. Diodes fabricated from these heterojunctions exhibit rectifying behavior, and the I-V characteristics are different from those for traditional semiconductor p-n junctions. A rather large ideality factor is ascribed to the complex nature of the interface.

Electronic and mechanical characteristics of stacked dimer molecular junctions.

PubMed

Magyarkuti, András; Adak, Olgun; Halbritter, Andras; Venkataraman, Latha

2018-02-15

Break-junction measurements are typically aimed at characterizing electronic properties of single molecules bound between two metal electrodes. Although these measurements have provided structure-function relationships for such devices, there is little work that studies the impact of molecule-molecule interactions on junction characteristics. Here, we use a scanning tunneling microscope based break-junction technique to study pi-stacked dimer junctions formed with two amine-terminated conjugated molecules. We show that the conductance, force and flicker noise of such dimers differ dramatically when compared with the corresponding monomer junctions and discuss the implications of these results on intra- and inter-molecular charge transport.

Nanostructure and Dynamics of Ionic and Non-Ionic PEO-Containing Polyureas

NASA Astrophysics Data System (ADS)

Chuayprakong, Sunanta; Runt, James

2013-03-01

A series of polyethylene oxide (PEO) - based diamines with molecular weights ranging from 250 - 6000 g/mol were polymerized in solution with 4,4'-methylene diphenyl diisocyanate (MDI). In addition, PEO soft segment diamines where modified to incorporate ionomeric species and also polymerized with MDI. The role of PEO soft segment molecular weight and the presence of ionic species on nanoscale segregation and cation conductivity were explored. The former was investigated using small-angle X-ray scattering and atomic force microscopy. Dielectric relaxation spectroscopy was used to investigate polymer and ion dynamics. Local environment and hydrogen bonding were identified by using FTIR spectroscopy.

Decoupled Ion Transport in a Protein-Based Solid Ion Conductor.

PubMed

Fu, Xuewei; Jewel, Yead; Wang, Yu; Liu, Jin; Zhong, Wei-Hong

2016-11-03

Simultaneous achievement of good electrochemical and mechanical properties is crucial for practical applications of solid ion conductors. Conventional polymer conductors suffer from low conductivity, low transference number, and deteriorated mechanical properties with the enhancement of conductivity, resulting from the coupling between ion transport and polymer movement. Here we present a successful fabrication and fundamental understanding of a high performance soy protein-based solid conductor. The conductor shows ionic conductivity of ∼10 -5 S/cm, transference number of 0.94, and modulus of 1 GPa at room temperature, and still remains flexible and easily processable. Molecular simulations indicate that this is due to appropriate manipulation of the protein structures for effective exploitation of protein functional groups. A decoupled transport mechanism, which is able to explain all results, is proposed. The new insights can be utilized to provide guidelines for design, optimization, and fabrication of high performance biosolid conductors.

Students' Learning with the Connected Chemistry (CC1) Curriculum: Navigating the Complexities of the Particulate World

ERIC Educational Resources Information Center

Levy, Sharona T.; Wilensky, Uri

2009-01-01

The focus of this study is students' learning with a Connected Chemistry unit, CC1 (denotes Connected Chemistry, chapter 1), a computer-based environment for learning the topics of gas laws and kinetic molecular theory in chemistry (Levy and Wilensky 2009). An investigation was conducted into high-school students' learning with Connected…

Poly(terphenylene) Anion Exchange Membranes: The Effect of Backbone Structure on Morphology and Membrane Property

DOE PAGES

Lee, Woo-Hyung; Park, Eun Joo; Han, Junyoung; ...

2017-05-05

A new design concept for ion-conducting polymers in anion exchange membranes (AEMs) fuel cells is proposed based on structural studies and conformational analysis of polymers and their effect on the properties of AEMs. Thermally, chemically, and mechanically stable terphenyl-based polymers with pendant quaternary ammonium alkyl groups were synthesized to investigate the effect of varying the arrangement of the polymer backbone and cation-tethered alkyl chains. The results demonstrate that the microstructure and morphology of these polymeric membranes significantly influence ion conductivity and fuel cell performance. Finally, the results of this study provide new insights that will guide the molecular design ofmore » polymer electrolyte materials to improve fuel cell performance.« less

Tailoring Functional Chitosan-based Composites for Food Applications.

PubMed

Nunes, Cláudia; Coimbra, Manuel A; Ferreira, Paula

2018-03-08

Chitosan-based functional materials are emerging for food applications. The covalent bonding of molecular entities demonstrates to enhance resistance to the typical acidity of food assigning mechanical and moisture/gas barrier properties. Moreover, the grafting to chitosan of some functional molecules, like phenolic compounds or essential oils, gives antioxidant, antimicrobial, among others properties to chitosan. The addition of nanofillers to chitosan and other biopolymers improves the already mentioned required properties for food applications and can attribute electrical conductivity and magnetic properties for active and intelligent packaging. Electrical conductivity is a required property for the processing of food at low temperature using electric fields or for sensors application. © 2018 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simultaneous improvement in ionic conductivity and flexibility of solid polymer electrolytes for thin film lithium ion batteries

NASA Astrophysics Data System (ADS)

Ji, Jianying

Solid polymer electrolytes (SPEs) provide advantages over liquid electrolytes in terms of safety, reliability, less temperature sensitive, and simplicity of design. With the use of a SPE in lithium batteries, high specific energy and specific power, safe operation, flexibility in packaging, and low cost of fabrication can be expected. However, after 30 years, SPEs have rarely found commercial success due to the low ionic conductivity and/or insufficient mechanical properties, both of which are related to the movement of the polymer chains. Many physical/chemical methods have been exploited to simultaneously create enhancement in ionic conductivity and mechanical properties, and some suggested ways have shown promise. However, the complex strategies have always introduced other challenge issues and incurred extra costs for manufacturing. In such a context, the development of dry solid state electrolytes is the central challenge to be faced worldwide. This thesis deals with the approaches to improving ionic conductivity and mechanical properties simultaneously. The method is to apply two kinds of controllable organic fillers: copolymer and protein. Our work revealed that the commercial available copolymer, poly (ethylene oxide)- block-polyethylene (PEO-b-PE), possesses a capability for enhancing the multiple performances of poly(ethylene oxide)(PEO)-based polymer electrolyte. And the effects of composition and molecular weight of the copolymers on performance of the resulting SPEs were examined. It was found that increasing the PE block percentage in the copolymer resulted in a significant increase in both ionic conductivity and mechanical properties, while increasing the molecular weight of the copolymer resulted in better mechanical properties, and an identical ionic conductivity. A rubber-like, soy protein-based SPE (s-SPE)was obtained by employing soy protein isolate (SPI), a soy product usually used as rigid fillers for enhancing mechanical properties of polymers, blended with poly(ethylene oxide)(PEO). The results indicated that the s-SPE with 55 wt% of SPI possesses a fully amorphous uniform structure having low Tg, in contrast with crystalline PEO-based SPE having discernable Tg and Tm. The conductivity and elasticity are both significantly improved with SPI involvement. Remarkably, this film has been elongated up to 100% without loss of ionic conductivity and 700% without mechanical damage.

Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

PubMed Central

Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

2016-01-01

Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

Monolayers and multilayers of conjugated polymers as nanosized electronic components.

PubMed

Zotti, Gianni; Vercelli, Barbara; Berlin, Anna

2008-09-01

Conjugated polymers (CPs) are interesting materials for preparing devices based on nanoscopic molecular architectures because they exhibit electrical, electronic, magnetic, and optical properties similar to those of metals or semiconductors while maintaining the flexibility and ease of processing of polymers. The production of well-defined mono- and multilayers of CPs on electrodes with nanometer-scale, one-dimensional resolution remains, however, an important challenge. In this Account, we describe the preparation and conductive properties of nanometer-sized CP molecular structures formed on electrode surfaces--namely, self-assembled monolayer (SAM), brush-type, and self-assembled multilayer CPs--and in combination with gold nanoparticles (AuNPs). We have electrochemically polymerized SAMs of carboxyalkyl-functionalized terthiophenes aligned either perpendicular or parallel to the electrode surface. Anodic coupling of various pyrrole- and thiophene-based monomers in solution with the oligothiophene-based SAMs produced brush-like films. Microcontact printing of these SAMs produced patterns that, after heterocoupling, exhibited large height enhancements, as measured using atomic force microscopy (AFM). We have employed layer-by-layer self-assembly of water-soluble polythiophene-based polyelectrolytes to form self-assembled multilayers. The combination of isostructural polycationic and polyanionic polythiophenes produced layers of chains aligned parallel to the substrate plane. These stable, robust, and dense layers formed with high regularity on the preformed monolayers, with minimal interchain penetration. Infrared reflection/adsorption spectroscopy and X-ray diffraction analyses revealed unprecedented degrees of order. Deposition of soluble polypyrroles produced molecular layers that, when analyzed using a gold-coated AFM tip, formed gold-polymer-gold junctions that were either ohmic or rectifying, depending of the layer sequence. We also describe the electronic conduction of model alpha,omega-capped sexithiophenes featuring a range of electron donor/acceptor units and lengths of additional conjugation. The sexithiophene cores exhibit redox-type conductivity, developing at the neutral/cation and cation/dication levels with values depending the nature of the substitution and the redox system. Extending the conjugation beyond the sexithiophene frame introduces further oxidation processes displaying enhanced conductivity. Finally, we discuss the ability of CP-based monolayers to coordinate AuNPs. Although thiophene- and pyrrole-based oligomers aggregate toluene-soluble AuNPs, alkyl substitution inhibits the aggregation process through steric restraint. Consequently, we investigated the interactions between AuNPs and polypyrrole or polythiophene monolayers, including those formed from star-shaped molecules. The hindered aggregation provided by alkyl substituents allowed us to adsorb thiol-functionalized oligothiophenes and oligopyrroles directly onto preformed AuNPs. Novel materials incorporating AuNPs of the same size but bearing different conjugated ends or bridges have great promise for applications in electrocatalysis, electroanalysis, and organic electronics.

Cation effect on small phosphonium based ionic liquid electrolytes with high concentrations of lithium salt

NASA Astrophysics Data System (ADS)

Chen, Fangfang; Kerr, Robert; Forsyth, Maria

2018-05-01

Ionic liquid electrolytes with high alkali salt concentrations have displayed some excellent electrochemical properties, thus opening up the field for further improvements to liquid electrolytes for lithium or sodium batteries. Fundamental computational investigations into these high concentration systems are required in order to gain a better understanding of these systems, yet they remain lacking. Small phosphonium-based ionic liquids with high concentrations of alkali metal ions have recently shown many promising results in experimental studies, thereby prompting us to conduct further theoretical exploration of these materials. Here, we conducted a molecular dynamics simulation on four small phosphonium-based ionic liquids with 50 mol. % LiFSI salt, focusing on the effect of cation structure on local structuring and ion diffusional and rotational dynamics—which are closely related to the electrochemical properties of these materials.

Disordered Nuclear Pasta, Magnetic Field Decay, and Crust Cooling in Neutron Stars

NASA Astrophysics Data System (ADS)

Horowitz, C. J.; Berry, D. K.; Briggs, C. M.; Caplan, M. E.; Cumming, A.; Schneider, A. S.

2015-01-01

Nuclear pasta, with nonspherical shapes, is expected near the base of the crust in neutron stars. Large-scale molecular dynamics simulations of pasta show long lived topological defects that could increase electron scattering and reduce both the thermal and electrical conductivities. We model a possible low-conductivity pasta layer by increasing an impurity parameter Qimp . Predictions of light curves for the low-mass x-ray binary MXB 1659-29, assuming a large Qimp, find continued late time cooling that is consistent with Chandra observations. The electrical and thermal conductivities are likely related. Therefore, observations of late time crust cooling can provide insight on the electrical conductivity and the possible decay of neutron star magnetic fields (assuming these are supported by currents in the crust).

Disordered nuclear pasta, magnetic field decay, and crust cooling in neutron stars.

PubMed

Horowitz, C J; Berry, D K; Briggs, C M; Caplan, M E; Cumming, A; Schneider, A S

2015-01-23

Nuclear pasta, with nonspherical shapes, is expected near the base of the crust in neutron stars. Large-scale molecular dynamics simulations of pasta show long lived topological defects that could increase electron scattering and reduce both the thermal and electrical conductivities. We model a possible low-conductivity pasta layer by increasing an impurity parameter Q_{imp}. Predictions of light curves for the low-mass x-ray binary MXB 1659-29, assuming a large Q_{imp}, find continued late time cooling that is consistent with Chandra observations. The electrical and thermal conductivities are likely related. Therefore, observations of late time crust cooling can provide insight on the electrical conductivity and the possible decay of neutron star magnetic fields (assuming these are supported by currents in the crust).

New leak assembly based on fluidic nanochannels

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

Zhu, Aiqing; Zhao, Yongheng; Wang, Xudi, E-mail: wxudi@hfut.edu.cn

2016-09-15

Fluidic nanochannels with a characteristic dimension of ∼280 nm were fabricated and designed as a leak assembly, where the nanochannels were formed on silicon wafers and enclosed with Pyrex{sup ®} glass. The geometric dimensions were characterized by scanning electron microscopy, and the gas flow conductance of He and other heavy gases (N{sub 2}, O{sub 2}, and Ar) was measured, and its uncertainty estimated, by the difference method. The results indicated that the measured flow conductance values were 45% less than the calculated flow conductance values. For helium, molecular flow was shown to occur at pressures ranging from vacuum to atmospheric pressure.more » As a consequence of the well-defined geometry, the prediction of flow conductance could be achieved for various gas species.« less

Synthesis, spectral and theoretical studies of Ni(II), Pd(II) and Pt(II) complexes of 5-mercapto-1,2,4-triazole-3-imine-2'-hydroxynaphthaline.

PubMed

Gaber, Mohamed; El-Ghamry, Hoda; Atlam, Faten; Fathalla, Shaimaa

2015-02-25

Ni(II), Pd(II) and Pt(II) complexes of 5-mercapto-1,2,4-triazole-3-imine-2'-hydroxynaphthaline have been isolated and characterized by elemental analysis, IR, (1)H NMR, EI-mass, UV-vis, molar conductance, magnetic moment measurements and thermogravimetric analysis. The molar conductance values indicated that the complexes are non-electrolytes. The magnetic moment values of the complexes displayed diamagnetic behavior for Pd(II) and Pt(II) complexes and tetrahedral geometrical structure for Ni(II) complex. From the bioinorganic applications point of view, the interaction of the ligand and its metal complexes with CT-DNA was investigated using absorption and viscosity titration techniques. The Schiff-base ligand and its metal complexes have also been screened for their antimicrobial and antitumor activities. Also, theoretical investigation of molecular and electronic structures of the studied ligand and its metal complexes has been carried out. Molecular orbital calculations were performed using DFT (density functional theory) at B3LYP level with standard 6-31G(d,p) and LANL2DZ basis sets to access reliable results to the experimental values. The calculations were performed to obtain the optimized molecular geometry, charge density distribution, extent of distortion from regular geometry, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), Mulliken atomic charges, reactivity index (ΔE), dipole moment (D), global hardness (η), softness (σ), electrophilicity index (ω), chemical potential and Mulliken electronegativity (χ). Copyright © 2014 Elsevier B.V. All rights reserved.

Electronic and transport properties of a molecular junction with asymmetric contacts.

PubMed

Tsai, M-H; Lu, T-H

2010-02-10

Asymmetric molecular junctions have been shown experimentally to exhibit a dual-conductance transport property with a pulse-like current-voltage characteristic, by Reed and co-workers. Using a recently developed first-principles integrated piecewise thermal equilibrium current calculation method and a gold-benzene-1-olate-4-thiolate-gold model molecular junction, this unusual transport property has been reproduced. Analysis of the electrostatics and the electronic structure reveals that the high-current state results from subtle bias induced charge transfer at the electrode-molecule contacts that raises molecular orbital energies and enhances the current-contributing molecular density of states and the probabilities of resonance tunneling of conduction electrons from one electrode to another.

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

PubMed

Hoadley, Katherine A; Yau, Christina; Hinoue, Toshinori; Wolf, Denise M; Lazar, Alexander J; Drill, Esther; Shen, Ronglai; Taylor, Alison M; Cherniack, Andrew D; Thorsson, Vésteinn; Akbani, Rehan; Bowlby, Reanne; Wong, Christopher K; Wiznerowicz, Maciej; Sanchez-Vega, Francisco; Robertson, A Gordon; Schneider, Barbara G; Lawrence, Michael S; Noushmehr, Houtan; Malta, Tathiane M; Stuart, Joshua M; Benz, Christopher C; Laird, Peter W

2018-04-05

We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular diodes in optical rectennas

NASA Astrophysics Data System (ADS)

Duché, David; Palanchoke, Ujwol; Terracciano, Luigi; Dang, Florian-Xuan; Patrone, Lionel; Le Rouzo, Judikael; Balaban, Téodore Silviu; Alfonso, Claude; Charai, Ahmed; Margeat, Olivier; Ackermann, Jorg; Gourgon, Cécile; Simon, Jean-Jacques; Escoubas, Ludovic

2016-09-01

The photo conversion efficiencies of the 1st and 2nd generat ion photovoltaic solar cells are limited by the physical phenomena involved during the photo-conversion processes. An upper limit around 30% has been predicted for a monojunction silicon solar cell. In this work, we study 3rd generation solar cells named rectenna which could direct ly convert visible and infrared light into DC current. The rectenna technology is at odds with the actual photovoltaic technologies, since it is not based on the use of semi-conducting materials. We study a rectenna architecture consist ing of plasmonic nano-antennas associated with rectifying self assembled molecular diodes. We first opt imized the geometry of plasmonic nano-antennas using an FDTD method. The optimal antennas are then realized using a nano-imprint process and associated with self assembled molecular diodes in 11- ferrocenyl-undecanethiol. Finally, The I(V) characterist ics in darkness of the rectennas has been carried out using an STM. The molecular diodes exhibit averaged rect ification ratios of 5.

Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers.

PubMed

Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J; Iqbal, Nayyer

2015-01-01

Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program.

Molecular simulation and mathematical modelling of glass transition temperature depression induced by CO2 plasticization in Polysulfone membranes

NASA Astrophysics Data System (ADS)

Lock, S. S. M.; Lau, K. K.; Lock Sow Mei, Irene; Shariff, A. M.; Yeong, Y. F.; Bustam, A. M.

2017-08-01

A sequence of molecular modelling procedure has been proposed to simulate experimentally validated membrane structure characterizing the effect of CO2 plasticization, whereby it can be subsequently employed to elucidate the depression in glass transition temperature (Tg ). Based on the above motivation, unswollen and swollen Polysulfone membrane structures with different CO2 loadings have been constructed, whereby the accuracy has been validated through good compliance with experimentally measured physical properties. It is found that the presence of CO2 constitutes to enhancement in polymeric chain relaxation, which consequently promotes the enlargement of molecular spacing and causes dilation in the membrane matrix. A series of glass transition temperature treatment has been conducted on the verified molecular structure to elucidate the effect of CO2 loadings to the depression in Tg induced by plasticization. Subsequently, a modified Michealis-Menten (M-M) function has been implemented to quantify the effect of CO2 loading attributed to plasticization towards Tg .

Transient variation of martian ground-atmosphere thermal boundary layer structure.

NASA Technical Reports Server (NTRS)

Pallmann, A. J.; Dannevik, W. P.

1972-01-01

Results of a numerical simulation of the diurnal redistribution of temperature by radiative and molecular-conductive processes in the Martian soil-atmosphere system. An attempt is made to assess the importance of atmospheric molecular conduction near the surface and to estimate the characteristic depth of the diurnal temperature wave. The computational results are found to indicate a dual structure in the diurnal temperature wave propagation pattern, with a diffusive-type wave in the lowest 150 m superimposed on a radiatively induced disturbance with a characteristic scale of 1.8 km. Atmospheric molecular thermal conduction typically accounts for about 15% of the total heating/cooling in the lowest 25 m. Thermal conduction in both the soil and atmosphere appears to be an important factor in the thermal coupling of these subsystems. A free-convection regime in the conduction layer is predicted by the model for about five hours of the Martian day.

The Effect of Structural Modifications on Ionic Conductivity in Newly-Designed Polyester Electrolytes

NASA Astrophysics Data System (ADS)

Pesko, Danielle; Jung, Yuki; Coates, Geoff; Balsara, Nitash

2015-03-01

Gaining a fundamental understanding of the relationship between molecular structure and ionic conductivity of polymer electrolytes is an essential step toward designing next generation materials for battery applications. In this study, we use a systematic set of newly-designed polyesters with varying side-chain lengths and oxygen functional groups to elucidate the effects of structural modifications on the conductive properties of the corresponding electrolytes. Mixtures of polyesters and lithium bis(trifluromethanesulfonyl)imide (LiTFSI) were characterized using ac impedance spectroscopy to measure the ionic conductivity at various temperatures and salt concentrations. The relative conductivities of these electrolytes in the dilute limit are directly comparable to results of molecular dynamics simulations performed using the same polymers. The simulations correspond well with the experimental results, and provide molecular level insight about the solvation environment of the lithium ions and how the ions transport through these polyesters.

Self-assembly of organic monolayers as protective and conductive bridges for nanometric surface-mount applications.

PubMed

Platzman, Ilia; Haick, Hossam; Tannenbaum, Rina

2010-09-01

In this work, we present a novel surface-mount placement process that could potentially overcome the inadequacies of the currently used stencil-printing technology, when applied to devices in which either their lateral and/or their horizontal dimensions approach the nanometric scale. Our novel process is based on the "bottom-up" design of an adhesive layer, operative in the molecular/nanoscale level, through the use of self-assembled monolayers (SAMs) that could form protective and conductive bridges between pads and components. On the basis of previous results, 1,4-phenylene diisocyanide (PDI) and terephthalic acid (TPA) were chosen to serve as the best candidates for the achievement of this goal. The quality and stability of these SAMs on annealed Cu surfaces (Rrms=0.15-1.1 nm) were examined in detail. Measurements showed that the SAMs of TPA and PDI molecules formed on top of Cu substrates created thermally stable organic monolayers with high surface coverage (∼90%), in which the molecules were closely packed and well-ordered. Moreover, the molecules assumed a standing-up phase conformation, in which the molecules bonded to the Cu substrate through one terminal functional group, with the other terminal group residing away from the substrate. To examine the ability of these monolayers to serve as "molecular wires," i.e., the capability to provide electrical conductivity, we developed a novel fabrication method of a parallel plate junction (PPJ) in order to create symmetric Cu-SAM-Cu electrical junctions. The current-bias measurements of these junctions indicated high tunneling efficiency. These achievements imply that the SAMs used in this study can serve as conductive molecular bridges that can potentially bind circuital pads/components.

Molecular identification of Entamoeba species in savanna woodland chimpanzees (Pan troglodytes schweinfurthii).

PubMed

Jirků-Pomajbíková, Kateřina; Čepička, Ivan; Kalousová, Barbora; Jirků, Milan; Stewart, Fiona; Levecke, Bruno; Modrý, David; Piel, Alex K; Petrželková, Klára J

2016-05-01

To address the molecular diversity and occurrence of pathogenic species of the genus Entamoeba spp. in wild non-human primates (NHP) we conducted molecular-phylogenetic analyses on Entamoeba from wild chimpanzees living in the Issa Valley, Tanzania. We compared the sensitivity of molecular [using a genus-specific polymerase chain reaction (PCR)] and coproscopic detection (merthiolate-iodine-formaldehyde concentration) of Entamoeba spp. We identified Entamoeba spp. in 72 chimpanzee fecal samples (79%) subjected to species-specific PCRs for six Entamoeba species/groups (Entamoeba histolytica, Entamoeba nuttalli, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba coli and Entamoeba polecki ST2). We recorded three Entamoeba species: E. coli (47%), E. dispar (16%), Entamoeba hartmanni (51%). Coproscopically, we could only distinguish the cysts of complex E. histolytica/dispar/moshkovskii/nuttalli and E. coli. Molecular prevalence of entamoebas was higher than the prevalence based on the coproscopic examination. Our molecular phylogenies showed that sequences of E. dispar and E. coli from Issa chimpanzees are closely related to sequences from humans and other NHP from GenBank. The results showed that wild chimpanzees harbour Entamoeba species similar to those occurring in humans; however, no pathogenic species were detected. Molecular-phylogenetic methods are critical to improve diagnostics of entamoebas in wild NHP and for determining an accurate prevalence of Entamoeba species.

Thermal conductivity of pillared graphene-epoxy nanocomposites using molecular dynamics

NASA Astrophysics Data System (ADS)

Lakshmanan, A.; Srivastava, S.; Ramazani, A.; Sundararaghavan, V.

2018-04-01

Thermal conductivity in a pillared graphene-epoxy nanocomposite (PGEN) is studied using equilibrium molecular dynamics simulations. PGEN is a proposed material for advanced thermal management applications because it combines high in-plane conductivity of graphene with high axial conductivity of a nanotube to significantly enhance the overall conductivity of the epoxy matrix material. Anisotropic conductivity of PGEN has been compared with that of pristine and functionalized carbon nanotube-epoxy nanocomposites, showcasing the advantages of the unique hierarchical structure of PGEN. Compared to pure carbon allotropes, embedding the epoxy matrix also promotes a weaker dependence of conductivity on thermal variations. These features make this an attractive material for thermal management applications.

Thermal conductivity of cross-linked polyethylene from molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Xiong, Xue; Yang, Ming; Liu, Changlin; Li, Xiaobo; Tang, Dawei

2017-07-01

The thermal conductivity of cross-linked bulk polyethylene is studied using molecular dynamics simulation. The atomic structure of the cross-linked polyethylene (PEX) is generated through simulated bond formation using LAMMPS. The thermal conductivity of PEX is studied with different degrees of crosslinking, chain length, and tensile strain. Generally, the thermal conductivity increases with the increasing degree of crosslinking. When the length of the primitive chain increases, the thermal conductivity increases linearly. When the polymer is stretched along one direction, the thermal conductivity increases in the stretched direction and decreases in the direction perpendicular to it. However, the thermal conductivity varies slightly when the polymer is stretched in three directions simultaneously.

Controlled, Site-Specific Functionalization of Carbon Nanotubes with Diazonium Salts

NASA Technical Reports Server (NTRS)

Tour, James M.

2013-01-01

This work uses existing technologies to prepare a crossbar architecture of nano tubes, wherein one nanotube is fixed to a substrate, and a second nanotube is suspended a finite distance above. Both nano tubes can be individually addressed electrically. Application of opposite potentials to the two tubes causes the top tube to deform and to essentially come into contact with the lower tube. Contact here refers not to actual, physical contact, but rather within an infinitesimally small distance referred to as van der Walls contact, in which the entities may influence each other on a molecular and electronic scale. First, the top tube is physically deformed, leading to a potentially higher chemical reactivity at the point of deformation, based on current understanding of the effects of curvature strain on reactivity. This feature would allow selective functionalization at the junction via reaction with diazonium salts. Secondly, higher potential is achieved at the point of "cross" between the tubes. In a pending patent application, a method is claimed for directed self-assembly of molecular components onto the surface of metal or conductive materials by application of potential to the metal or conductive surface. In another pending patent application, a method is claimed for attaching molecules to the surface of nanotubes via the use of reactive diazonium salts. In the present invention, the directed functionalization of the crossed-nanotube junctions by applying a potential to the ends of the nanotubes in the presence of reactive diazonium slats, or other reactive molecular species is claimed. The diazonium salts are directed by the potential existing at the junction to react with the surface of the nanotube, thus placing functional molecular components at the junctions. The crossed nano tubes therefore provide a method of directly addressing the functionalized molecules, which have been shown to function as molecular switches, molecular wires, and in other capacities and uses. Site-specific functionalization may enable the use of nanotubes in molecular electronic applications because device functionality is critical at the cross points.

Coupled electron-ion Monte Carlo simulation of hydrogen molecular crystals

NASA Astrophysics Data System (ADS)

Rillo, Giovanni; Morales, Miguel A.; Ceperley, David M.; Pierleoni, Carlo

2018-03-01

We performed simulations for solid molecular hydrogen at high pressures (250 GPa ≤ P ≤ 500 GPa) along two isotherms at T = 200 K (phase III) and at T = 414 K (phase IV). At T = 200 K, we considered likely candidates for phase III, the C2c and Cmca12 structures, while at T = 414 K in phase IV, we studied the Pc48 structure. We employed both Coupled Electron-Ion Monte Carlo (CEIMC) and Path Integral Molecular Dynamics (PIMD). The latter is based on Density Functional Theory (DFT) with the van der Waals approximation (vdW-DF). The comparison between the two methods allows us to address the question of the accuracy of the exchange-correlation approximation of DFT for thermal and quantum protons without recurring to perturbation theories. In general, we find that atomic and molecular fluctuations in PIMD are larger than in CEIMC which suggests that the potential energy surface from vdW-DF is less structured than the one from quantum Monte Carlo. We find qualitatively different behaviors for systems prepared in the C2c structure for increasing pressure. Within PIMD, the C2c structure is dynamically partially stable for P ≤ 250 GPa only: it retains the symmetry of the molecular centers but not the molecular orientation; at intermediate pressures, it develops layered structures like Pbcn or Ibam and transforms to the metallic Cmca-4 structure at P ≥ 450 GPa. Instead, within CEIMC, the C2c structure is found to be dynamically stable at least up to 450 GPa; at increasing pressure, the molecular bond length increases and the nuclear correlation decreases. For the other two structures, the two methods are in qualitative agreement although quantitative differences remain. We discuss various structural properties and the electrical conductivity. We find that these structures become conducting around 350 GPa but the metallic Drude-like behavior is reached only at around 500 GPa, consistent with recent experimental claims.

Better Proton-Conducting Polymers for Fuel-Cell Membranes

NASA Technical Reports Server (NTRS)

Narayan, Sri; Reddy, Prakash

2012-01-01

Polyoxyphenylene triazole sulfonic acid has been proposed as a basis for development of improved proton-conducting polymeric materials for solid-electrolyte membranes in hydrogen/air fuel cells. Heretofore, the proton-conducting membrane materials of choice have been exemplified by a family of perfluorosulfonic acid-based polymers (Nafion7 or equivalent). These materials are suitable for operation in the temperature of 75 to 85 C, but in order to reduce the sizes and/or increase the energy-conversion efficiencies of fuel-cell systems, it would be desirable to increase temperatures to as high as 120 C for transportation applications, and to as high as 180 C for stationary applications. However, at 120 C and at relative humidity values below 50 percent, the loss of water from perfluorosulfonic acid-based polymer membranes results in fuel-cell power densities too low to be of practical value. Therefore, membrane electrolyte materials that have usefully high proton conductivity in the temperature range of 180 C at low relative humidity and that do not rely on water for proton conduction at 180 C would be desirable. The proposed polyoxyphenylene triazole sulfonic acid-based materials have been conjectured to have these desirable properties. These materials would be free of volatile or mobile acid constituents. The generic molecular structure of these materials is intended to exploit the fact, demonstrated in previous research, that materials that contain ionizable acid and base groups covalently attached to thermally stable polymer backbones exhibit proton conduction even in the anhydrous state.

Conductance of Single Molecule Junctions: Dependence on Structure and Conformation

NASA Astrophysics Data System (ADS)

Venkataraman, Latha

2007-03-01

We recently demonstrated that the conductance of single molecule junctions formed by breaking Au point contacts in an environment of molecules with amine linkages can be measured reliably and reproducibly^1. We have now studied junctions formed by approximately 30 different amine terminated molecules, allowing systematic study of the correlation between molecular properties and single molecule junction conductance. This talk will focus on the relation between molecular conductance and molecule conformation for the simple case of a biphenyl, two benzene rings linked together by a single C-C bond. Our results from a series of seven biphenyl derivatives show that the molecular junction conductance depends on the twist angle. Specifically, we find that the planar molecule has the highest conductance, and the conductance for the series decreases with increasing twist angle, consistent with a cosine squared relation predicted theoretically^2. 1. L. Venkataraman, J.E. Klare, I.W. Tam, C. Nuckolls, M.S Hybertsen and M. Steigerwald, Nano Letters, vol. 5, pp. 458-462, 2006. 2. L. Venkataraman, J.E. Klare, C. Nuckolls, M.S Hybertsen and M. Steigerwald, Nature, vol. 442, pp. 904-907, 2006.

Role of direct electron-phonon coupling across metal-semiconductor interfaces in thermal transport via molecular dynamics.

PubMed

Lin, Keng-Hua; Strachan, Alejandro

2015-07-21

Motivated by significant interest in metal-semiconductor and metal-insulator interfaces and superlattices for energy conversion applications, we developed a molecular dynamics-based model that captures the thermal transport role of conduction electrons in metals and heat transport across these types of interface. Key features of our model, denoted eleDID (electronic version of dynamics with implicit degrees of freedom), are the natural description of interfaces and free surfaces and the ability to control the spatial extent of electron-phonon (e-ph) coupling. Non-local e-ph coupling enables the energy of conduction electrons to be transferred directly to the semiconductor/insulator phonons (as opposed to having to first couple to the phonons in the metal). We characterize the effect of the spatial e-ph coupling range on interface resistance by simulating heat transport through a metal-semiconductor interface to mimic the conditions of ultrafast laser heating experiments. Direct energy transfer from the conduction electrons to the semiconductor phonons not only decreases interfacial resistance but also increases the ballistic transport behavior in the semiconductor layer. These results provide new insight for experiments designed to characterize e-ph coupling and thermal transport at the metal-semiconductor/insulator interfaces.

Identification of the functional binding pocket for compounds targeting small-conductance Ca2+-activated potassium channels

PubMed Central

Zhang, Miao; Pascal, John M.; Schumann, Marcel; Armen, Roger S.; Zhang, Ji-fang

2012-01-01

Small- and intermediate-conductance Ca2+-activated potassium channels, activated by Ca2+-bound calmodulin, play an important role in regulating membrane excitability. These channels are also linked to clinical abnormalities. A tremendous amount of effort has been devoted to developing small molecule compounds targeting these channels. However, these compounds often suffer from low potency and lack of selectivity, hindering their potentials for clinical use. A key contributing factor is the lack of knowledge of the binding site(s) for these compounds. Here we demonstrate by X-ray crystallography that the binding pocket for the compounds of the 1-EBIO class is located at the calmodulin-channel interface. We show that, based on structure data and molecular docking, mutations of the channel can effectively change the potency of these compounds. Our results provide insight into the molecular nature of the binding pocket and its contribution to the potency and selectivity of the compounds of the 1-EBIO class. PMID:22929778

Identification of the functional binding pocket for compounds targeting small-conductance Ca²⁺-activated potassium channels.

PubMed

Zhang, Miao; Pascal, John M; Schumann, Marcel; Armen, Roger S; Zhang, Ji-Fang

2012-01-01

Small- and intermediate-conductance Ca(2+)-activated potassium channels, activated by Ca(2+)-bound calmodulin, have an important role in regulating membrane excitability. These channels are also linked to clinical abnormalities. A tremendous amount of effort has been devoted to developing small molecule compounds targeting these channels. However, these compounds often suffer from low potency and lack of selectivity, hindering their potential for clinical use. A key contributing factor is the lack of knowledge of the binding site(s) for these compounds. Here we demonstrate by X-ray crystallography that the binding pocket for the compounds of the 1-ethyl-2-benzimidazolinone (1-EBIO) class is located at the calmodulin-channel interface. We show that, based on structure data and molecular docking, mutations of the channel can effectively change the potency of these compounds. Our results provide insight into the molecular nature of the binding pocket and its contribution to the potency and selectivity of the compounds of the 1-EBIO class.

Silk/nano-material hybrid: properties and functions

NASA Astrophysics Data System (ADS)

Steven, Eden; Lebedev, Victor; Laukhina, Elena; Laukhin, Vladimir; Alamo, Rufina G.; Rovira, Concepcio; Veciana, Jaume; Brooks, James S.

2014-03-01

Silk continues to emerge as a material of interest in electronics. In this work, the interaction between silk and conducting nano-materials are investigated. Simple fabrication methods, physical, electronic, thermal, and actuation properties are reported for spider silk / carbon nanotube (CNT-SS) and Bombyx mori / (BEDT-TTF)-based organic molecular conductor hybrids (ET-S). The CNT-SS fibers are produced via water and shear assisted method, resulting in fibers that are tough, custom-shapeable, flexible, and electrically conducting. For ET-S bilayer films, a layer transfer technique is developed to deposit linked crystallites of (BEDT-TTF)2I3 molecular conductor onto silk films, generating highly piezoresistive semi-transparent films. In both cases, the hybridization allows us to gain additional functions by harnessing the water-dependent properties of silk materials, for example, as humidity sensor and electrical current- or water-driven actuators. SEM, TEM, FT-IR, and resistance measurements under varying temperature, strain, and relative humidity reveal the synergistic interactions between the bio- and nano-materials. E.S. is supported by NSF-DMR 1005293.

Functionalization mediates heat transport in graphene nanoflakes

PubMed Central

Han, Haoxue; Zhang, Yong; Wang, Nan; Samani, Majid Kabiri; Ni, Yuxiang; Mijbil, Zainelabideen Y.; Edwards, Michael; Xiong, Shiyun; Sääskilahti, Kimmo; Murugesan, Murali; Fu, Yifeng; Ye, Lilei; Sadeghi, Hatef; Bailey, Steven; Kosevich, Yuriy A.; Lambert, Colin J.; Liu, Johan; Volz, Sebastian

2016-01-01

The high thermal conductivity of graphene and few-layer graphene undergoes severe degradations through contact with the substrate. Here we show experimentally that the thermal management of a micro heater is substantially improved by introducing alternative heat-escaping channels into a graphene-based film bonded to functionalized graphene oxide through amino-silane molecules. Using a resistance temperature probe for in situ monitoring we demonstrate that the hotspot temperature was lowered by ∼28 °C for a chip operating at 1,300 W cm−2. Thermal resistance probed by pulsed photothermal reflectance measurements demonstrated an improved thermal coupling due to functionalization on the graphene–graphene oxide interface. Three functionalization molecules manifest distinct interfacial thermal transport behaviour, corroborating our atomistic calculations in unveiling the role of molecular chain length and functional groups. Molecular dynamics simulations reveal that the functionalization constrains the cross-plane phonon scattering, which in turn enhances in-plane heat conduction of the bonded graphene film by recovering the long flexural phonon lifetime. PMID:27125636

TOPICAL REVIEW: Tetrathiapentalene-based organic conductors

NASA Astrophysics Data System (ADS)

Misaki, Yohji

2009-04-01

The synthesis, structure and properties of tetrathiapentalene-based (TTP) organic conductors are reviewed. Among various TTP-type donors, bis-fused tetrathiafulvalene, 2,5-bis(1,3-dithiol-2-ylidene)-1,3,4,6-tetrathiapentalene (BDT-TTP) and its derivatives afford many metallic radical cation salts stable down to low temperatures, regardless of the size and shape of the counter anions. Most BDT-TTP conductors have a β-type donor arrangement with almost uniform stacks. Introduction of appropriate substituents results in molecular packing that differs from the β-type. A vinylogous TTP, 2-(1,3-dithiol-2-ylidene)-5-(2-ethanediylidene-1,3-dithiole)-1,3,4,6-tetrathiapentalene (DTEDT) has yielded an organic superconductor (DTEDT)3Au(CN)2 as well as metallic radical cation salts, regardless of the counter anions. (Thio)pyran analogs of TTP, namely (T)PDT-TTP and its derivatives produce molecular conductors with novel molecular arrangements. A TTP analog with reduced π-electron system 2,5-bis(1,3-dithian-2-ylidene)-1,3,4,6-tetrathiapentalene (BDA-TTP) has afforded several organic superconductors. Highly conducting molecular metals with unusual oxidation states (+1, +5/3 and neutral) have been developed on the basis of 2,5-bis(1,3-dithiol-2-ylidene)-1,3,4,6-tetrathiapentalene (BDT-TTP) derivatives and analogous metal derivatives M(dt)2 (M = Ni, Au).

Internal Electric Field Modulation in Molecular Electronic Devices by Atmosphere and Mobile Ions.

PubMed

Chandra Mondal, Prakash; Tefashe, Ushula M; McCreery, Richard L

2018-06-13

The internal potential profile and electric field are major factors controlling the electronic behavior of molecular electronic junctions consisting of ∼1-10 nm thick layers of molecules oriented in parallel between conducting contacts. The potential profile is assumed linear in the simplest cases, but can be affected by internal dipoles, charge polarization, and electronic coupling between the contacts and the molecular layer. Electrochemical processes in solutions or the solid state are entirely dependent on modification of the electric field by electrolyte ions, which screen the electrodes and form the ionic double layers that are fundamental to electrode kinetics and widespread applications. The current report investigates the effects of mobile ions on nominally solid-state molecular junctions containing aromatic molecules covalently bonded between flat, conducting carbon surfaces, focusing on changes in device conductance when ions are introduced into an otherwise conventional junction design. Small changes in conductance were observed when a polar molecule, acetonitrile, was present in the junction, and a large decrease of conductance was observed when both acetonitrile (ACN) and lithium ions (Li + ) were present. Transient experiments revealed that conductance changes occur on a microsecond-millisecond time scale, and are accompanied by significant alteration of device impedance and temperature dependence. A single molecular junction containing lithium benzoate could be reversibly transformed from symmetric current-voltage behavior to a rectifier by repetitive bias scans. The results are consistent with field-induced reorientation of acetonitrile molecules and Li + ion motion, which screen the electrodes and modify the internal potential profile and provide a potentially useful means to dynamically alter junction electronic behavior.

Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti- resonances

NASA Astrophysics Data System (ADS)

Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevinçli, Hâldun; Gutierrez, Rafael; Cuniberti, Gianaurelio

2013-03-01

Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method to predict the appearance of quantum interference, Fano resonances or anti- resonances, and its position in the conductance spectrum by introducing a simple graphical representation (parabolic model). Using it we can easily visualize the relation between the key electronic parameters and the positions of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules and the coupling between side group and main conduction channel from transmission spectra.

Towards molecular electronics with large-area molecular junctions.

PubMed

Akkerman, Hylke B; Blom, Paul W M; de Leeuw, Dago M; de Boer, Bert

2006-05-04

Electronic transport through single molecules has been studied extensively by academic and industrial research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes, break junctions, metallic crossbars and nanopores. For technological applications, molecular tunnel junctions must be reliable, stable and reproducible. The conductance per molecule, however, typically varies by many orders of magnitude. Self-assembled monolayers (SAMs) may offer a promising route to the fabrication of reliable devices, and charge transport through SAMs of alkanethiols within nanopores is well understood, with non-resonant tunnelling dominating the transport mechanism. Unfortunately, electrical shorts in SAMs are often formed upon vapour deposition of the top electrode, which limits the diameter of the nanopore diodes to about 45 nm. Here we demonstrate a method to manufacture molecular junctions with diameters up to 100 microm with high yields (> 95 per cent). The junctions show excellent stability and reproducibility, and the conductance per unit area is similar to that obtained for benchmark nanopore diodes. Our technique involves processing the molecular junctions in the holes of a lithographically patterned photoresist, and then inserting a conducting polymer interlayer between the SAM and the metal top electrode. This simple approach is potentially low-cost and could pave the way for practical molecular electronics.

First-principles and molecular dynamics study of thermoelectric transport properties of N-type silicon-based superlattice-nanocrystalline heterostructures

NASA Astrophysics Data System (ADS)

Zhou, Yanguang; Gong, Xiaojing; Xu, Ben; Hu, Ming

2017-08-01

Electrical and thermal transport in silicon germanium superlattice nanostructures has received extensive attention from scientists for understanding carrier properties at the nanoscale, and the figure-of-merit (ZT) reported in such structures has inspired engineers to develop cost-effective waste heat recovery systems. In this paper, the thermoelectric transport properties of the silicon-based superlattice- and anti-superlattice-nanocrystalline heterostructures are systematically studied by first-principles and molecular dynamics simulations combined with the Boltzmann transport theory. The thermal conductivity, which is thought to be the essential bottleneck for bulk crystalline Si to gain a high ZT value, of such structures is found to be reduced by two orders of magnitude and reaches a level far below the amorphous limit of Si. This is achieved due to the extremely strong phonon-boundary scattering at both grain boundaries and Si-Ge interfaces, which will lead to the phonon mean free path being much smaller than the grain size (Casmir limit): for instance, the dominant phonons are in range of 0.5 to 3 nm for the heterostructures with a grain size of around 8 nm. Meanwhile, the power factor can be preserved at the level comparable to bulk crystalline because of the quantum confinement effect, which resulted from the conduction band minima converge, reduction of band gap, and the short mean free path of carriers. As a result, the ZT of such superlattice based nanomembranes can reach around 0.3 at room temperature, which is two orders of magnitude higher than the bulk crystalline case. The corresponding bulk superlattice-nanocrystalline heterostructures possess a ZT value of 0.5 at room temperature, which is superior to all other bulk silicon-based thermoelectrics. Our results here show that nanostructuring the superlattice structure can further decrease the thermal conductivity while keeping the electrical transport properties at the bulk comparable level, and provides a new strategy for enhancing the thermoelectric performance of the silicon-based nanostructures.

Statistical inference on censored data for targeted clinical trials under enrichment design.

PubMed

Chen, Chen-Fang; Lin, Jr-Rung; Liu, Jen-Pei

2013-01-01

For the traditional clinical trials, inclusion and exclusion criteria are usually based on some clinical endpoints; the genetic or genomic variability of the trial participants are not totally utilized in the criteria. After completion of the human genome project, the disease targets at the molecular level can be identified and can be utilized for the treatment of diseases. However, the accuracy of diagnostic devices for identification of such molecular targets is usually not perfect. Some of the patients enrolled in targeted clinical trials with a positive result for the molecular target might not have the specific molecular targets. As a result, the treatment effect may be underestimated in the patient population truly with the molecular target. To resolve this issue, under the exponential distribution, we develop inferential procedures for the treatment effects of the targeted drug based on the censored endpoints in the patients truly with the molecular targets. Under an enrichment design, we propose using the expectation-maximization algorithm in conjunction with the bootstrap technique to incorporate the inaccuracy of the diagnostic device for detection of the molecular targets on the inference of the treatment effects. A simulation study was conducted to empirically investigate the performance of the proposed methods. Simulation results demonstrate that under the exponential distribution, the proposed estimator is nearly unbiased with adequate precision, and the confidence interval can provide adequate coverage probability. In addition, the proposed testing procedure can adequately control the size with sufficient power. On the other hand, when the proportional hazard assumption is violated, additional simulation studies show that the type I error rate is not controlled at the nominal level and is an increasing function of the positive predictive value. A numerical example illustrates the proposed procedures. Copyright © 2013 John Wiley & Sons, Ltd.

Electrochemical sensor for catechol and dopamine based on a catalytic molecularly imprinted polymer-conducting polymer hybrid recognition element.

PubMed

Lakshmi, Dhana; Bossi, Alessandra; Whitcombe, Michael J; Chianella, Iva; Fowler, Steven A; Subrahmanyam, Sreenath; Piletska, Elena V; Piletsky, Sergey A

2009-05-01

One of the difficulties with using molecularly imprinted polymers (MIPs) and other electrically insulating materials as the recognition element in electrochemical sensors is the lack of a direct path for the conduction of electrons from the active sites to the electrode. We have sought to address this problem through the preparation and characterization of novel hybrid materials combining a catalytic MIP, capable of oxidizing the template, catechol, with an electrically conducting polymer. In this way a network of "molecular wires" assists in the conduction of electrons from the active sites within the MIP to the electrode surface. This was made possible by the design of a new monomer that combines orthogonal polymerizable functionality; comprising an aniline group and a methacrylamide. Conducting films were prepared on the surface of electrodes (Au on glass) by electropolymerization of the aniline moiety. A layer of MIP was photochemically grafted over the polyaniline, via N,N'-diethyldithiocarbamic acid benzyl ester (iniferter) activation of the methacrylamide groups. Detection of catechol by the hybrid-MIP sensor was found to be specific, and catechol oxidation was detected by cyclic voltammetry at the optimized operating conditions: potential range -0.6 V to +0.8 V (vs Ag/AgCl), scan rate 50 mV/s, PBS pH 7.4. The calibration curve for catechol was found to be linear to 144 microM, with a limit of detection of 228 nM. Catechol and dopamine were detected by the sensor, whereas analogues and potentially interfering compounds, including phenol, resorcinol, hydroquinone, serotonin, and ascorbic acid, had minimal effect (< or = 3%) on the detection of either analyte. Non-imprinted hybrid electrodes and bare gold electrodes failed to give any response to catechol at concentrations below 0.5 mM. Finally, the catalytic properties of the sensor were characterized by chronoamperometry and were found to be consistent with Michaelis-Menten kinetics.

A national comparison of biochemistry and molecular biology capstone experiences.

PubMed

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, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices. © 2015 The International Union of Biochemistry and Molecular Biology.

Ferrocene-Alkynyl Conjugated Molecular Wires: Synthesis, Characterization, and Conductance Properties.

PubMed

Yuan, Ye; Yan, Jian-Feng; Lin, Da-Qiang; Mao, Bing-Wei; Yuan, Yao-Feng

2018-03-07

A novel series of 1,2,3-substituted ferrocene-based wires a1-a2 and b4-b5 have been synthesized by using an iterative Pd-mediated Sonogashira cross-coupling methodology. The molecular structures of a2 and b3 were determined by single-crystal X-ray analysis. Electrochemical data showed that there was a strong electronic communication among the ferrocenyl moieties in b1-b5. The UV absorption spectra indicated that replacing the 1,1'-substituted ferrocene unit with a 1,2,3-substituted ferrocene moiety causes delocalization of electrons in the extended π orbitals. The self-assembled monolayers of wire a1 and a2 on Au surfaces have been comprehensively characterized by electrochemistry and scanning tunneling microscopy break junction. The data demonstrated that 1,2,3-substituted ferrocene-based wires reduced the intermolecular π-π stacking, and furthermore solved the rotation problem in the 1,1'-substituted ferrocene-based wires. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-world cost analysis of chemotherapy for colorectal cancer in Japan: detailed costs of various regimens during the entire course of chemotherapy.

PubMed

Yajima, Shuichi; Shimizu, Hisanori; Sakamaki, Hiroyuki; Ikeda, Shunya; Ikegami, Naoki; Murayama, Jun-Ichiro

2016-01-04

Various chemotherapy regimens for advanced colorectal cancer have been introduced to clinical practice in Japan over the past decade. The cost profiles of these regimens, however, remain unclear in Japan. To explore the detailed costs of different regimens used to treat advanced colorectal cancer during the entire course of chemotherapy in patients treated in a practical setting, we conducted a so-called "real-world" cost analysis. A detailed cost analysis was performed retrospectively. Patients with advanced colorectal cancer who had received chemotherapy in a practical healthcare setting from July 2004 through October 2010 were extracted from the ordering system database of Showa University Hospital. Direct medical costs of chemotherapy regimens were calculated from the hospital billing data of the patients. The analysis was conducted from a payer's perspective. A total of 30 patients with advanced colorectal cancer were identified. Twenty patients received up to second-line treatment, and 8 received up to third-line treatment. The regimens identified from among all courses of treatment in all patients were 13 oxaliplatin-based regimens, 31 irinotecan-based regimens, and 11 regimens including molecular targeted agents. The average (95% confidence interval [95% CI]) monthly cost during the overall period from the beginning of treatment to the end of treatment was 308,363 (258,792 to 357,933) Japanese yen (JPY). According to the type of regimen, the average monthly cost was 418,463 (357,413 to 479,513) JPY for oxaliplatin-based regimens, 215,499 (188,359 to 242,639) JPY for irinotecan-based regimens, and 705,460 (586,733 to 824,187) JPY for regimens including molecular targeted agents. Anticancer drug costs and hospital fees accounted for 50 to 77% and 11 to 25% of the overall costs of chemotherapy, respectively. The costs of irinotecan-based regimens were lower than those of oxaliplatin-based regimens and regimens including molecular targeted agents in Japan. Using a lower cost regimen for first-line treatment can potentially reduce the overall cost of chemotherapy. The main cost drivers were the anticancer drug costs and hospitalization costs.

Thermal cracking of poly α-olefin aviation lubricating base oil

NASA Astrophysics Data System (ADS)

Fei, Yiwei; Wu, Nan; Ma, Jun; Hao, Jingtuan

2018-02-01

Thermal cracking of poly α-olefin (PAO) was conducted under different temperatures among 190 °C to 300 °C. The reacted mixtures were sequentially detected by gas chromatography-mass spectrometer (GC/MS). A series of small molecular normal alkanes, branched alkanes and olefins were identified. PAO perfect structure of aligned comb-likely side-chains has been seriously cracked under high temperatures. Property changes about kinematic viscosity and pour point of PAO samples reacted under high temperatures were also investigated. The appearance of small molecular compounds weakened the thermal stability, viscosity temperature performance and low temperature fluidity of PAO samples. Property of PAO samples was deteriorated due to thermal cracking under high temperatures.

Spin filter and molecular switch based on bowtie-shaped graphene nanoflake

NASA Astrophysics Data System (ADS)

Kang, Jun; Wu, Fengmin; Li, Jingbo

2012-11-01

The magnetic and transport properties of bowtie-shaped graphene nanoflake (BGNF) are investigated from first principles calculations. The eigen states of ferromagnetic (FM) BGNF near Fermi level are found to be delocalized over the whole flake, whereas those of antiferromagnetic (AFM) BGNF are localized in one side. The different characters result in different transport properties for FM and AFM BGNFs. FM BGNF exhibits perfect spin filtering effect and can serve as a spin filter. Moreover, the conductance of BGNF is much larger in FM state than in AFM state, thus BGNF can serve as a molecular switch. These results suggest that BGNF is a good candidate for future nanoelectronics.

Tungsten nanoparticles influence on radiation protection properties of polymers

NASA Astrophysics Data System (ADS)

Gavrish, V. M.; Baranov, G. A.; Chayka, T. V.; Derbasova, N. M.; Lvov, A. V.; Matsuk, Y. M.

2016-02-01

In the presented article the results of the study of metal-polymer composites based on the ultra-high molecular weight polyethylene GUR 4122 with the addition of superdispersed tungsten nanopowders with 5, 10, 20, 40, and 50 mass percent content levels are given, their thermophysical, radiation-shielding, and mechanical properties are shown, and the influence of content levels of tungsten superdispersed nanopowders on these properties is analyzed. The conducted studies have shown the increase in the listed properties depending on the content level of tungsten superdispersed and nanopowders in the ultra-high molecular weight polyethylene GUR 4122. Owing to their properties, the obtained materials may be used in various fields, such as aviation, space technologies, mechanical engineering, etc.

Electrospinning bioactive supramolecular polymers from water.

PubMed

Tayi, Alok S; Pashuck, E Thomas; Newcomb, Christina J; McClendon, Mark T; Stupp, Samuel I

2014-04-14

Electrospinning is a high-throughput, low-cost technique for manufacturing long fibers from solution. Conventionally, this technique is used with covalent polymers with large molecular weights. We report here the electrospinning of functional peptide-based supramolecular polymers from water at very low concentrations (<4 wt %). Molecules with low molecular weights (<1 kDa) could be electrospun because they self-assembled into one-dimensional supramolecular polymers upon solvation and the critical parameters of viscosity, solution conductivity, and surface tension were optimized for this technique. The supramolecular structure of the electrospun fibers could ensure that certain residues, like bioepitopes, are displayed on the surface even after processing. This system provides an opportunity to electrospin bioactive supramolecular materials from water for biomedical applications.

Exploring Carbon Nanotubes for Nanoscale Devices

NASA Technical Reports Server (NTRS)

Han, Jie; Dai; Anantram; Jaffe; Saini, Subhash (Technical Monitor)

1998-01-01

Carbon nanotubes (CNTs) are shown to promise great opportunities in nanoelectronic devices and nanoelectromechanical systems (NEMS) because of their inherent nanoscale sizes, intrinsic electric conductivities, and seamless hexagonal network architectures. I present our collaborative work with Stanford on exploring CNTs for nanodevices in this talk. The electrical property measurements suggest that metallic tubes are quantum wires. Furthermore, two and three terminal CNT junctions have been observed experimentally. We have proposed and studied CNT-based molecular switches and logic devices for future digital electronics. We also have studied CNTs based NEMS inclusing gears, cantilevers, and scanning probe microscopy tips. We investigate both chemistry and physics based aspects of the CNT NEMS. Our results suggest that CNT have ideal stiffness, vibrational frequencies, Q-factors, geometry-dependent electric conductivities, and the highest chemical and mechanical stabilities for the NEMS. The use of CNT SPM tips for nanolithography is presented for demonstration of the advantages of the CNT NEMS.

Development of a tritium monitor combined with an electrochemical tritium pump using a proton conducting oxide

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

Tanaka, M.; Sugiyama, T.

2015-03-15

The detection of low level tritium is one of the key issues for tritium management in tritium handling facilities. Such a detection can be performed by tritium monitors based on proton conducting oxide technique. We tested a tritium monitoring system composed of a commercial proportional counter combined with an electrochemical hydrogen pump equipped with CaZr{sub 0.9}In{sub 0.1}O{sub 3-α} as proton conducting oxide. The hydrogen pump operated at 973 K under electrolysis conditions using tritiated water vapor (HTO). The proton conducting oxide extracts tritium molecules (HT) from HTO and tritium concentration is measured by the proportional counter. The advantage of themore » proposed tritium monitoring system is that it is able to convert HTO into molecular hydrogen.« less

Modelling heat conduction in polycrystalline hexagonal boron-nitride films

PubMed Central

Mortazavi, Bohayra; Pereira, Luiz Felipe C.; Jiang, Jin-Wu; Rabczuk, Timon

2015-01-01

We conducted extensive molecular dynamics simulations to investigate the thermal conductivity of polycrystalline hexagonal boron-nitride (h-BN) films. To this aim, we constructed large atomistic models of polycrystalline h-BN sheets with random and uniform grain configuration. By performing equilibrium molecular dynamics (EMD) simulations, we investigated the influence of the average grain size on the thermal conductivity of polycrystalline h-BN films at various temperatures. Using the EMD results, we constructed finite element models of polycrystalline h-BN sheets to probe the thermal conductivity of samples with larger grain sizes. Our multiscale investigations not only provide a general viewpoint regarding the heat conduction in h-BN films but also propose that polycrystalline h-BN sheets present high thermal conductivity comparable to monocrystalline sheets. PMID:26286820

Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Keller, Nicholas A.; Migliori, Amy D.; Arya, Gaurav; Rao, Venigalla B.; Smith, Douglas E.

2013-09-01

Many double-stranded DNA viruses employ a molecular motor to package DNA into preformed capsid shells. Based on structures of phage T4 motor proteins determined by X-ray crystallography and cryo-electron microscopy, Rao, Rossmann and coworkers recently proposed a structural model for motor function. They proposed that DNA is ratcheted by a large conformational change driven by electrostatic interactions between charged residues at an interface between two globular domains of the motor protein. We have conducted experiments to test this model by studying the effect on packaging under applied load of site-directed changes altering these residues. We observe significant impairment of packaging activity including reductions in packaging rate, percent time packaging, and time active under high load. We show that these measured impairments correlate well with alterations in free energies associated with the conformational change predicted by molecular dynamics simulations.

A Bio-Inspired Two-Layer Sensing Structure of Polypeptide and Multiple-Walled Carbon Nanotube to Sense Small Molecular Gases

PubMed Central

Wang, Li-Chun; Su, Tseng-Hsiung; Ho, Cheng-Long; Yang, Shang-Ren; Chiu, Shih-Wen; Kuo, Han-Wen; Tang, Kea-Tiong

2015-01-01

In this paper, we propose a bio-inspired, two-layer, multiple-walled carbon nanotube (MWCNT)-polypeptide composite sensing device. The MWCNT serves as a responsive and conductive layer, and the nonselective polypeptide (40 mer) coating the top of the MWCNT acts as a filter into which small molecular gases pass. Instead of using selective peptides to sense specific odorants, we propose using nonselective, peptide-based sensors to monitor various types of volatile organic compounds. In this study, depending on gas interaction and molecular sizes, the randomly selected polypeptide enabled the recognition of certain polar volatile chemical vapors, such as amines, and the improved discernment of low-concentration gases. The results of our investigation demonstrated that the polypeptide-coated sensors can detect ammonia at a level of several hundred ppm and barely responded to triethylamine. PMID:25751078

Molecular systematics and global phylogeography of angel sharks (genus Squatina).

PubMed

Stelbrink, Björn; von Rintelen, Thomas; Cliff, Geremy; Kriwet, Jürgen

2010-02-01

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe-North Africa-Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events. Copyright (c) 2009. Published by Elsevier Inc.

Self-doped molecular composite battery electrolytes

DOEpatents

Harrup, Mason K.; Wertsching, Alan K.; Stewart, Frederick F.

2003-04-08

This invention is in solid polymer-based electrolytes for battery applications. It uses molecular composite technology, coupled with unique preparation techniques to render a self-doped, stabilized electrolyte material suitable for inclusion in both primary and secondary batteries. In particular, a salt is incorporated in a nano-composite material formed by the in situ catalyzed condensation of a ceramic precursor in the presence of a solvated polymer material, utilizing a condensation agent comprised of at least one cation amenable to SPE applications. As such, the counterion in the condensation agent used in the formation of the molecular composite is already present as the electrolyte matrix develops. This procedure effectively decouples the cation loading levels required for maximum ionic conductivity from electrolyte physical properties associated with condensation agent loading levels by utilizing the inverse relationship discovered between condensation agent loading and the time domain of the aging step.

The role of amine ligands in governing film morphology and electrical properties of copper films derived from copper formate-based molecular inks.

PubMed

Paquet, Chantal; Lacelle, Thomas; Liu, Xiangyang; Deore, Bhavana; Kell, Arnold J; Lafrenière, Sylvie; Malenfant, Patrick R L

2018-04-19

Copper formate complexes with various primary amines, secondary amines and pyridines were prepared, and their decomposition into conductive films was characterized. A comparison of the various complexes reveals that the temperature of thermolysis depends on the number of hydrogen bonds that can be formed between the amine and formate ligands. The particle size resulting from sintering of the copper complexes is shown to depend on the fraction of amine ligand released during the thermolysis reaction. The particle size in turn is shown to govern the electrical properties of the copper films. Correlations between the properties of the amines, such as boiling point and coordination strength, with the morphology and electrical performance of the copper films were established and provide a basis for the molecular design of copper formate molecular inks.

Can the scaling behavior of electric conductivity be used to probe the self-organizational changes in solution with respect to the ionic liquid structure? The case of [C8MIM][NTf2].

PubMed

Paluch, Marian; Wojnarowska, Zaneta; Goodrich, Peter; Jacquemin, Johan; Pionteck, Jürgen; Hensel-Bielowka, Stella

2015-08-28

Electrical conductivity of the supercooled ionic liquid [C8MIM][NTf2], determined as a function of temperature and pressure, highlights strong differences in its ionic transport behavior between low and high temperature regions. To date, the crossover effect which is very well known for low molecular van der Waals liquids has been rarely described for classical ionic liquids. This finding highlights that the thermal fluctuations could be dominant mechanisms driving the dramatic slowing down of ion motions near Tg. An alternative way to analyze separately low and high temperature dc-conductivity data using a density scaling approach was then proposed. Based on which a common value of the scaling exponent γ = 2.4 was obtained, indicating that the applied density scaling is insensitive to the crossover effect. By comparing the scaling exponent γ reported herein along with literature data for other ionic liquids, it appears that γ decreases by increasing the alkyl chain length on the 1-alkyl-3-methylimidazolium-based ionic liquids. This observation may be related to changes in the interaction between ions in solution driven by an increase in the van der Waals type interaction by increasing the alkyl chain length on the cation. This effect may be related to changes in the ionic liquid nanostructural organization with the alkyl chain length on the cation as previously reported in the literature based on molecular dynamic simulations. In other words, the calculated scaling exponent γ may be then used as a key parameter to probe the interaction and/or self-organizational changes in solution with respect to the ionic liquid structure.

Molecular medicine of fragile X syndrome: based on known molecular mechanisms.

PubMed

Luo, Shi-Yu; Wu, Ling-Qian; Duan, Ran-Hui

2016-02-01

Extensive research on fragile X mental retardation gene knockout mice and mutant Drosophila models has largely expanded our knowledge on mechanism-based treatment of fragile X syndrome (FXS). In light of these findings, several clinical trials are now underway for therapeutic translation to humans. Electronic literature searches were conducted using the PubMed database and ClinicalTrials.gov. The search terms included "fragile X syndrome", "FXS and medication", "FXS and therapeutics" and "FXS and treatment". Based on the publications identified in this search, we reviewed the neuroanatomical abnormalities in FXS patients and the potential pathogenic mechanisms to monitor the progress of FXS research, from basic studies to clinical trials. The pathological mechanisms of FXS were categorized on the basis of neuroanatomy, synaptic structure, synaptic transmission and fragile X mental retardation protein (FMRP) loss of function. The neuroanatomical abnormalities in FXS were described to motivate extensive research into the region-specific pathologies in the brain responsible for FXS behavioural manifestations. Mechanism-directed molecular medicines were classified according to their target pathological mechanisms, and the most recent progress in clinical trials was discussed. Current mechanism-based studies and clinical trials have greatly contributed to the development of FXS pharmacological therapeutics. Research examining the extent to which these treatments provided a rescue effect or FMRP compensation for the developmental impairments in FXS patients may help to improve the efficacy of treatments.

Versatile Molecular Silver Ink Platform for Printed Flexible Electronics.

PubMed

Kell, Arnold J; Paquet, Chantal; Mozenson, Olga; Djavani-Tabrizi, Iden; Deore, Bhavana; Liu, Xiangyang; Lopinski, Gregory P; James, Robert; Hettak, Khelifa; Shaker, Jafar; Momciu, Adrian; Ferrigno, Julie; Ferrand, Olivier; Hu, Jian Xiong; Lafrenière, Sylvie; Malenfant, Patrick R L

2017-05-24

A silver molecular ink platform formulated for screen, inkjet, and aerosol jet printing is presented. A simple formulation comprising silver neodecanoate, ethyl cellulose, and solvent provides improved performance versus that of established inks, yet with improved economics. Thin, screen-printed traces with exceptional electrical (<10 mΩ/□/mil or 12 μΩ·cm) and mechanical properties are achieved following thermal or photonic sintering, the latter having never been demonstrated for silver-salt-based inks. Low surface roughness, submicron thicknesses, and line widths as narrow as 41 μm outperform commercial ink benchmarks based on flakes or nanoparticles. These traces are mechanically robust to flexing and creasing (less than 10% change in resistance) and bind strongly to epoxy-based adhesives. Thin traces are remarkably conformal, enabling fully printed metal-insulator-metal band-pass filters. The versatility of the molecular ink platform enables an aerosol jet-compatible ink that yields conductive features on glass with 2× bulk resistivity and strong adhesion to various plastic substrates. An inkjet formulation is also used to print top source/drain contacts and demonstrate printed high-mobility thin film transistors (TFTs) based on semiconducting single-walled carbon nanotubes. TFTs with mobility values of ∼25 cm 2 V -1 s -1 and current on/off ratios >10 4 were obtained, performance similar to that of evaporated metal contacts in analogous devices.

Application of Petri Nets in Bone Remodeling

PubMed Central

Li, Lingxi; Yokota, Hiroki

2009-01-01

Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings. PMID:19838338

Molecular optoelectronics: the interaction of molecular conduction junctions with light.

PubMed

Galperin, Michael; Nitzan, Abraham

2012-07-14

The interaction of light with molecular conduction junctions is attracting growing interest as a challenging experimental and theoretical problem on one hand, and because of its potential application as a characterization and control tool on the other. It stands at the interface between two important fields, molecular electronics and molecular plasmonics and has attracted attention as a challenging scientific problem with potentially important technological consequences. Here we review the present state of the art of this field, focusing on several key phenomena and applications: using light as a switching device, using light to control junction transport in the adiabatic and non-adiabatic regimes, light generation in biased junctions and Raman scattering from such systems. This field has seen remarkable progress in the past decade, and the growing availability of scanning tip configurations that can combine optical and electrical probes suggests that further progress towards the goal of realizing molecular optoelectronics on the nanoscale is imminent.

Interactions between avidin and graphene for development of a biosensing platform.

PubMed

Macwan, Isaac; Khan, Md Daud Hossain; Aphale, Ashish; Singh, Shrishti; Liu, Juan; Hingorani, Manju; Patra, Prabir

2017-03-15

Fundamental understanding of interactions at the interface of biological molecules, such as proteins, and nanomaterials is crucial for developing various biocompatible hybrid materials and biosensing platforms. Biosensors comprising of graphene-based conductive nanomaterials offer the advantage of higher sensitivity and reliable diagnosis mainly due to their superior specific surface area and ballistic conductivity. Furthermore, conductive nanocomposite structures that immobilize proteins can synergize the properties of both transducers and molecular recognition elements improving the performance of the biosensing device. Here we report for the first time, using a combined molecular dynamics simulations and experimental approach, the interactions between avidin and graphene for the development of a sensing platform that can be used for the detection of biological macromolecules such as mismatch repair proteins through biotinylated DNA substrates. We find that the interactive forces between avidin and graphene are mainly hydrophobic, along with some van der Waals, electrostatic and hydrogen bonding interactions. Notably, the structure and function of the avidin molecule are largely preserved after its adsorption on the graphene surface. The MD results agree well with scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS) analysis of avidin immobilized on a graphenated polypyrrole (G-PPy) conductive nanocomposite confirming the adsorption of avidin on graphene nanoplatelets as observed from the Fourier-transform infrared spectroscopy (FTIR). Copyright © 2016 Elsevier B.V. All rights reserved.

Photoresponses in Gold Nanoparticle Single-Electron Transistors with Molecular Floating Gates

NASA Astrophysics Data System (ADS)

Noguchi, Yutaka; Yamamoto, Makoto; Ishii, Hisao; Ueda, Rieko; Terui, Toshifumi; Imazu, Keisuke; Tamada, Kaoru; Sakano, Takeshi; Matsuda, Kenji

2013-11-01

We have proposed a simple method of activating advanced functions in single-electron transistors (SETs) based on the specific properties of individual molecules. As a prototype, we fabricated a copper phthalocyanine (CuPc)-doped SET. The device consists of a gold-nanoparticle (GNP)-based SET doped with CuPc as a photoresponsive floating gate. In this paper, we report the details of the photoresponses of the CuPc-doped SET, such as conductance switching, sensitivity to the wavelength of the incident light, and multiple induced states.

Detection of glutamate and acetylcholine with organic electrochemical transistors based on conducting polymer/platinum nanoparticle composites.

PubMed

Kergoat, Loïg; Piro, Benoît; Simon, Daniel T; Pham, Minh-Chau; Noël, Vincent; Berggren, Magnus

2014-08-27

The aim of the study is to open a new scope for organic electrochemical transistors based on PEDOT:PSS, a material blend known for its stability and reliability. These devices can leverage molecular electrocatalysis by incorporating small amounts of nano-catalyst during the transistor manufacturing (spin coating). This methodology is very simple to implement using the know-how of nanochemistry and results in efficient enzymatic activity transduction, in this case utilizing choline oxidase and glutamate oxidase. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A molecular dynamics study of thermal transport in nanoparticle doped Argon like solid

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

Shahadat, Muhammad Rubayat Bin, E-mail: rubayat37@gmail.com; Ahmed, Shafkat; Morshed, A. K. M. M.

2016-07-12

Interfacial phenomena such as mass and type of the interstitial atom, nano scale material defect influence heat transfer and the effect become very significant with the reduction of the material size. Non Equilibrium Molecular Dynamics (NEMD) simulation was carried out in this study to investigate the effect of the interfacial phenomena on solid. Argon like solid was considered in this study and LJ potential was used for atomic interaction. Nanoparticles of different masses and different molecular defects were inserted inside the solid. From the molecular simulation, it was observed that a large interfacial mismatch due to change in mass inmore » the homogenous solid causes distortion of the phonon frequency causing increase in thermal resistance. Position of the doped nanoparticles have more profound effect on the thermal conductivity of the solid whereas influence of the mass ratio is not very significant. Interstitial atom positioned perpendicular to the heat flow causes sharp reduction in thermal conductivity. Structural defect caused by the molecular defect (void) also observed to significantly affect the thermal conductivity of the solid.« less

Spin transport properties of n-polyacene molecules (n = 1–15) connected to Ni surface electrodes: Theoretical analysis

PubMed Central

Caliskan, S.; Laref, A.

2014-01-01

Using non-equilibrium Green function formalism in conjunction with density functional theory, we explore the spin-polarized transport characteristics of several planar n-acene molecules suspended between two semi-infinite Ni electrodes via the thiol group. We examine the spin-dependence transport on Ni-n-acenes-Ni junctions, while the number of fused benzene rings varies between 1 and 15. Intriguingly, the induced magnetic moments of small acene molecules are higher than that of longer acene rings. The augmentation of fused benzene rings affects both the magnetic and transport features, such as the transmission function and conductance owing to their coupling to the Ni surface contacts via the anchoring group. The interplay between the spin-polarized transport properties, structural configuration and molecular electronic is a fortiori essential in these attractive molecular devices. Thus, this can conduct to the engineering of the electron spin transport in atomistic and molecular junctions. These prominent molecules convincingly infer that the molecular spin valves can conduct to thriving molecular devices. PMID:25482076

A DAG Scheduling Scheme on Heterogeneous Computing Systems Using Tuple-Based Chemical Reaction Optimization

PubMed Central

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems. PMID:25143977

A DAG scheduling scheme on heterogeneous computing systems using tuple-based chemical reaction optimization.

PubMed

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems.

Enhanced n-Doping Efficiency of a Naphthalenediimide-Based Copolymer through Polar Side Chains for Organic Thermoelectrics

PubMed Central

2018-01-01

N-doping of conjugated polymers either requires a high dopant fraction or yields a low electrical conductivity because of their poor compatibility with molecular dopants. We explore n-doping of the polar naphthalenediimide–bithiophene copolymer p(gNDI-gT2) that carries oligoethylene glycol-based side chains and show that the polymer displays superior miscibility with the benzimidazole–dimethylbenzenamine-based n-dopant N-DMBI. The good compatibility of p(gNDI-gT2) and N-DMBI results in a relatively high doping efficiency of 13% for n-dopants, which leads to a high electrical conductivity of more than 10–1 S cm–1 for a dopant concentration of only 10 mol % when measured in an inert atmosphere. We find that the doped polymer is able to maintain its electrical conductivity for about 20 min when exposed to air and recovers rapidly when returned to a nitrogen atmosphere. Overall, solution coprocessing of p(gNDI-gT2) and N-DMBI results in a larger thermoelectric power factor of up to 0.4 μW K–2 m–1 compared to other NDI-based polymers. PMID:29457139

Enhanced n-Doping Efficiency of a Naphthalenediimide-Based Copolymer through Polar Side Chains for Organic Thermoelectrics.

PubMed

Kiefer, David; Giovannitti, Alexander; Sun, Hengda; Biskup, Till; Hofmann, Anna; Koopmans, Marten; Cendra, Camila; Weber, Stefan; Anton Koster, L Jan; Olsson, Eva; Rivnay, Jonathan; Fabiano, Simone; McCulloch, Iain; Müller, Christian

2018-02-09

N-doping of conjugated polymers either requires a high dopant fraction or yields a low electrical conductivity because of their poor compatibility with molecular dopants. We explore n-doping of the polar naphthalenediimide-bithiophene copolymer p(gNDI-gT2) that carries oligoethylene glycol-based side chains and show that the polymer displays superior miscibility with the benzimidazole-dimethylbenzenamine-based n-dopant N-DMBI. The good compatibility of p(gNDI-gT2) and N-DMBI results in a relatively high doping efficiency of 13% for n-dopants, which leads to a high electrical conductivity of more than 10 -1 S cm -1 for a dopant concentration of only 10 mol % when measured in an inert atmosphere. We find that the doped polymer is able to maintain its electrical conductivity for about 20 min when exposed to air and recovers rapidly when returned to a nitrogen atmosphere. Overall, solution coprocessing of p(gNDI-gT2) and N-DMBI results in a larger thermoelectric power factor of up to 0.4 μW K -2 m -1 compared to other NDI-based polymers.

Charge transport in organic multi-layer devices under electric and optical fields

NASA Astrophysics Data System (ADS)

Park, June Hyoung

2007-12-01

Charge transport in small organic molecules and conjugated conducting polymers under electric or optical fields is studied by using field effect transistors and photo-voltaic cells with multiple thin layers. With these devices, current under electric field, photo-current under optical field, and luminescence of optical materials are measured to characterize organic and polymeric materials. For electric transport studies, poly(3,4-ethylenedioxythiophene) doped by polystyrenesulfonic acid is used, which is conductive with conductivity of approximately 25 S/cm. Despite their high conductance, field effect transistors based on the films are successfully built and characterized by monitoring modulations of drain current by gate voltage and IV characteristic curves. Due to very thin insulating layers of poly(vinylphenol), the transistors are relative fast under small gate voltage variation although heavy ions are involved in charge transport. In IV characteristic curves, saturation effects can be observed. Analysis using conventional field effect transistor model indicates high mobility of charge carriers, 10 cm2/V·sec, which is not consistent with the mobility of the conducting polymer. It is proposed that the effect of a small density of ions injected via polymer dielectric upon application of gate voltage and the ion compensation of key hopping sites accounts for the operation of the field effect transistors. For the studies of transport under optical field, photovoltaic cells with 3 different dendrons, which are efficient to harvest photo-excited electrons, are used. These dendrons consist of two electron-donors (tetraphenylporphyrin) and one electron-accepter (naphthalenediimide). Steady-state fluorescence measurements show that inter-molecular interaction is dominant in solid dendron film, although intra-molecular interaction is still present. Intra-molecular interaction is suggested by different fluorescence lifetimes between solutions of donor and dendrons. This intra-molecular interaction has two processes, transport via pi-stackings and transport via linking functional groups in the dendrons. IV characteristic spectra of the photovoltaic cells suggest that the transport route of photo-excited charges depends on wavelength of incident light on the cells. For excitation by the Soret band and the lowest Q band, a photo-excited electron can transport directly to a neighbor dendron. For excitation by high-energy Q bands, a photo-excited electron transports via the electron-accepters.

Recombinant Peptides as Biomarkers for Metastatic Breast Cancer Response

DTIC Science & Technology

2007-10-01

could be specific to breast cancer tumor models has just been concluded. In vivo biopanning wsa conducted with a T7 phage -based random peptide library...peptides selected from phage -displayed libraries. 15. SUBJECT TERMS Breast cancer, phage display, molecular imaging, personalized medicine 16...recombinant peptides from phage -displayed peptide libraries can be selected that bind to receptors activated in response to therapy. These peptides in turn

Mode-coupling theoretical analysis of transport and relaxation properties of liquid dimethylimidazolium chloride

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Koda, S.

2010-03-01

The mode-coupling theory for molecular liquids based on the interaction-site model is applied to a representative molecular ionic liquid, dimethylimidazolium chloride, and dynamic properties such as shear viscosity, self-diffusion coefficients, reorientational relaxation time, electric conductivity, and dielectric relaxation spectrum are analyzed. Molecular dynamics (MD) simulation is also performed on the same system for comparison. The theory captures the characteristics of the dynamics of the ionic liquid qualitatively, although theoretical relaxation times are several times larger than those from the MD simulation. Large relaxations are found in the 100 MHz region in the dispersion of the shear viscosity and the dielectric relaxation, in harmony with various experiments. The relaxations of the self-diffusion coefficients are also found in the same frequency region. The dielectric relaxation spectrum is divided into the contributions of the translational and reorientational modes, and it is demonstrated that the relaxation in the 100 MHz region mainly stems from the translational modes. The zero-frequency electric conductivity is close to the value predicted by the Nernst-Einstein equation in both MD simulation and theoretical calculation. However, the frequency dependence of the electric conductivity is different from those of self-diffusion coefficients in that the former is smaller than the latter in the gigahertz-terahertz region, which is compensated by the smaller dispersion of the former in the 100 MHz region. The analysis of the theoretical calculation shows that the difference in their frequency dependence is due to the different contribution of the short- and long-range liquid structures.

Electrical Matching at Metal/Molecule Contacts for Efficient Heterogeneous Charge Transfer.

PubMed

Sato, Shino; Iwase, Shigeru; Namba, Kotaro; Ono, Tomoya; Hara, Kenji; Fukuoka, Atsushi; Uosaki, Kohei; Ikeda, Katsuyoshi

2018-02-27

In a metal/molecule hybrid system, unavoidable electrical mismatch exists between metal continuum states and frontier molecular orbitals. This causes energy loss in the electron conduction across the metal/molecule interface. For efficient use of energy in a metal/molecule hybrid system, it is necessary to control interfacial electronic structures. Here we demonstrate that electrical matching between a gold substrate and π-conjugated molecular wires can be obtained by using monatomic foreign metal interlayers, which can change the degree of d-π* back-donation at metal/anchor contacts. This interfacial control leads to energy level alignment between the Fermi level of the metal electrode and conduction molecular orbitals, resulting in resonant electron conduction in the metal/molecule hybrid system. When this method is applied to molecule-modified electrocatalysts, the heterogeneous electrochemical reaction rate is considerably improved with significant suppression of energy loss at the internal electron conduction.

On the dielectric conductivity of molecular ionic liquids.

PubMed

Schröder, Christian; Steinhauser, Othmar

2009-09-21

The contribution of the conductivity to the spectrum of the generalized dielectric constant or susceptibility of molecular ionic liquids is analyzed, both in theoretical terms and computationally by means of molecular dynamics simulation of the concrete system 1-ethyl-3-methyl-imidazolium dicyanoamide at 300 K. As a central quantity the simulated current autocorrelation function is modeled by a carefully designed fit function. This not only gives a satisfactory numerical representation but yields the correct conductivity upon integration. In addition the fit function can be Fourier-Laplace transformed analytically. Both, the real and imaginary parts of the transform show expected behavior, in particular, the right limits for zero frequency. This altogether demonstrates that the components of the fit function are of physical relevance.

Thermoelectric effect in molecular electronics

NASA Astrophysics Data System (ADS)

Paulsson, Magnus; Datta, Supriyo

2003-06-01

We provide a theoretical estimate of the thermoelectric current and voltage over a Phenyldithiol molecule. We also show that the thermoelectric voltage is (1) easy to analyze, (2) insensitive to the detailed coupling to the contacts, (3) large enough to be measured, and (4) give valuable information, which is not readily accessible through other experiments, on the location of the Fermi energy relative to the molecular levels. The location of the Fermi-energy is poorly understood and controversial even though it is a central factor in determining the nature of conduction (n or p type). We also note that the thermoelectric voltage measured over Guanine molecules with a scanning tunneling microscope by Poler et al., indicate conduction through the highest occupied molecular orbital level, i.e., p-type conduction.

Transforming Benzophenoxazine Laser Dyes into Chromophores for Dye-Sensitized Solar Cells: A Molecular Engineering Approach

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

Schröder, Florian A. Y. N.; Cole, Jacqueline M.; Waddell, Paul G.

2015-02-03

The re-functionalization of a series of four well-known industrial laser dyes, based on benzophenoxazine, is explored with the prospect of molecularly engineering new chromophores for dye-sensitized solar cell (DSC) applications. Such engineering is important since a lack of suitable dyes is stifling the progress of DSC technology. The conceptual idea involves making laser dyes DSC-active by chemical modification, while maintaining their key property attributes that are attractive to DSC applications. This molecular engineering follows a step-wise approach. Firstly, molecular structures and optical absorption properties are determined for the parent laser dyes: Cresyl Violet (1); Oxazine 170 (2); Nile Blue Amore » (3), Oxazine 750 (4). These reveal structure-property relationships which define the prerequisites for computational molecular design of DSC dyes; the nature of their molecular architecture (D-π-A) and intramolecular charge transfer. Secondly, new DSC dyes are computationally designed by the in silico addition of a carboxylic acid anchor at various chemical substitution points in the parent laser dyes. A comparison of the resulting frontier molecular orbital energy levels with the conduction band edge of a TiO2 DSC photoanode and the redox potential of two electrolyte options I-/I3- and Co(II/III)tris(bipyridyl) suggests promise for these computationally designed dyes as co-sensitizers for DSC applications.« less

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

PubMed

Ryu, Taekhee; Lansac, Yves; Jang, Yun Hee

2017-07-12

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC 6 H 4 ) 5 HC 60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

Reduced thermal conductivity of nanotwinned random layer structures: a promising nanostructuring towards efficient Si and Si/Ge thermoelectric materials

NASA Astrophysics Data System (ADS)

Samaraweera, Nalaka; Chan, Kin L.; Mithraratne, Kumar

2018-05-01

Si and Si/Ge based nanostructures of reduced lattice thermal conductivity are widely attractive for developing efficient thermoelectric materials. In this study, we demonstrate the reduced thermal conductivity of Si nanotwinned random layer (NTRL) structures over corresponding superlattice and twin-free counterparts. The participation ratio analysis of vibrational modes shows that a possible cause of thermal conductivity reduction is phonon localization due to the random arrangement of twin boundaries. Via non-equilibrium molecular dynamic simulations, it is shown that ~23 and ~27% reductions over superlattice counterparts and ~55 and 53% over twin-free counterparts can be attained for the structures of total lengths of 90 and 170 nm, respectively. Furthermore, a random twin boundary distribution is applied for Si/Ge random layer structures seeking further reduction of thermal conductivity. A significant reduction in thermal conductivity of Si/Ge structures exceeding the thermal insulating performance of the corresponding amorphous Si structure by ~31% for a total length of 90 nm can be achieved. This reduction is as high as ~98% compared to the twin-free Si counterpart. It is demonstrated that application of randomly organised nanoscale twin boundaries is a promising nanostructuring strategy towards developing efficient Si and Si/Ge based thermoelectric materials in the future.

Low-molecular-weight heparin for prevention of placenta-mediated pregnancy complications: protocol for a systematic review and individual patient data meta-analysis (AFFIRM)

PubMed Central

2014-01-01

Background Placenta-mediated pregnancy complications include pre-eclampsia, late pregnancy loss, placental abruption, and the small-for-gestational age newborn. They are leading causes of maternal, fetal, and neonatal morbidity and mortality in developed nations. Women who have experienced these complications are at an elevated risk of recurrence in subsequent pregnancies. However, despite decades of research no effective strategies to prevent recurrence have been identified, until recently. We completed a pooled summary-based meta-analysis that strongly suggests that low-molecular-weight heparin reduces the risk of recurrent placenta-mediated complications. The proposed individual patient data meta-analysis builds on this successful collaboration. The project is called AFFIRM, An individual patient data meta-analysis oF low-molecular-weight heparin For prevention of placenta-medIated pRegnancy coMplications. Methods/Design We conducted a systematic review to identify randomized controlled trials with a low-molecular-weight heparin intervention for the prevention of recurrent placenta-mediated pregnancy complications. Investigators and statisticians representing eight trials met to discuss the outcomes and analysis plan for an individual patient data meta-analysis. An additional trial has since been added for a total of nine eligible trials. The primary analyses from the original trials will be replicated for quality assurance prior to recoding the data from each trial and combining it into a common dataset for analysis. Using the anonymized combined data we will conduct logistic regression and subgroup analyses aimed at identifying which women with previous pregnancy complications benefit most from treatment with low-molecular-weight heparin during pregnancy. Discussion The goal of the proposed individual patient data meta-analysis is a thorough estimation of treatment effects in patients with prior individual placenta-mediated pregnancy complications and exploration of which complications are specifically prevented by low-molecular-weight heparin. Systematic review registration PROSPERO (International Prospective Registry of Systematic Reviews) 23 December 2013, CRD42013006249 PMID:24969227

A DICOM-based 2nd generation Molecular Imaging Data Grid implementing the IHE XDS-i integration profile.

PubMed

Lee, Jasper; Zhang, Jianguo; Park, Ryan; Dagliyan, Grant; Liu, Brent; Huang, H K

2012-07-01

A Molecular Imaging Data Grid (MIDG) was developed to address current informatics challenges in archival, sharing, search, and distribution of preclinical imaging studies between animal imaging facilities and investigator sites. This manuscript presents a 2nd generation MIDG replacing the Globus Toolkit with a new system architecture that implements the IHE XDS-i integration profile. Implementation and evaluation were conducted using a 3-site interdisciplinary test-bed at the University of Southern California. The 2nd generation MIDG design architecture replaces the initial design's Globus Toolkit with dedicated web services and XML-based messaging for dedicated management and delivery of multi-modality DICOM imaging datasets. The Cross-enterprise Document Sharing for Imaging (XDS-i) integration profile from the field of enterprise radiology informatics was adopted into the MIDG design because streamlined image registration, management, and distribution dataflow are likewise needed in preclinical imaging informatics systems as in enterprise PACS application. Implementation of the MIDG is demonstrated at the University of Southern California Molecular Imaging Center (MIC) and two other sites with specified hardware, software, and network bandwidth. Evaluation of the MIDG involves data upload, download, and fault-tolerance testing scenarios using multi-modality animal imaging datasets collected at the USC Molecular Imaging Center. The upload, download, and fault-tolerance tests of the MIDG were performed multiple times using 12 collected animal study datasets. Upload and download times demonstrated reproducibility and improved real-world performance. Fault-tolerance tests showed that automated failover between Grid Node Servers has minimal impact on normal download times. Building upon the 1st generation concepts and experiences, the 2nd generation MIDG system improves accessibility of disparate animal-model molecular imaging datasets to users outside a molecular imaging facility's LAN using a new architecture, dataflow, and dedicated DICOM-based management web services. Productivity and efficiency of preclinical research for translational sciences investigators has been further streamlined for multi-center study data registration, management, and distribution.

Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

NASA Technical Reports Server (NTRS)

Wilson, Michael A.; Wei, Chenyu; Bjelkmar, Paer; Wallace, B. A.; Pohorille, Andrew

2011-01-01

Molecular dynamics simulations were carried out in order to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistant with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive.The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be non-conducting. The conductance of the hexamer was estimated to be 115+/-34 pS and 74+/-20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K(+) and Cl(-) with their first solvation shells intact. The free energy barrier encountered by K(+) is only 2.2 kcal/mol whereas Cl(-) encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. keywords: ion channels, peptaibols, channel conductance, molecular dynamics

The principle of respect for autonomy--concordant with the experience of oncology physicians and molecular biologists in their daily work?

PubMed

Ebbesen, Mette; Pedersen, Birthe D

2008-03-26

This article presents results from a qualitative empirical investigation of how Danish oncology physicians and Danish molecular biologists experience the principle of respect for autonomy in their daily work. This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. We found that that molecular biologists consider the principle of respect for autonomy as a negative obligation, where the informed consent of patients or research subjects should be respected. Furthermore, molecular biologists believe that very sick patients are constraint by the circumstances to a certain choice. However, in contrast to molecular biologists, oncology physicians experience the principle of respect for autonomy as a positive obligation, where the physician in dialogue with the patient performs a medical prognosis based on the patient's wishes and ideas, mutual understanding and respect. Oncology physicians believe that they have a positive obligation to adjust to the level of the patient when providing information making sure that the patient understands. Oncology physicians experience situations where the principle of respect for autonomy does not apply because the patient is in a difficult situation. In this study we explore the moral views and attitudes of oncology physicians and molecular biologists and compare these views with bioethical theories of the American bioethicists Tom L. Beauchamp & James F. Childress and the Danish philosophers Jakob Rendtorff & Peter Kemp. This study shows that essential parts of the two bioethical theories are reflected in the daily work of Danish oncology physicians and Danish molecular biologists. However, the study also explores dimensions where the theories can be developed further to be concordant with biomedical practice. The hope is that this study enhances the understanding of the principle of respect for autonomy and the way it is practiced.

Initiative for Molecular Profiling and Advanced Cancer Therapy and challenges in the implementation of precision medicine.

PubMed

Tsimberidou, Apostolia-Maria

In the last decade, breakthroughs in technology have improved our understanding of genomic, transcriptional, proteomic, epigenetic aberrations and immune mechanisms in carcinogenesis. Genomics and model systems have enabled the validation of novel therapeutic strategies. Based on these developments, in 2007, we initiated the IMPACT (Initiative for Molecular Profiling and Advanced Cancer Therapy) study, the first personalized medicine program for patients with advanced cancer at The University of Texas MD Anderson Cancer Center. We demonstrated that in patients referred for Phase I clinical trials, the use of tumor molecular profiling and treatment with matched targeted therapy was associated with encouraging rates of response, progression-free survival and overall survival compared to non-matched therapy. We are currently conducting IMPACT2, a randomized study evaluating molecular profiling and targeted agents in patients with metastatic cancer. Optimization of innovative biomarker-driven clinical trials that include targeted therapy and/or immunotherapeutic approaches for carefully selected patients will accelerate the development of novel drugs and the implementation of precision medicine. Copyright © 2017 Elsevier Inc. All rights reserved.

Alloying effects on superionic conductivity in lithium indium halides for all-solid-state batteries

NASA Astrophysics Data System (ADS)

Zevgolis, Alysia; Wood, Brandon C.; Mehmedović, Zerina; Hall, Alex T.; Alves, Thomaz C.; Adelstein, Nicole

2018-04-01

Alloying of anions is a promising engineering strategy for tuning ionic conductivity in halide-based inorganic solid electrolytes. We explain the alloying effects in Li3InBr6-xClx, in terms of strain, chemistry, and microstructure, using first-principles molecular dynamics simulations and electronic structure analysis. We find that strain and bond chemistry can be tuned through alloying and affect the activation energy and maximum diffusivity coefficient. The similar conductivities of the x = 3 and x = 6 compositions can be understood by assuming that the alloy separates into Br-rich and Cl-rich regions. Phase-separation increases diffusivity at the interface and in the expanded Cl-region, suggesting microstructure effects are critical. Similarities with other halide superionic conductors are highlighted.

Reinterpretation of Mariner 9 IRIS data on the basis of a simulation of radiative-conductive convective transfer in the dust laden Martian atmosphere

NASA Technical Reports Server (NTRS)

Pallman, A. J.

1974-01-01

Time dependent vertical distributions of atmospheric temperature and static stability were determined by a radiative-convective-conductive heat transfer model attuned to Mariner 9 IRIS radiance data. Of particular interest were conditions of both the dust-laden and dust-free atmosphere in the middle latitudes on Mars during the late S.H. summer season. The numerical model simulates at high spatial and temporal resolution (52 atmospheric and 30 subsurface levels; with a time-step of 7.5 min.) the heat transports in the ground-atmosphere system. The algorithm is based on the solution of the appropriate heating rate equation which includes radiative, molecular-conductive and convective heat transfer terms. Ground and atmosphere are coupled by an internal thermal boundary condition.

Vibrational Heat Transport in Molecular Junctions

NASA Astrophysics Data System (ADS)

Segal, Dvira; Agarwalla, Bijay Kumar

2016-05-01

We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.

The mechanism of proton conduction in phosphoric acid

NASA Astrophysics Data System (ADS)

Vilčiauskas, Linas; Tuckerman, Mark E.; Bester, Gabriel; Paddison, Stephen J.; Kreuer, Klaus-Dieter

2012-06-01

Neat liquid phosphoric acid (H3PO4) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.

Thermal conductance of suspended nanoribbons: interplay between strain and interatomic potential nonlinearity

NASA Astrophysics Data System (ADS)

Barreto, Roberto; Florencia Carusela, M.; Monastra, Alejandro G.

2017-10-01

We investigate the role that nonlinearity in the interatomic potential has on the thermal conductance of a suspended nanoribbon when it is subjected to a longitudinal strain. To focus on the first cubic and quartic nonlinear terms of a general potential, we propose an atomic system based on an α-β Fermi-Pasta-Ulam nearest neighbor interaction. We perform classical molecular dynamics simulations to investigate the contribution of longitudinal, transversal and flexural modes to the thermal conductance as a function of the α-β parameters and the applied strain. We compare the cases where atoms are allowed to vibrate only in plane (2D) with the case of vibrations in and out of plane (3D). We find that the dependence of conductance on α and β relies on a crossover phenomenon between linear/nonlinear delocalized/localized flexural and transversal modes, driven by an on/off switch of the strain.

Disordered nuclear pasta, magnetic field decay, and crust cooling in neutron stars

NASA Astrophysics Data System (ADS)

Horowitz, C. J.; Berry, D. K.; Briggs, C. M.; Caplan, M. E.; Cumming, A.; Schneider, A. S.

2015-04-01

Nuclear pasta, with non-spherical shapes, is expected near the base of the crust in neutron stars. Large scale molecular dynamics simulations of pasta show long lived topological defects that could increase electron scattering and reduce both the thermal and electrical conductivities. We model a possible low conductivity pasta layer by increasing an impurity parameter Qimp. Predictions of light curves for the low mass X-ray binary MXB 1659-29, assuming a large Qimp, find continued late time cooling that is consistent with Chandra observations. The electrical and thermal conductivities are likely related. Therefore observations of late time crust cooling can provide insight on the electrical conductivity and the possible decay of neutron star magnetic fields (assuming these are supported by currents in the crust). This research was supported in part by DOE Grants DE-FG02-87ER40365 (Indiana University) and DE-SC0008808 (NUCLEI SciDAC Collaboration).

Ab initio electron propagator calculations of transverse conduction through DNA nucleotide bases in 1-nm nanopore corroborate third generation sequencing.

PubMed

Kletsov, Aleksey A; Glukhovskoy, Evgeny G; Chumakov, Aleksey S; Ortiz, Joseph V

2016-01-01

The conduction properties of DNA molecule, particularly its transverse conductance (electron transfer through nucleotide bridges), represent a point of interest for DNA chemistry community, especially for DNA sequencing. However, there is no fully developed first-principles theory for molecular conductance and current that allows one to analyze the transverse flow of electrical charge through a nucleotide base. We theoretically investigate the transverse electron transport through all four DNA nucleotide bases by implementing an unbiased ab initio theoretical approach, namely, the electron propagator theory. The electrical conductance and current through DNA nucleobases (guanine [G], cytosine [C], adenine [A] and thymine [T]) inserted into a model 1-nm Ag-Ag nanogap are calculated. The magnitudes of the calculated conductance and current are ordered in the following hierarchies: gA>gG>gC>gT and IG>IA>IT>IC correspondingly. The new distinguishing parameter for the nucleobase identification is proposed, namely, the onset bias magnitude. Nucleobases exhibit the following hierarchy with respect to this parameter: Vonset(A)

Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

NASA Astrophysics Data System (ADS)

Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.; Franco, Ignacio

2017-03-01

The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green's function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to interrogate basic structure-transport relations at the single-molecule limit.

Standards-based curation of a decade-old digital repository dataset of molecular information.

PubMed

Harvey, Matthew J; Mason, Nicholas J; McLean, Andrew; Murray-Rust, Peter; Rzepa, Henry S; Stewart, James J P

2015-01-01

The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the "supporting information") should be conducted in a manner that facilitates automatic periodic curation. Graphical abstractStandards and metadata-based curation of a decade-old digital repository dataset of molecular information.

The molecular, electronic structures and vibrational spectra of metal-free, N,N'-dideuterio and magnesium tetra-2,3-pyridino-porphyrazines: Density functional calculations.

PubMed

Liu, Zhongqiang; Zhang, Xianxi; Zhang, Yuexing; Li, Renjie; Jiang, Jianzhuang

2006-10-01

A theoretical investigation of the fully optimized geometries and electronic structures of the metal-free (TPdPzH(2)), N,N'-dideuterio (TPdPzD(2)), and magnesium (TPdPzMg) tetra-2,3-pyridino-porphyrazine has been conducted based on density functional theory. The optimized geometries at density functional theory level for these compounds are reported here for the first time. A comparison between the different molecules for the geometry, molecular orbital, and atomic charge is made. The substituent effect of the N atoms on the molecular structures of these compounds is discussed. The IR and Raman spectra for these three compounds have also been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH, NM, and pyridine ring vibrational bands in the IR and Raman spectra have been made based on assistance of animated pictures. The simulated IR spectra of TPdPzH(2) are compared with the experimental absorption spectra, and very good consistency has been found. The isotope effect on the IR and Raman spectra is also discussed.

Altitudinal distribution and advertisement call of Colostethus latinasus (Amphibia: Dendrobatidae), endemic species from eastern Panama and type species of Colostethus , with a molecular assessment of similar sympatric species.

PubMed

Ibáñez, Roberto D; Griffith, Edgardo J; Lips, Karen R; Crawford, Andrew J

2017-04-12

We conducted a molecular assessment of Colostethus-like frogs along an elevational gradient in the Serranía de Pirre, above Santa Cruz de Cana, eastern Panama, aiming to establish their species identity and to determine the altitudinal distribution of C. latinasus. Our findings confirm the view of C. latinasus as an endemic species restricted to the highlands of this mountain range, i.e., 1350-1475 m.a.s.l., considered to be type locality of this species. We described the advertisement call of C. latinasus that consists of a series of 4-18 single, short and relatively loud "peep"-like notes given in rapid succession, and its spectral and temporal features were compared with calls of congeneric species. For the first time, DNA sequences from C. latinasus were obtained, since previously reported sequences were based on misidentified specimens. This is particularly important because C. latinasus is the type species of Colostethus, a genus considered paraphyletic according to recent phylogenetic analyses based on molecular data.

Structure formation in fibrous materials based on poly-3-hydroxybutyrate for traumatology

NASA Astrophysics Data System (ADS)

Olkhov, A. A.; Sklyanchuk, E. D.; Staroverova, O. V.; Abbasov, T. A.; Guryev, V. V.; Akatov, V. S.; Fadeyeva, I. S.; Fesenko, N. I.; Filatov, Yu. N.; Iordanskii, A. L.

2015-10-01

The paper reviews the structure formation of fibrous materials based on poly-3-hydroxybutyrate depending on parameters of electrospinning and characteristics of polymer solution. Fiber structure was studied by DSC, ESR and SEM. The molecular weight affects the diameter and uniformity of the fiber. An electromechanical impact leads to an orientation of crystalline structure in the fiber. The design of an artificial bioresorbable implant based on nano- and microfibers of poly-3-hydroxybutyrate is created. Dynamics of growth of mesenchymal stem cells on poly-3-hydroxybutyrate scaffolds is studied. Successful field tests of implants of the Achilles tendon in Wistar rats are conducted.

Imaging of Tumor Characteristics and Molecular Pathways With PET: Developments Over the Last Decade Toward Personalized Cancer Therapy.

PubMed

Marcu, Loredana Gabriela; Moghaddasi, Leyla; Bezak, Eva

2018-05-04

Improvements in personalized therapy are made possible by the advances in molecular biology that led to developments in molecular imaging, allowing highly specific in vivo imaging of biological processes. Positron emission tomography (PET) is the most specific and sensitive imaging technique for in vivo molecular targets and pathways, offering quantification and evaluation of functional properties of the targeted anatomy. This work is an integrative research review that summarizes and evaluates the accumulated current status of knowledge of recent advances in PET imaging for cancer diagnosis and treatment, concentrating on novel radiotracers and evaluating their advantages and disadvantages in cancer characterization. Medline search was conducted, limited to English publications from 2007 onward. Identified manuscripts were evaluated for most recent developments in PET imaging of cancer hypoxia, angiogenesis, proliferation, and clonogenic cancer stem cells (CSC). There is an expansion observed from purely metabolic-based PET imaging toward antibody-based PET to achieve more information on cancer characteristics to identify hypoxia, proangiogenic factors, CSC, and others. 64 Cu-ATSM, for example, can be used both as a hypoxia and a CSC marker. Progress in the field of functional imaging will possibly lead to more specific tumor targeting and personalized treatment, increasing tumor control and improving quality of life. Copyright © 2018 Elsevier Inc. All rights reserved.

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

PubMed

Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

2010-07-28

Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

PubMed

San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

2014-12-01

Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

Carbon Fibers Conductivity Studies

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Butkus, A. M.

1980-01-01

In an attempt to understand the process of electrical conduction in polyacrylonitrile (PAN)-based carbon fibers, calculations were carried out on cluster models of the fiber consisting of carbon, nitrogen, and hydrogen atoms using the modified intermediate neglect of differential overlap (MINDO) molecular orbital (MO) method. The models were developed based on the assumption that PAN carbon fibers obtained with heat treatment temperatures (HTT) below 1000 C retain nitrogen in a graphite-like lattice. For clusters modeling an edge nitrogen site, analysis of the occupied MO's indicated an electron distribution similar to that of graphite. A similar analysis for the somewhat less stable interior nitrogen site revealed a partially localized II electron distribution around the nitrogen atom. The differences in bonding trends and structural stability between edge and interior nitrogen clusters led to a two-step process proposed for nitrogen evolution with increasing HTT.

Synergistic gelation of silica nanoparticles and a sorbitol-based molecular gelator to yield highly-conductive free-standing gel electrolytes.

PubMed

Basrur, Veidhes R; Guo, Juchen; Wang, Chunsheng; Raghavan, Srinivasa R

2013-01-23

Lithium-ion batteries have emerged as the preferred type of rechargeable batteries, but there is a need to improve the performance of the electrolytes therein. Specifically, the challenge is to obtain electrolytes with the mechanical rigidity of solids but with liquid-like conductivities. In this study, we report a class of nanostructured gels that are able to offer this unique combination of properties. The gels are prepared by utilizing the synergistic interactions between a molecular gelator, 1,3:2,4-di-O-methyl-benzylidene-d-sorbitol (MDBS), and a nanoscale particulate material, fumed silica (FS). When MDBS and FS are combined in a liquid consisting of propylene carbonate with dissolved lithium perchlorate salt, the liquid electrolyte is converted into a free-standing gel due to the formation of a strong MDBS-FS network. The gels exhibit elastic shear moduli around 1000 kPa and yield stresses around 11 kPa-both values considerably exceed those obtainable by MDBS or FS alone in the same liquid. At the same time, the gel also exhibits electrochemical properties comparable to the parent liquid, including a high ionic conductivity (~5 × 10(-3) S/cm at room temperature) and a wide electrochemical stability window (up to 4.5 V).

Uncertainty for calculating transport on Titan: A probabilistic description of bimolecular diffusion parameters

NASA Astrophysics Data System (ADS)

Plessis, S.; McDougall, D.; Mandt, K.; Greathouse, T.; Luspay-Kuti, A.

2015-11-01

Bimolecular diffusion coefficients are important parameters used by atmospheric models to calculate altitude profiles of minor constituents in an atmosphere. Unfortunately, laboratory measurements of these coefficients were never conducted at temperature conditions relevant to the atmosphere of Titan. Here we conduct a detailed uncertainty analysis of the bimolecular diffusion coefficient parameters as applied to Titan's upper atmosphere to provide a better understanding of the impact of uncertainty for this parameter on models. Because temperature and pressure conditions are much lower than the laboratory conditions in which bimolecular diffusion parameters were measured, we apply a Bayesian framework, a problem-agnostic framework, to determine parameter estimates and associated uncertainties. We solve the Bayesian calibration problem using the open-source QUESO library which also performs a propagation of uncertainties in the calibrated parameters to temperature and pressure conditions observed in Titan's upper atmosphere. Our results show that, after propagating uncertainty through the Massman model, the uncertainty in molecular diffusion is highly correlated to temperature and we observe no noticeable correlation with pressure. We propagate the calibrated molecular diffusion estimate and associated uncertainty to obtain an estimate with uncertainty due to bimolecular diffusion for the methane molar fraction as a function of altitude. Results show that the uncertainty in methane abundance due to molecular diffusion is in general small compared to eddy diffusion and the chemical kinetics description. However, methane abundance is most sensitive to uncertainty in molecular diffusion above 1200 km where the errors are nontrivial and could have important implications for scientific research based on diffusion models in this altitude range.

Spin-Controlled Conductivity in a Thiophene-Functionalized Iron-Bis(dicarbollide)

NASA Astrophysics Data System (ADS)

Beach, Benjamin; Sauriol, Dustin; Derosa, Pedro

2016-04-01

The relationship between spin state and conductivity is studied for a thiophene-functionalized iron(III)-bis(dicarbollide) with one or two thiophenes at each end of the cage. Iron has a high ground state spin that can be adjusted by external electromagnetic fields to produce different magnetic states. The hypothesis explored here is that changes in the spin state of these Fe-containing molecules can lead to significant changes in molecular conductivity. Two examples of the possible application of such spin-dependent conductivity are its use as a molecular switch, the basic building block in digital logic, or as a memory bit. The molecules were first optimized using the Becke-3 Lee-Yang-Parr functional (B3LYP) with the 6-31G(d) basis set. A relaxed molecular geometry at each spin state was then placed between gold electrodes to conduct spin-polarized electron transport calculations with the density functional theory/non-equilibrium Green's functions formalism. The revised Perdew-Burke-Ernzerhf solids exchange-correlation functional (PBES) with double zeta polarized basis set was used. The result of these calculations show that the conductivity increases with the spin state. The cage structure is shown to exhibit fully delocalized molecular orbitals (MOs) appropriate for high conductivity and thus, in this system, the conductivity depends on the position of the MOs relative to the Fermi level. Minority spins are responsible for the conductivity of the doublet spin state while majority spins dominate for the quartet and sextet spin states as they are found closer to the Fermi level when they are occupied. Energy calculations predict a difference in energy between the more and the less conductive spin states (sextet and doublet respectively) that is 15-20 times greater than the thermal energy, which would imply stability at room temperature; however, the energy difference is sufficiently small that transitions between spin states can be induced.

Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

PubMed Central

Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

2014-01-01

Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

Comparison of Steady State Evaporation Models for Toxic Chemical Spills: Development of a New Evaporation Model

DTIC Science & Technology

1989-11-29

for diffusivity based on theory : DVab- 0.002e6 703/2 eS/s(bPM11 t/ ,cm/s (28) ab ab 1) where DV-b a molecular diffusion coefflcient of chemical a In...24 Ugt W m -K (48)S[(/hg) + (1/h)] m- K- where ha is the coefficient of heat conduction through the ground, and hl is the liquid heat transfer

An overview of the first half-century of molecular electronics.

PubMed

Hush, Noel S

2003-12-01

The seminal ideas from which molecular electronics has developed were the theories of molecular conduction advanced in the late 1940s by Robert S. Mulliken and Albert Szent-Gyorgi. These were, respectively, the concept of donor-acceptor charge transfer complexes and the possibility that proteins might in fact not be insulators The next two decades saw a burgeoning of experimental and theoretical work on electron transfer systems, together with a lone effort by D.D. Eley on conduction in proteins. The call by Feynman in his famous 1959 lecture There's Plenty of Room at the Bottom for chemists, engineers and physicists to combine to build up structures from the molecular level was influential in turning attention to the possibility of engineering single molecules to function as elements in information-processing systems. This was made tangible by the proposal of Aviram and Ratner in 1974 to use a Mulliken-like electron donor-acceptor molecule as a molecular diode, generalizing molecular conduction into molecular electronics. In the early 1970s the remarkably visionary work of Forrest L. Carter of the U.S. Naval Research Laboratories began to appear: designs for molecular wires, switches, complex molecular logic elements, and a host of related ideas were advanced. Shortly after that, conferences on molecular electronics began to be held, and the interdisciplinary programs that Feynman envisaged. There was a surge in both experimental and theoretical work in molecular electronics, and the establishment of many research centres. The past five years or so have seen extraordinarily rapid progress in fabrication and theoretical understanding. The history of how separate lines of research emanating from fundamental insights of about 50 years ago have coalesced into a thriving international research program in what might be called the ultimate nanotechnology is the subject of this review; it concentrates on the lesser-appreciated early developments in the field.

Synthesis, spectroscopic, molecular orbital calculation, cytotoxic, molecular docking of DNA binding and DNA cleavage studies of transition metal complexes with N-benzylidene-N'-salicylidene-1,1-diaminopropane

NASA Astrophysics Data System (ADS)

Al-Mogren, Muneerah M.; Alaghaz, Abdel-Nasser M. A.; Elbohy, Salwa A. H.

2013-10-01

Eight mononuclear chromium(III), manganese(II), iron(III), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of Schiff's base ligand were synthesized and determined by different physical techniques. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the eight metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff base is found to act as tridentate ligand using N2O donor set of atoms leading to an octahedral geometry for the complexes around all the metal ions. Quantum chemical calculations were performed with semi-empirical method to find the optimum geometry of the ligand and its complexes. Additionally in silico, the docking studies and the calculated pharmacokinetic parameters show promising futures for application of the ligand and complexes as high potency agents for DNA binding activity. The interaction of the complexes with calf thymus DNA (CT-DNA) has been investigated by UV absorption method, and the mode of CT-DNA binding to the complexes has been explored. Furthermore, the DNA cleavage activity by the complexes was performed. The Schiff base and their complexes have been screened for their antibacterial activity against bacterial strains [Staphylococcus aureus (RCMB010027), Staphylococcus epidermidis (RCMB010024), Bacillis subtilis (RCMB010063), Proteous vulgaris (RCMB 010085), Klebsiella pneumonia (RCMB 010093) and Shigella flexneri (RCMB 0100542)] and fungi [(Aspergillus fumigates (RCMB 02564), Aspergillus clavatus (RCMB 02593) and Candida albicans (RCMB05035)] by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligand.

Electrochemical immobilization of Fluorescent labelled probe molecules on a FTO surface for affinity detection based on photo-excited current

NASA Astrophysics Data System (ADS)

Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro

2011-10-01

Photo-excited current can be generated at a molecular interface between a photo-excited molecules and a semi-conductive material in appropriate condition. The system has been recognized for promoting photo-energy devices such as an organic dye sensitized solar-cell. The photo-current generated reactions are totally dependent on the interfacial energy reactions, which are in a highly fluctuated interfacial environment. The authors investigated the photo-excited current reaction to develop a smart affinity detection method. However, in order to perform both an affinity reaction and a photo-excited current reaction at a molecular interface, ordered fabrications of the functional (affinity, photo-excitation, etc.) molecules layer on a semi-conductive surface is required. In the present research, we would like to present the fabrication and functional performance of photo-excited current-based affinity assay device and its application for detection of endocrine disrupting chemicals. On the FTO surface, fluorescent pigment labelled affinity peptide was immobilized through the EC tag (electrochemical-tag) method. The modified FTO produced a current when it was irradiated with diode laser light. However, the photo current decreased drastically when estrogen (ES) coexisted in the reaction solution. In this case, immobilized affinity probe molecules formed a complex with ES and estrogen receptor (ER). The result strongly suggests that the photo-excited current transduction between probe molecule-labelled cyanine pigment and the FTO surface was partly inhibited by a complex that formed at the affinity oligo-peptide region in a probe molecule on the FTO electrode. The bound bulky complex may act as an impediment to perform smooth transduction of photo-excited current in the molecular interface. The present system is new type of photo-reaction-based analysis. This system can be used to perform simple high-sensitive homogeneous assays.

Oligoyne Molecular Junctions for Efficient Room Temperature Thermoelectric Power Generation.

PubMed

Sadeghi, Hatef; Sangtarash, Sara; Lambert, Colin J

2015-11-11

Understanding phonon transport at a molecular scale is fundamental to the development of high-performance thermoelectric materials for the conversion of waste heat into electricity. We have studied phonon and electron transport in alkane and oligoyne chains of various lengths and find that, due to the more rigid nature of the latter, the phonon thermal conductances of oligoynes are counterintuitively lower than that of the corresponding alkanes. The thermal conductance of oligoynes decreases monotonically with increasing length, whereas the thermal conductance of alkanes initially increases with length and then decreases. This difference in behavior arises from phonon filtering by the gold electrodes and disappears when higher-Debye-frequency electrodes are used. Consequently a molecule that better transmits higher-frequency phonon modes, combined with a low-Debye-frequency electrode that filters high-energy phonons is a viable strategy for suppressing phonon transmission through the molecular junctions. The low thermal conductance of oligoynes, combined with their higher thermopower and higher electrical conductance lead to a maximum thermoelectric figure of merit of ZT = 1.4, which is several orders of magnitude higher than that of alkanes.

Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

PubMed

Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

2017-04-01

The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

A molecular dynamics study of the effect of thermal boundary conductance on thermal transport of ideal crystal of n-alkanes with different number of carbon atoms

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

Rastgarkafshgarkolaei, Rouzbeh; Zeng, Yi; Khodadadi, J. M., E-mail: khodajm@auburn.edu

2016-05-28

Phase change materials such as n-alkanes that exhibit desirable characteristics such as high latent heat, chemical stability, and negligible supercooling are widely used in thermal energy storage applications. However, n-alkanes have the drawback of low thermal conductivity values. The low thermal conductivity of n-alkanes is linked to formation of randomly oriented nano-domains of molecules in their solid structure that is responsible for excessive phonon scattering at the grain boundaries. Thus, understanding the thermal boundary conductance at the grain boundaries can be crucial for improving the effectiveness of thermal storage systems. The concept of the ideal crystal is proposed in thismore » paper, which describes a simplified model such that all the nano-domains of long-chain n-alkanes are artificially aligned perfectly in one direction. In order to study thermal transport of the ideal crystal of long-chain n-alkanes, four (4) systems (C{sub 20}H{sub 42}, C{sub 24}H{sub 50}, C{sub 26}H{sub 54}, and C{sub 30}H{sub 62}) are investigated by the molecular dynamics simulations. Thermal boundary conductance between the layers of ideal crystals is determined using both non-equilibrium molecular dynamics (NEMD) and equilibrium molecular dynamics (EMD) simulations. Both NEMD and EMD simulations exhibit no significant change in thermal conductance with the molecular length. However, the values obtained from the EMD simulations are less than the values from NEMD simulations with the ratio being nearly three (3) in most cases. This difference is due to the nature of EMD simulations where all the phonons are assumed to be in equilibrium at the interface. Thermal conductivity of the n-alkanes in three structures including liquid, solid, and ideal crystal is investigated utilizing NEMD simulations. Our results exhibit a very slight rise in thermal conductivity values as the number of carbon atoms of the chain increases. The key understanding is that thermal transport can be significantly altered by how the molecules and the nano-domains are oriented in the structure rather than by the length of the n-alkane molecules.« less

Thermoelectric transport properties in graphene connected molecular junctions

NASA Astrophysics Data System (ADS)

Rodriguez, S. T.; Grosu, I.; Crisan, M.; Ţifrea, I.

2018-02-01

We study the electronic contribution to the main thermoelectric properties of a molecular junction consisting of a single quantum dot coupled to graphene external leads. The system electrical conductivity (G), Seebeck coefficient (S), and the thermal conductivity (κ), are numerically calculated based on a Green's function formalism that includes contributions up to the Hartree-Fock level. We consider the system leads to be made either of pure or gapped-graphene. To describe the free electrons in the gapped-graphene electrodes we used two possible scenarios, the massive gap scenario, and the massless gap scenario, respectively. In all cases, the Fano effect is responsible for a strong violation of the Wiedemann-Franz law and we found a substantial increase of the system figure of merit ZT due to a drastic reduction of the system thermal coefficient. In the case of gapped-graphene electrodes, the system figure of merit presents a maximum at an optimal value of the energy gap of the order of Δ / D ∼ 0.002 (massive gap scenario) and Δ / D ∼ 0.0026 (massless gap scenario). Additionally, for all cases, the system figure of merit is temperature dependent.

Sub-μL measurements of the thermal conductivity and heat capacity of liquids.

PubMed

López-Bueno, C; Bugallo, D; Leborán, V; Rivadulla, F

2018-03-07

We present the analysis of the thermal conductivity, κ, and heat capacity, C p , of a wide variety of liquids, covering organic molecular solvents, ionic liquids and water-polymer mixtures. These data were obtained from ≈0.6 μL samples, using an experimental development based on the 3ω method, capable of the simultaneous measurement of κ and C p . In spite of the different type and strength of interactions, expected in a priori so different systems, the ratio of κ to the sound velocity is approximately constant for all of them. This is the consequence of a similar atomic density for all these liquids, notwithstanding their different molecular structures. This was corroborated experimentally by the observation of a C p /V ≈ 1.89 × 10 6 J K -1 m -3 (≈3R/2 per atom), for all liquids studied in this work. Finally, the very small volume of the sample required in this experimental method is an important advantage for the characterization of systems like nanofluids, in which having a large amount of the dispersed phase is sometimes extremely challenging.

Emergence of innovative properties by replacement of nitrogen atom with phosphorus atom in quaternary ammonium ionic liquids: Insights from ab initio calculations and MD simulations

NASA Astrophysics Data System (ADS)

Ghatee, Mohammad Hadi; Bahrami, Maryam

2017-06-01

We investigate to contrasting structure, dynamic and thermophysical properties of quaternary ammonium and phosphonium ionic liquids (ILs) based on triethylalkylammonium [N222n]+ and triethylalkylphosphonium [P222n]+ cations (n = 5, 8, 12) and (bis(trifluoromethylsulfonyl)imide) anion [NTf2]- by quantum chemical calculations (QCC) and molecular dynamics (MD) simulations. QCCs conform to previous studies, showing that phosphonium cation alkyl chain rotational-energy-barrier is lower than ammonium cation. These molecular nature leads to no appreciable differences in their liquid density. However, their simulated transport properties (self-diffusion, conductivity, etc) are appreciably different. In particular, viscosity of phosphoniums are much lower than ammoniums. Ammoniums make nano-scale structural domains larger than phosphoniums. Employed analysis, vector re-orientational dynamics, ion-pair lifetime and nanostructure domain are in favor of faster dynamic for phosphoniums than ammoniums. [NTf2]- anion features a long lived pairing with ammoniums than phosphoniums. Overall, phosphoniums possess higher transference number, higher conductivity, and appreciably lower viscosity favorable for higher electrochemical performances.

Investigation on Fluorescence Quenching Mechanism of Perylene Diimide Dyes by Graphene Oxide.

PubMed

Zhao, Yuzhen; Li, Kexuan; He, Zemin; Zhang, Yongming; Zhao, Yang; Zhang, Haiquan; Miao, Zongcheng

2016-11-30

Perylene diimide derivatives were used as probes to investigate the effect of the molecular structures on the fluorescence quenching mechanism in a perylene diimide/graphene oxide system. The electrons transferred from the excited state of dyes to the conductive band of graphene oxide with different concentrations were determined by fluorescence spectra. The results indicated that the quenching efficiency of perylene diimides by graphene oxide was not only dependent on the difference between the lowest unoccupied molecular orbital level of dyes and the conduction band of the graphene oxide, but also mainly on the difference in the molecular structures.

Pronounced low-frequency vibrational thermal transport in C60 fullerite realized through pressure-dependent molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Giri, Ashutosh; Hopkins, Patrick E.

2017-12-01

Fullerene condensed-matter solids can possess thermal conductivities below their minimum glassy limit while theorized to be stiffer than diamond when crystallized under pressure. These seemingly disparate extremes in thermal and mechanical properties raise questions into the pressure dependence on the thermal conductivity of C60 fullerite crystals, and how the spectral contributions to vibrational thermal conductivity changes under applied pressure. To answer these questions, we investigate the effect of strain on the thermal conductivity of C60 fullerite crystals via pressure-dependent molecular dynamics simulations under the Green-Kubo formalism. We show that the thermal conductivity increases rapidly with compressive strain, which demonstrates a power-law relationship similar to their stress-strain relationship for the C60 crystals. Calculations of the density of states for the crystals under compressive strains reveal that the librational modes characteristic in the unstrained case are diminished due to densification of the molecular crystal. Over a large compression range (0-20 GPa), the Leibfried-Schlömann equation is shown to adequately describe the pressure dependence of thermal conductivity, suggesting that low-frequency intermolecular vibrations dictate heat flow in the C60 crystals. A spectral decomposition of the thermal conductivity supports this hypothesis.

Charge Transport Processes in Molecular Junctions

NASA Astrophysics Data System (ADS)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (<4 nm) conjugated molecular wires, and 3) quantitatively extract interfacial properties characteristic to macroscopic junctions, such as energy level alignment and molecule-contact electronic coupling from experimental I-V curves. Here, we lay ground work for creating a more complete picture of charge transport in macroscopically ordered molecular junctions of controlled architecture, length and charge carrier. The polaronic nature of hopping transport has been predicted in long, conjugated molecular wires. Using quantum-based calculations, we modeled 'p-type' polaron transport through oligophenylenethiophene (OPTI) wires and assigned transport activation energies to specific modes of nuclear motion. We also show control over 'n-type', LUMO-mediated transport in short ( 2 nm) redox-active perylenediimide (PDI) SAMs bound to contacts through isocyano linkers. By changing the contact work function (φ) and temperature, we were able to verify thermally-assisted LUMO transport. Transition voltage spectroscopy and the single level model was employed to fit the experimental I-V curves and extract the electronic coupling (epsilon) and the EF-LUMO offset (epsilonl). It was found that epsilonl does not change with φ (LUMO pinning), while Gamma changes with both φ and temperature. Further, the PDI SAMs could be reversibly chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

Some critical issues in the characterization of nanoscale thermal conductivity by molecular dynamics analysis

NASA Astrophysics Data System (ADS)

Ehsan Khaled, Mohammad; Zhang, Liangchi; Liu, Weidong

2018-07-01

The nanoscale thermal conductivity of a material can be significantly different from its value at the macroscale. Although a number of studies using the equilibrium molecular dynamics (EMD) with Green–Kubo (GK) formula have been conducted for nano-conductivity predictions, there are many problems in the analysis that have made the EMD results unreliable or misleading. This paper aims to clarify such critical issues through a thorough investigation on the effect and determination of the vital physical variables in the EMD-GK analysis, using the prediction of the nanoscale thermal conductivity of Si as an example. The study concluded that to have a reliable prediction, quantum correction, time step, simulation time, correlation time and system size are all crucial.

Current-voltage characteristics of single-molecule diarylethene junctions measured with adjustable gold electrodes in solution.

PubMed

Briechle, Bernd M; Kim, Youngsang; Ehrenreich, Philipp; Erbe, Artur; Sysoiev, Dmytro; Huhn, Thomas; Groth, Ulrich; Scheer, Elke

2012-01-01

We report on an experimental analysis of the charge transport through sulfur-free photochromic molecular junctions. The conductance of individual molecules contacted with gold electrodes and the current-voltage characteristics of these junctions are measured in a mechanically controlled break-junction system at room temperature and in liquid environment. We compare the transport properties of a series of molecules, labeled TSC, MN, and 4Py, with the same switching core but varying side-arms and end-groups designed for providing the mechanical and electrical contact to the gold electrodes. We perform a detailed analysis of the transport properties of TSC in its open and closed states. We find rather broad distributions of conductance values in both states. The analysis, based on the assumption that the current is carried by a single dominating molecular orbital, reveals distinct differences between both states. We discuss the appearance of diode-like behavior for the particular species 4Py that features end-groups, which preferentially couple to the metal electrode by physisorption. We show that the energetic position of the molecular orbital varies as a function of the transmission. Finally, we show for the species MN that the use of two cyano end-groups on each side considerably enhances the coupling strength compared to the typical behavior of a single cyano group.

Quasi-monodimensional polyaniline nanostructures for enhanced molecularly imprinted polymer-based sensing.

PubMed

Berti, Francesca; Todros, Silvia; Lakshmi, Dhana; Whitcombe, Michael J; Chianella, Iva; Ferroni, Matteo; Piletsky, Sergey A; Turner, Anthony P F; Marrazza, Giovanna

2010-10-15

Recent advances in nanotechnology have allowed significant progress in utilising cutting-edge techniques associated with nanomaterials and nano-fabrication to expand the scope and capability of biosensors to a new level of novelty and functionality. The aim of this work was the development and characterisation of conductive polyaniline (PANI) nanostructures for applications in electrochemical biosensing. We explore a simple, inexpensive and fast route to grow PANI nanotubes, arranged in an ordered structure directly on an electrode surface, by electrochemical polymerisation using alumina nanoporous membranes as a 'nano-mould'. The deposited nanostructures have been characterised electrochemically and morphologically prior to grafting with a molecularly imprinted polymer (MIP) receptor in order to create a model sensor for catechol detection. In this way, PANI nanostructures resulted in a conductive nanowire system which allowed direct electrical connection between the electrode and the synthetic receptor (MIP). To our knowledge, this is the first example of integration between molecularly imprinted polymers and PANI nanostructured electrodes. The advantages of using nanostructures in this particular biosensing application have been evaluated by comparing the analytical performance of the sensor with an analogous non-nanostructured MIP-sensor for catechol detection that was previously developed. A significantly lower limit of detection for catechol has been obtained (29 nM, one order of magnitude), thus demonstrating that the nanostructures are capable of improving the analytical performance of the sensor. Copyright © 2010 Elsevier B.V. All rights reserved.

Generative Mechanistic Explanation Building in Undergraduate Molecular and Cellular Biology

ERIC Educational Resources Information Center

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-01-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among…

Cofacial Assembly of Metallomacrocycles. A Molecular Engineering Approach to Electrically Conductive Polymers.

DTIC Science & Technology

1981-05-13

34molecular metals." THE COFACIAL ASSEMBLY STRATEGY Although the above molecular macrocycle, halogen cocrystalli - zation approach to the synthesis of...substitute various oxidizing quinones for halogens in the cocrystallization synthesis have failed because integrated stacK (Figure 2C,D) insulators are

Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Widawsky, Jonathan R.

In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine-terminated and pyridine-terminated molecules (which exhibit hole transport and electron transport, respectively). We also report the thermopower of the highly conducting, covalently bound molecular junctions that we have recently been able to form, and learn that, because of their unique transport properties, the junction power factors, GS2, are extremely high. Finally, we discuss the measurement of molecular current-voltage curves and consider the electronic and physical effects of applying a large bias to the system. We conclude with a summary of the work discussed and an outlook on related scientific studies.

Ion transport and structural dynamics in homologous ammonium and phosphonium-based room temperature ionic liquids

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

Griffin, Philip J., E-mail: pgrif@seas.upenn.edu; Holt, Adam P.; Tsunashima, Katsuhiko

2015-02-28

Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphoniummore » IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range—indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs.« less

FTIR and molecular mechanics studies of H-bonds in aliphatic polyurethane and polyamide-66 model molecules.

PubMed

Wang, Guoqing; Zhang, Chunxia; Guo, Xiaohe; Ren, Zhiyong

2008-02-01

Model aliphatic polyurethane (APU) hard segment based on 1,6-hexamethylene diisocyanate (HDI) and 1,4-butanediol (BDO) were prepared. FTIR and molecular mechanics (MM) simulation were used to conduct the systematic studies on APU and polyamide-66 (PA-66) whose sole difference lies in the alkoxyl oxygen. It was found that the introduction of the alkoxyl not only increases the conformations in APU, makes it a possible H-bond acceptor, but also weakens the H-bond between NH and O=C in APU. There are two conformers stably existed in APU with lowest energy, leading to eight H-bond complexes based on NH as donor and (1) O=C as acceptor, and another two complexes based on (2) alkoxyl O and (3) urethane N as acceptors, whereas there is only one stable conformer in PA-66, leading to one H-bond complex. One predominant H-bond complex has been found in APU with probability of about 95%. The simulated results are consistent with the nuNH and nuC=O band shifting in FTIR.

FTIR and molecular mechanics studies of H-bonds in aliphatic polyurethane and polyamide-66 model molecules

NASA Astrophysics Data System (ADS)

Wang, Guoqing; Zhang, Chunxia; Guo, Xiaohe; Ren, Zhiyong

2008-02-01

Model aliphatic polyurethane (APU) hard segment based on 1,6-hexamethylene diisocyanate (HDI) and 1,4-butanediol (BDO) were prepared. FTIR and molecular mechanics (MM) simulation were used to conduct the systematic studies on APU and polyamide-66 (PA-66) whose sole difference lies in the alkoxyl oxygen. It was found that the introduction of the alkoxyl not only increases the conformations in APU, makes it a possible H-bond acceptor, but also weakens the H-bond between NH and O dbnd C in APU. There are two conformers stably existed in APU with lowest energy, leading to eight H-bond complexes based on NH as donor and (1) O dbnd C as acceptor, and another two complexes based on (2) alkoxyl O and (3) urethane N as acceptors, whereas there is only one stable conformer in PA-66, leading to one H-bond complex. One predominant H-bond complex has been found in APU with probability of about 95%. The simulated results are consistent with the νNH and νC dbnd O band shifting in FTIR.

Forensic molecular genetic diversity analysis of Chinese Hui ethnic group based on a novel STR panel.

PubMed

Fang, Yating; Guo, Yuxin; Xie, Tong; Jin, Xiaoye; Lan, Qiong; Zhou, Yongsong; Zhu, Bofeng

2018-03-26

In present study, the genetic polymorphisms of 22 autosomal short tandem repeat (STR) loci were analyzed in 496 unrelated Chinese Xinjiang Hui individuals. These autosomal STR loci were multiplex amplified and genotyped based on a novel STR panel. There were 246 observed alleles with the allele frequencies ranging from 0.0010 to 0.3609. All polymorphic information content values were higher than 0.7. The combined power of discrimination and the combined probability of exclusion were 0.999999999999999999999999999426766 and 0.999999999860491, respectively. Based on analysis of molecular variance method, genetic differentiation analysis between the Xinjiang Hui and other reported groups were conducted at these 22 loci. The results indicated that there were no significant differences in statistics between Hui group and Northern Han group (including Han groups from Hebei, Henan, Shaanxi provinces), and significant deviations with Southern Han group (including those from Guangdong, Guangxi provinces) at 7 loci, and Uygur group at 10 loci. To sum up, these 22 autosomal STR loci were high genetic polymorphic in Xinjiang Hui group.

Ion transport and structural dynamics in homologous ammonium and phosphonium-based room temperature ionic liquids

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

Griffin, Phillip J.; Holt, Adam P.; Tsunashima, Katsuhiko

2015-02-01

Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphoniummore » IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range-indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs.« less

Preparation of highly thermally stable and conductive Schiff base polymer: Molecular weight monitoring and investigation of antimicrobial properties

NASA Astrophysics Data System (ADS)

Yılmaz Baran, Nuray; Saçak, Mehmet

2018-07-01

A novel thermally stable polyazomethine with phenol group, Poly(4-[[4-(dimethylamino)benzylidene]amino]phenol) P(4-DBAP), was synthesized from 4-[[4-(dimethylamino)benzylidene]amino]phenol) (4-DBAP) in aqueous alkaline medium via oxidative polycondensation with NaOCl, H2O2, and O2 oxidants. The change of the yield and molecular weight distribution of P(4-DBAP) with oxidant type and concentration, monomer concentration, and polymerization temperature and time were analyzed. The structures of the monomer and polymer were confirmed by UV-Vis, FTIR, 1H-NMR, 13C-NMR and TGA techniques. The conductivity value of the polymer which was doped with iodine vapor for 24 h was reached 3.2 × 10-5 S/cm and 1.1 × 10-4 S/cm values by increasing 107 and 108 folds compared to the initial conductivity value at 20 °C and 60 °C, respectively. This conductivity value which was measured at 20 °C is the highest value reported in the literature for polyazomethines having phenol group in such a short time and at low temperature. Moreover, antimicrobial activity test was performed for 4-DBAP and P(4-DBAP) against Sarcina lutea, Enterobacter aerogenes, Escherichia coli, Enterococcus Feacalis, Klebsiella pneumoniae, Bacillus subtilis bacteria, and Candida albicans and Saccharomyces cerevisiae fungi. Although both monomer and polymer showed antibacterial activity, the polymer was more efficient compared to the monomer.

A three-dimensional nitrogen-doped graphene structure: a highly efficient carrier of enzymes for biosensors

NASA Astrophysics Data System (ADS)

Guo, Jingxing; Zhang, Tao; Hu, Chengguo; Fu, Lei

2015-01-01

In recent years, graphene-based enzyme biosensors have received considerable attention due to their excellent performance. Enormous efforts have been made to utilize graphene oxide and its derivatives as carriers of enzymes for biosensing. However, the performance of these sensors is limited by the drawbacks of graphene oxide such as slow electron transfer rate, low catalytic area and poor conductivity. Here, we report a new graphene-based enzyme carrier, i.e. a highly conductive 3D nitrogen-doped graphene structure (3D-NG) grown by chemical vapour deposition, for highly effective enzyme-based biosensors. Owing to the high conductivity, large porosity and tunable nitrogen-doping ratio, this kind of graphene framework shows outstanding electrical properties and a large surface area for enzyme loading and biocatalytic reactions. Using glucose oxidase (GOx) as a model enzyme and chitosan (CS) as an efficient molecular binder of the enzyme, our 3D-NG based biosensors show extremely high sensitivity for the sensing of glucose (226.24 μA mM-1 m-2), which is almost an order of magnitude higher than those reported in most of the previous studies. The stable adsorption and outstanding direct electrochemical behaviour of the enzyme on the nanocomposite indicate the promising application of this 3D enzyme carrier in high-performance electrochemical biosensors or biofuel cells.In recent years, graphene-based enzyme biosensors have received considerable attention due to their excellent performance. Enormous efforts have been made to utilize graphene oxide and its derivatives as carriers of enzymes for biosensing. However, the performance of these sensors is limited by the drawbacks of graphene oxide such as slow electron transfer rate, low catalytic area and poor conductivity. Here, we report a new graphene-based enzyme carrier, i.e. a highly conductive 3D nitrogen-doped graphene structure (3D-NG) grown by chemical vapour deposition, for highly effective enzyme-based biosensors. Owing to the high conductivity, large porosity and tunable nitrogen-doping ratio, this kind of graphene framework shows outstanding electrical properties and a large surface area for enzyme loading and biocatalytic reactions. Using glucose oxidase (GOx) as a model enzyme and chitosan (CS) as an efficient molecular binder of the enzyme, our 3D-NG based biosensors show extremely high sensitivity for the sensing of glucose (226.24 μA mM-1 m-2), which is almost an order of magnitude higher than those reported in most of the previous studies. The stable adsorption and outstanding direct electrochemical behaviour of the enzyme on the nanocomposite indicate the promising application of this 3D enzyme carrier in high-performance electrochemical biosensors or biofuel cells. Electronic supplementary information (ESI) available: Procedures for CVD growth of 3D-NG, XRD and TEM measurements, a comparison with other graphene-based biosensors, a detailed study on the universality of 3D-NG as an enzyme carrier and more CV data on selectivity and stability. See DOI: 10.1039/c4nr05325g

Fabrication of reproducible, integration-compatible hybrid molecular/si electronics.

PubMed

Yu, Xi; Lovrinčić, Robert; Kraynis, Olga; Man, Gabriel; Ely, Tal; Zohar, Arava; Toledano, Tal; Cahen, David; Vilan, Ayelet

2014-12-29

Reproducible molecular junctions can be integrated within standard CMOS technology. Metal-molecule-semiconductor junctions are fabricated by direct Si-C binding of hexadecane or methyl-styrene onto oxide-free H-Si(111) surfaces, with the lateral size of the junctions defined by an etched SiO2 well and with evaporated Pb as the top contact. The current density, J, is highly reproducible with a standard deviation in log(J) of 0.2 over a junction diameter change from 3 to 100 μm. Reproducibility over such a large range indicates that transport is truly across the molecules and does not result from artifacts like edge effects or defects in the molecular monolayer. Device fabrication is tested for two n-Si doping levels. With highly doped Si, transport is dominated by tunneling and reveals sharp conductance onsets at room temperature. Using the temperature dependence of current across medium-doped n-Si, the molecular tunneling barrier can be separated from the Si-Schottky one, which is a 0.47 eV, in agreement with the molecular-modified surface dipole and quite different from the bare Si-H junction. This indicates that Pb evaporation does not cause significant chemical changes to the molecules. The ability to manufacture reliable devices constitutes important progress toward possible future hybrid Si-based molecular electronics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dependence of Ion Dynamics on the Polymer Chain Length in Poly(ethylene oxide)-Based Polymer Electrolytes.

PubMed

Chattoraj, Joyjit; Knappe, Marisa; Heuer, Andreas

2015-06-04

It is known from experiments that in the polymer electrolyte system, which contains poly(ethylene oxide) chains (PEO), lithium-cations (Li(+)), and bis(trifluoromethanesulfonyl)imide-anions (TFSI(-)), the cation and the anion diffusion and the ionic conductivity exhibit a similar chain-length dependence: with increasing chain length, they start dropping steadily, and later, they saturate to constant values. These results are surprising because Li-cations are strongly correlated with the polymer chains, whereas TFSI-anions do not have such bonding. To understand this phenomenon, we perform molecular dynamics simulations of this system for four different polymer chain lengths. The diffusion results obtained from our simulations display excellent agreement with the experimental data. The cation transport model based on the Rouse dynamics can successfully quantify the Li-diffusion results, which correlates Li diffusion with the polymer center-of-mass motion and the polymer segmental motion. The ionic conductivity as a function of the chain length is then estimated based on the chain-length-dependent ion diffusion, which shows a temperature-dependent deviation for short chain lengths. We argue that in the first regime, counterion correlations modify the conductivity, whereas for the long chains, the system behaves as a strong electrolyte.

Patterns of diagnostic marker assessment in adult diffuse glioma: a survey of the European Confederation of Neuropathological Societies (Euro-CNS)

PubMed Central

Woehrer, Adelheid; Kristensen, Bjarne W.; Vital, Anne; Hainfellner, Johannes A.

2017-01-01

The 2016 update of the WHO classification has introduced an integrated diagnostic approach that incorporates both tumor morphology and molecular information. This conceptual change has far-reaching implications, especially for neuropathologists who are in the forefront of translating molecular markers to routine diagnostic use. Adult diffuse glioma is a prototypic example for a group of tumors that underwent substantial regrouping, and it represents a major workload for surgical neuropathologists. Hence, we conducted a survey among members of the European Confederation of Neuropathological Societies (Euro-CNS) in order to assess 1) the extent to which molecular markers have already been incorporated in glioma diagnoses, 2) which molecular techniques are in daily use, and 3) to set a baseline for future surveys in this field. Based on 130 responses from participants across 40 nations neuropathologists uniformly rate molecular marker testing as highly relevant and already incorporate molecular information in their diagnostic assessments. At the same time however, the survey documents substantial differences in access to crucial biomarkers and molecular techniques across geographic regions and within individual countries. Concerns are raised concerning the validity of test assays with MGMT, 1p19q, and ATRX; being perceived as most problematic. Neuropathologists advocate the need for international harmonization of standards and consensus guidelines, and the majority is willing to actively engage in interlaboratory trials aiming at quality control (Figure 1). PMID:27966427

Molecular Dynamics Simulations of the Thermal Conductivity of Single-Wall Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Osman, M.; Srivastava, Deepak; Govindan,T. R. (Technical Monitor)

2000-01-01

Carbon nanotubes (CNT) have very attractive electronic, mechanical. and thermal properties. Recently, measurements of thermal conductivity in single wall CNT mats showed estimated thermal conductivity magnitudes ranging from 17.5 to 58 W/cm-K at room temperature. which are better than bulk graphite. The cylinderical symmetry of CNT leads to large thermal conductivity along the tube axis, additionally, unlike graphite. CNTs can be made into ropes that can be used as heat conducting pipes for nanoscale applications. The thermal conductivity of several single wall carbon nanotubes has been calculated over temperature range from l00 K to 600 K using non-equilibrium molecular dynamics using Tersoff-Brenner potential for C-C interactions. Thermal conductivity of single wall CNTs shows a peaking behavior as a function of temperature. Dependence of the peak position on the chirality and radius of the tube will be discussed and explained in this presentation.

Gliomatosis cerebri: Prognosis based on current molecular markers.

PubMed

Maharaj, Monish M; Phan, Kevin; Xu, Joshua; Fairhall, Jacob; Reddy, Rajesh; Rao, Prashanth J V

2017-09-01

This study aims to review the literature and identify key molecular markers affecting the prognosis of Gliomatosis cerebri (2) to evaluate the level of evidence and identify outstanding markers requiring further study. A literature search was conducted across 5 major databases using the key terms: "Molecular markers" AND "Gliomatosis cerebri" OR "diffuse astrocytoma." Critical appraisal and data presentation was performed inline with the PRISMA guidelines. Following search strategy implementation, 11 studies were included in the final review process. Our data demonstrates significant prognostic value associated with IDH1 132H mutation and variable evidence surrounding the role of INA expression, MGMT promoter methylation and other factors. However, there are significant limitations in the level of evidence obtained. As the genetic basis for the pathogenesis of Gliomatosis cerebri continues to widen, there is little data on markers aside from IDH1 mutation available. IDH1 132H mutation has been demonstrated to have significant effect on survival, particularly in patients with Gliomatosis cerebri type 2. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spin resolved electronic transport through N@C20 fullerene molecule between Au electrodes: A first principles study

NASA Astrophysics Data System (ADS)

Caliskan, Serkan

2018-05-01

Using first principles study, through Density Functional Theory combined with Non Equilibrium Green's Function Formalism, electronic properties of endohedral N@C20 fullerene molecule joining Au electrodes (Au-N@C20) was addressed in the presence of spin property. The electronic transport behavior across the Au-N@C20 molecular junction was investigated by spin resolved transmission, density of states, molecular orbitals, differential conductance and current-voltage (I-V) characteristics. Spin asymmetric variation was clearly observed in the results due to single N atom encapsulated in the C20 fullerene cage, where the N atom played an essential role in the electronic behavior of Au-N@C20. This N@C20 based molecular bridge, exhibiting a spin dependent I-V variation, revealed a metallic behavior within the bias range from -1 V to 1 V. The induced magnetic moment, spin polarization and other relevant quantities associated with the spin resolved transport were elucidated.

Friction and morphology of magnetic tapes in sliding contact with nickel-zinc ferrite

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Buckley, D. H.; Bhushan, B.

1984-01-01

Friction and morphological studies were conducted with magnetic tapes containing a Ni-Zn ferrite hemispherical pin in laboratory air at a relative humidity of 40 percent and at 23 C. The results indicate that the binder plays a significant role in the friction properties, morphology, and microstructure of the tape. Comparisons were made with four binders: nitrocellulose; poly (vinyledene) chloride; cellulose acetate; and hydroxyl-terminated, low molecular weight polyester added to the base polymer, polyester-polyurethane. The coefficient of friction was lowest for the tape with the nitrocellulose binder and increased in the order hydroxylterminated, low molecular weight polyester resin; poly (vinyledene) chloride; and cellulose acetate. The degree of enclosure of the oxide particles by the binder was highest for hydroxyl-terminated, low molecular weight polyester and decreased in the order cellulose acetate, poly (vinyledene) chloride, and nitrocellulose. The nature of deformation of the tape was a factor in controlling friction. The coefficient of friction under elastic contact conditions was considerably lower than under conditions that produced plastic contacts.

Personalizing therapies for gastric cancer: Molecular mechanisms and novel targeted therapies

PubMed Central

Luis, Michael; Tavares, Ana; Carvalho, Liliana S; Lara-Santos, Lúcio; Araújo, António; de Mello, Ramon Andrade

2013-01-01

Globally, gastric cancer is the 4th most frequently diagnosed cancer and the 2nd leading cause of death from cancer, with an estimated 990000 new cases and 738000 deaths registered in 2008. In the advanced setting, standard chemotherapies protocols acquired an important role since last decades in prolong survival. Moreover, recent advances in molecular therapies provided a new interesting weapon to treat advanced gastric cancer through anti-human epidermal growth factor receptor 2 (HER2) therapies. Trastuzumab, an anti-HER2 monoclonal antibody, was the first target drug in the metastatic setting that showed benefit in overall survival when in association with platinum-5-fluorouracil based chemotherapy. Further, HER2 overexpression analysis acquired a main role in predict response for trastuzumab in this field. Thus, we conducted a review that will discuss the main points concerning trastuzumab and HER2 in gastric cancer, providing a comprehensive overview of molecular mechanisms and novel trials involved. PMID:24151357

Meta-review of protein network regulating obesity between validated obesity candidate genes in the white adipose tissue of high-fat diet-induced obese C57BL/6J mice.

PubMed

Kim, Eunjung; Kim, Eun Jung; Seo, Seung-Won; Hur, Cheol-Goo; McGregor, Robin A; Choi, Myung-Sook

2014-01-01

Worldwide obesity and related comorbidities are increasing, but identifying new therapeutic targets remains a challenge. A plethora of microarray studies in diet-induced obesity models has provided large datasets of obesity associated genes. In this review, we describe an approach to examine the underlying molecular network regulating obesity, and we discuss interactions between obesity candidate genes. We conducted network analysis on functional protein-protein interactions associated with 25 obesity candidate genes identified in a literature-driven approach based on published microarray studies of diet-induced obesity. The obesity candidate genes were closely associated with lipid metabolism and inflammation. Peroxisome proliferator activated receptor gamma (Pparg) appeared to be a core obesity gene, and obesity candidate genes were highly interconnected, suggesting a coordinately regulated molecular network in adipose tissue. In conclusion, the current network analysis approach may help elucidate the underlying molecular network regulating obesity and identify anti-obesity targets for therapeutic intervention.

Optimal thermoelectric figure of merit of a molecular junction

NASA Astrophysics Data System (ADS)

Murphy, Padraig; Mukerjee, Subroto; Moore, Joel

2008-10-01

We show that a molecular junction can give large values of the thermoelectric figure of merit ZT , and so it could be used as a solid-state energy-conversion device that operates close to the Carnot efficiency. The mechanism is similar to the Mahan-Sofo model for bulk thermoelectrics—the Lorenz number goes to zero violating the Wiedemann-Franz law while the thermopower remains nonzero. The molecular state through which charge is transported must be weakly coupled to the leads, and the energy level of the state must be of order kBT away from the Fermi energy of the leads. In practice, the figure of merit is limited by the phonon thermal conductance; we show that the largest possible Z Ttilde ( Gtilde thph)-1/2 , where Gtilde thph is the phonon thermal conductance divided by the thermal conductance quantum.

Can we better predict the biologic behavior of incidental IPMN? A comprehensive analysis of molecular diagnostics and biomarkers in intraductal papillary mucinous neoplasms of the pancreas.

PubMed

Tulla, Kiara A; Maker, Ajay V

2018-03-01

Predicting the biologic behavior of intraductal papillary mucinous neoplasm (IPMN) remains challenging. Current guidelines utilize patient symptoms and imaging characteristics to determine appropriate surgical candidates. However, the majority of resected cysts remain low-risk lesions, many of which may be feasible to have under surveillance. We herein characterize the most promising and up-to-date molecular diagnostics in order to identify optimal components of a molecular signature to distinguish levels of IPMN dysplasia. A comprehensive systematic review of pertinent literature, including our own experience, was conducted based on the PRISMA guidelines. Molecular diagnostics in IPMN patient tissue, duodenal secretions, cyst fluid, saliva, and serum were evaluated and organized into the following categories: oncogenes, tumor suppressor genes, glycoproteins, markers of the immune response, proteomics, DNA/RNA mutations, and next-generation sequencing/microRNA. Specific targets in each of these categories, and in aggregate, were identified by their ability to both characterize a cyst as an IPMN and determine the level of cyst dysplasia. Combining molecular signatures with clinical and imaging features in this era of next-generation sequencing and advanced computational analysis will enable enhanced sensitivity and specificity of current models to predict the biologic behavior of IPMN.

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations.

PubMed

Druliner, Brooke R; Wang, Panwen; Bae, Taejeong; Baheti, Saurabh; Slettedahl, Seth; Mahoney, Douglas; Vasmatzis, Nikolaos; Xu, Hang; Kim, Minsoo; Bockol, Matthew; O'Brien, Daniel; Grill, Diane; Warner, Nathaniel; Munoz-Gomez, Miguel; Kossick, Kimberlee; Johnson, Ruth; Mouchli, Mohamad; Felmlee-Devine, Donna; Washechek-Aletto, Jill; Smyrk, Thomas; Oberg, Ann; Wang, Junwen; Chia, Nicholas; Abyzov, Alexej; Ahlquist, David; Boardman, Lisa A

2018-02-16

The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients. CAPs had significantly more mutations, altered expression and hypermethylation compared to CFPs. APC was significantly mutated in both polyp groups, but mutations in TP53, FBXW7, PIK3CA, KIAA1804 and SMAD2 were exclusive to CAPs. We found significant expression changes between CAPs and CFPs in GREM1, IGF2, CTGF, and PLAU, and both expression and methylation alterations in FES and HES1. Integrative analyses revealed 124 genes with alterations in at least two platforms, and ERBB3 and E2F8 showed aberrations specific to CAPs across all platforms. These findings provide a resource of molecular distinctions between polyps with and without cancer, which have the potential to enhance the diagnosis, risk assessment and management of polyps.

Ni-DNA-based nanowires and nanodevices

NASA Astrophysics Data System (ADS)

Chang, Chia-Ching; Yuan, Chiun-Jye; Jian, Wen-Bin; Chen, Yu-Chang; di Ventra, Massimiliano

DNA is a highly versatile biopolymer that has been a recent focus in the field of nanomachines and nanoelectronics. DNA exhibits high stability, adjustable conductance, self-organizing capability, programmability and vast information storage. It is an ideal material in the applications of nanodevices, nanoelectronics, and molecular computing. Low conductance of native DNA renders applications difficult. However, doping with nickel ions tunes the DNA into a conducting polymer. Further studies showed that nickel ions containing DNA (Ni-DNA) nanowires exhibit characteristics of memristor and memcapacitor making them a potential mass information storage system. In summary, Ni-DNA has promising applications in a variety of fields, including nanoelectronics, biosensors and memcomputing. This study was supported in part by the Ministry of Science and Technology (MOST), Taiwan (ROC) MOST 103-2112-M-009-011 -MY3, and MOST 105-2627-M-009-006.

Electronically Transparent Au-N Bonds for Molecular Junctions.

PubMed

Zang, Yaping; Pinkard, Andrew; Liu, Zhen-Fei; Neaton, Jeffrey B; Steigerwald, Michael L; Roy, Xavier; Venkataraman, Latha

2017-10-25

We report a series of single-molecule transport measurements carried out in an ionic environment with oligophenylenediamine wires. These molecules exhibit three discrete conducting states accessed by electrochemically modifying the contacts. Transport in these junctions is defined by the oligophenylene backbone, but the conductance is increased by factors of ∼20 and ∼400 when compared to traditional dative junctions. We propose that the higher-conducting states arise from in situ electrochemical conversion of the dative Au←N bond into a new type of Au-N contact. Density functional theory-based transport calculations establish that the new contacts dramatically increase the electronic coupling of the oligophenylene backbone to the Au electrodes, consistent with experimental transport data. The resulting contact resistance is the lowest reported to date; more generally, our work demonstrates a facile method for creating electronically transparent metal-organic interfaces.

Ab initio studies of electronic transport through amine-Au-linked junctions of photoactive molecules

NASA Astrophysics Data System (ADS)

Strubbe, David A.; Quek, Su Ying; Venkataraman, Latha; Choi, Hyoung Joon; Neaton, J. B.; Louie, Steven G.

2008-03-01

Molecules linked to Au electrodes via amine groups have been shown to result in reproducible molecular conductance values for a wide range of single-molecule junctions [1,2]. Recent calculations have shown that these linkages result in a junction conductance relatively insensitive to atomic structure [3]. Here we exploit these well-defined linkages to study the effect of isomerization on conductance for the photoactive molecule 4,4'-diaminoazobenzene. We use a first-principles scattering-state method based on density-functional theory to explore structure and transport properties of the cis and trans isomers of the molecule, and we discuss implications for experiment. [1] L Venkataraman et al., Nature 442, 904-907 (2006); [2] L Venkataraman et al., Nano Lett. 6, 458-462 (2006); [3] SY Quek et al., Nano Lett. 7, 3477-3482 (2007).

How Dynamic Visualization Technology Can Support Molecular Reasoning

ERIC Educational Resources Information Center

Levy, Dalit

2013-01-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

Use of Ionic Liquids in Rod-Coil Block Copolyimides for Improved Lithium Ion Conduction

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B.; Tigelaar, Dean M.; Chapin, Kara; Bennett, William R.

2007-01-01

Solvent-free, solid polymer electrolytes (SPE) have the potential to improve safety, increase design flexibility and enhance performance of rechargeable lithium batteries. Solution based electrolytes are flammable and typically incompatible with lithium metal anodes, limiting energy density. We have previously demonstrated use of polyimide rod coil block copolymers doped with lithium salts as electrolytes for lithium polymer batteries. The polyimide rod blocks provide dimensional stability while the polyethylene oxide (PEO) coil portions conduct ions. Phase separation of the rods and coils in these highly branched polymers provide channels with an order of magnitude improvement in lithium conduction over polyethylene oxide itself at room temperature. In addition, the polymers have been demonstrated in coin cells to be compatible with lithium metal. For practical use at room temperature and below, however, at least an order of magnitude improvement in ion conduction is still required. The addition of nonvolatile, room temperature ionic liquids has been shown to improve the ionic conductivity of high molecular weight PEO. Herein we describe use of these molten salts to improve ionic conductivity in the rod-coil block copolymers.

SIMULATION OF ION CONDUCTION IN α-HEMOLYSIN NANOPORES WITH COVALENTLY ATTACHED β-CYCLODEXTRIN BASED ON BOLTZMANN TRANSPORT MONTE CARLO MODEL

PubMed Central

Toghraee, Reza; Lee, Kyu-Il; Papke, David; Chiu, See-Wing; Jakobsson, Eric; Ravaioli, Umberto

2009-01-01

Ion channels, as natures’ solution to regulating biological environments, are particularly interesting to device engineers seeking to understand how natural molecular systems realize device-like functions, such as stochastic sensing of organic analytes. What’s more, attaching molecular adaptors in desired orientations inside genetically engineered ion channels, enhances the system functionality as a biosensor. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator, offers a powerful and general approach to study ion channel permeation. BioMOCA is based on the Boltzmann Transport Monte Carlo (BTMC) and Particle-Particle-Particle-Mesh (P3M) methodologies developed at the University of Illinois at Urbana-Champaign. In this paper, we have employed BioMOCA to study two engineered mutations of α-HL, namely (M113F)6(M113C-D8RL2)1-β-CD and (M113N)6(T117C-D8RL3)1-β-CD. The channel conductance calculated by BioMOCA is slightly higher than experimental values. Permanent charge distributions and the geometrical shape of the channels gives rise to selectivity towards anions and also an asymmetry in I-V curves, promoting a rectification largely for cations. PMID:20938493

Charge transport and ac response under light illumination in gate-modulated DNA molecular junctions.

PubMed

Zhang, Yan; Zhu, Wen-Huan; Ding, Guo-Hui; Dong, Bing; Wang, Xue-Feng

2015-05-22

Using a two-strand tight-binding model and within nonequilibrium Green's function approach, we study charge transport through DNA sequences (GC)NGC and (GC)1(TA)NTA (GC)3 sandwiched between two Pt electrodes. We show that at low temperature DNA sequence (GC)NGC exhibits coherent charge carrier transport at very small bias, since the highest occupied molecular orbital in the GC base pair can be aligned with the Fermi energy of the metallic electrodes by a gate voltage. A weak distance dependent conductance is found in DNA sequence (GC)1(TA)NTA (GC)3 with large NTA. Different from the mechanism of thermally induced hopping of charges proposed by the previous experiments, we find that this phenomenon is dominated by quantum tunnelling through discrete quantum well states in the TA base pairs. In addition, ac response of this DNA junction under light illumination is also investigated. The suppression of ac conductances of the left and right lead of DNA sequences at some particular frequencies is attributed to the excitation of electrons in the DNA to the lead Fermi surface by ac potential, or the excitation of electrons in deep DNA energy levels to partially occupied energy levels in the transport window. Therefore, measuring ac response of DNA junctions can reveal a wealth of information about the intrinsic dynamics of DNA molecules.

Empirical investigation of the ethical reasoning of physicians and molecular biologists - the importance of the four principles of biomedical ethics.

PubMed

Ebbesen, Mette; Pedersen, Birthe D

2007-10-25

This study presents an empirical investigation of the ethical reasoning and ethical issues at stake in the daily work of physicians and molecular biologists in Denmark. The aim of this study was to test empirically whether there is a difference in ethical considerations and principles between Danish physicians and Danish molecular biologists, and whether the bioethical principles of the American bioethicists Tom L. Beauchamp and James F. Childress are applicable to these groups. This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. In this sample, the authors found that oncology physicians and molecular biologists employed in a private biopharmaceutical company have the specific principle of beneficence in mind in their daily work. Both groups are motivated to help sick patients. According to the study, molecular biologists explicitly consider nonmaleficence in relation to the environment, the researchers' own health, and animal models; and only implicitly in relation to patients or human subjects. In contrast, considerations of nonmaleficence by oncology physicians relate to patients or human subjects. Physicians and molecular biologists both consider the principle of respect for autonomy as a negative obligation in the sense that informed consent of patients should be respected. However, in contrast to molecular biologists, physicians experience the principle of respect for autonomy as a positive obligation as the physician, in dialogue with the patient, offers a medical prognosis based upon the patients wishes and ideas, mutual understanding, and respect. Finally, this study discloses utilitarian characteristics in the overall conception of justice as conceived by oncology physicians and molecular biologists from the private biopharmaceutical company. Molecular biologists employed at a public university are, in this study, concerned with allocation, however, they do not propose a specific theory of justice. This study demonstrates that each of the four bioethical principles of the American bioethicists Tom L. Beauchamp & James F. Childress - respect for autonomy, beneficence, nonmaleficence and justice - are reflected in the daily work of physicians and molecular biologists in Denmark. Consequently, these principles are applicable in the Danish biomedical setting.

Empirical investigation of the ethical reasoning of physicians and molecular biologists – the importance of the four principles of biomedical ethics

PubMed Central

Ebbesen, Mette; Pedersen, Birthe D

2007-01-01

Background This study presents an empirical investigation of the ethical reasoning and ethical issues at stake in the daily work of physicians and molecular biologists in Denmark. The aim of this study was to test empirically whether there is a difference in ethical considerations and principles between Danish physicians and Danish molecular biologists, and whether the bioethical principles of the American bioethicists Tom L. Beauchamp and James F. Childress are applicable to these groups. Method This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. Results In this sample, the authors found that oncology physicians and molecular biologists employed in a private biopharmaceutical company have the specific principle of beneficence in mind in their daily work. Both groups are motivated to help sick patients. According to the study, molecular biologists explicitly consider nonmaleficence in relation to the environment, the researchers' own health, and animal models; and only implicitly in relation to patients or human subjects. In contrast, considerations of nonmaleficence by oncology physicians relate to patients or human subjects. Physicians and molecular biologists both consider the principle of respect for autonomy as a negative obligation in the sense that informed consent of patients should be respected. However, in contrast to molecular biologists, physicians experience the principle of respect for autonomy as a positive obligation as the physician, in dialogue with the patient, offers a medical prognosis based upon the patients wishes and ideas, mutual understanding, and respect. Finally, this study discloses utilitarian characteristics in the overall conception of justice as conceived by oncology physicians and molecular biologists from the private biopharmaceutical company. Molecular biologists employed at a public university are, in this study, concerned with allocation, however, they do not propose a specific theory of justice. Conclusion This study demonstrates that each of the four bioethical principles of the American bioethicists Tom L. Beauchamp & James F. Childress – respect for autonomy, beneficence, nonmaleficence and justice – are reflected in the daily work of physicians and molecular biologists in Denmark. Consequently, these principles are applicable in the Danish biomedical setting. PMID:17961251

Assessment of Knowledge of Participants on Basic Molecular Biology Techniques after 5-Day Intensive Molecular Biology Training Workshops in Nigeria

ERIC Educational Resources Information Center

Yisau, J. I.; Adagbada, A. O.; Bamidele, T.; Fowora, M.; Brai, B. I. C.; Adebesin, O.; Bamidele, M.; Fesobi, T.; Nwaokorie, F. O.; Ajayi, A.; Smith, S. I.

2017-01-01

The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of…

Numerical Investigation of the Microscopic Heat Current Inside a Nanofluid System Based on Molecular Dynamics Simulation and Wavelet Analysis.

PubMed

Jia, Tao; Gao, Di

2018-04-03

Molecular dynamics simulation is employed to investigate the microscopic heat current inside an argon-copper nanofluid. Wavelet analysis of the microscopic heat current inside the nanofluid system is conducted. The signal of the microscopic heat current is decomposed into two parts: one is the approximation part; the other is the detail part. The approximation part is associated with the low-frequency part of the signal, and the detail part is associated with the high-frequency part of the signal. Both the probability distributions of the high-frequency and the low-frequency parts of the signals demonstrate Gaussian-like characteristics. The curves fit to data of the probability distribution of the microscopic heat current are established, and the parameters including the mean value and the standard deviation in the mathematical formulas of the curves show dramatic changes for the cases before and after adding copper nanoparticles into the argon base fluid.

Molecular performance of commercial MTG variety oil palm based on RAPD markers

NASA Astrophysics Data System (ADS)

Putri, L. A. P.; Setyo, I. E.; Basyuni, M.; Bayu, E. S.; Setiado, H.; Reynaldi, N. F.; Laia, H.; Puteri, S. A. K.; Arifiyanto, D.; Syahputra, I.

2018-02-01

The oil palm, an economically important tree in Indonesia, has been one of the world’s major sources of edible oil and a significant precursor of biodiesel fuel. This research is conducted by taking individual tree sample of commercial MTG variety germplasm oil palm one years old. The purpose of this research is to analyse molecular performance of some oil palm MTG variety based on RAPD markers. In this experiment, the DNA profile diversity was assessed using markers of oil palm’s random RAPD markers (OPD-20, SB-19, OPM-01 and OPO-11). A total of 15 trees commercial MTG oil palm variety were used for analysis. The results of the experiment indicated out of 4 RAPD markers (OPD-20, SB-19, OPM-01 and OPO-11) showed polymorphic of PCR product. These preliminary results demonstrated RAPD marker can be used to evaluate genetic relatedness among trees of commercial MTG variety oil palm and detecting either genetic variants or mislabelled.

Diagnostic of students' misconceptions using the Biological Concepts Instrument (BCI): A method for conducting an educational needs assessment

PubMed Central

Champagne Queloz, Annie; Klymkowsky, Michael W.; Stern, Elsbeth; Hafen, Ernst; Köhler, Katja

2017-01-01

Concept inventories, constructed based on an analysis of students’ thinking and their explanations of scientific situations, serve as diagnostics for identifying misconceptions and logical inconsistencies and provide data that can help direct curricular reforms. In the current project, we distributed the Biological Concepts Instrument (BCI) to 17-18-year-old students attending the highest track of the Swiss school system (Gymnasium). Students’ performances on many questions related to evolution, genetics, molecular properties and functions were diverse. Important common misunderstandings were identified in the areas of evolutionary processes, molecular properties and an appreciation of stochastic processes in biological systems. Our observations provide further evidence that the BCI is efficient in identifying specific areas where targeted instruction is required. Based on these observations we have initiated changes at several levels to reconsider how biological systems are presented to university biology studies with the goal of improving student’s foundational understanding. PMID:28493960

Chemical, electrochemical and photochemical molecular water oxidation catalysts.

PubMed

Bofill, Roger; García-Antón, Jordi; Escriche, Lluís; Sala, Xavier

2015-11-01

Hydrogen release from the splitting of water by simply using sunlight as the only energy source is an old human dream that could finally become a reality. This process involves both the reduction and oxidation of water into hydrogen and oxygen, respectively. While the first process has been fairly overcome, the conversion of water into oxygen has been traditionally the bottleneck process hampering the development of a sustainable hydrogen production based on water splitting. Fortunately, a revolution in this field has occurred during the past decade, since many research groups have been conducting an intense research in this area. Thus, while molecular, well-characterized catalysts able to oxidize water were scarce just five years ago, now a wide range of transition metal based compounds has been reported as active catalysts for this transformation. This review reports the most prominent key advances in the field, covering either examples where the catalysis is triggered chemically, electrochemically or photochemically. Copyright © 2014 Elsevier B.V. All rights reserved.

Negative differential resistance observation in complex convoluted fullerene junctions

NASA Astrophysics Data System (ADS)

Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

2018-04-01

In this work, we simulated the smallest fullerene molecule, C20 in a two-probe device model with gold electrodes. The gold electrodes comprised of (011) miller planes were carved to construct the novel geometry based four unique shapes, which were strung to fullerene molecules through mechanically controlled break junction techniques. The organized devices were later scrutinized using non-equilibrium Green's function based on the density functional theory to calculate their molecular orbitals, energy levels, charge transfers, and electrical parameters. After intense scrutiny, we concluded that five-edged and six-edged devices have the lowest and highest current-conductance values, which result from their electrode-dominating and electrode-subsidiary effects, respectively. However, an interesting observation was that the three-edged and four-edged electrodes functioned as semi-metallic in nature, allowing the C20 molecule to demonstrate its performance with the complementary effect of these electrodes in the electron conduction process of a two-probe device.

Learning through ferroelectric domain dynamics in solid-state synapses

NASA Astrophysics Data System (ADS)

Boyn, Sören; Grollier, Julie; Lecerf, Gwendal; Xu, Bin; Locatelli, Nicolas; Fusil, Stéphane; Girod, Stéphanie; Carrétéro, Cécile; Garcia, Karin; Xavier, Stéphane; Tomas, Jean; Bellaiche, Laurent; Bibes, Manuel; Barthélémy, Agnès; Saïghi, Sylvain; Garcia, Vincent

2017-04-01

In the brain, learning is achieved through the ability of synapses to reconfigure the strength by which they connect neurons (synaptic plasticity). In promising solid-state synapses called memristors, conductance can be finely tuned by voltage pulses and set to evolve according to a biological learning rule called spike-timing-dependent plasticity (STDP). Future neuromorphic architectures will comprise billions of such nanosynapses, which require a clear understanding of the physical mechanisms responsible for plasticity. Here we report on synapses based on ferroelectric tunnel junctions and show that STDP can be harnessed from inhomogeneous polarization switching. Through combined scanning probe imaging, electrical transport and atomic-scale molecular dynamics, we demonstrate that conductance variations can be modelled by the nucleation-dominated reversal of domains. Based on this physical model, our simulations show that arrays of ferroelectric nanosynapses can autonomously learn to recognize patterns in a predictable way, opening the path towards unsupervised learning in spiking neural networks.

Room temperature stable single molecule rectifiers with graphite electrodes

NASA Astrophysics Data System (ADS)

Rungger, Ivan; Kaliginedi, V.; Droghetti, A.; Ozawa, H.; Kuzume, A.; Haga, M.; Broekmann, P.; Rudnev, A. V.

In this combined theoretical and experimental study we present new molecular electronics device characteristics of unprecedented stability at room temperature by using electrodes based on highly oriented pyrolytic graphite with covalently attached molecules. To this aim, we explore the effect of the anchoring group chemistry on the charge transport properties of graphite/molecule contacts by means of the scanning tunneling microscopy break-junction technique and ab initio simulations. The theoretical approach to evaluate the conductance is based on density functional theory calculations combined with the non-equilibrium Greens function technique, as implemented in the Smeagol electron transport code. We also demonstrate a strong bias dependence and rectification of the single molecule conductance induced by the anchoring chemistry in combination with the very low density of states of graphite around the Fermi energy. We show that the direction of tunneling current rectification can be tuned by anchoring group chemistry.

The Workshop on Conductive Polymers: Final Report

DOE R&D Accomplishments Database

1985-10-01

Reports are made by groups on: polyacetylene, polyphenylene, polyaniline, and related systems; molecular, crystallographic, and defect structures in conducting polymers; heterocyclic polymers; synthesis of new and improved conducting polymers; future applications possibilities for conducting polymers; and challenges for improved understanding of properties. (DLC)

Observation of molecular level behavior in molecular electronic junction device

NASA Astrophysics Data System (ADS)

Maitani, Masato

In this dissertation, I utilize AFM based scanning probe measurement and surface enhanced Raman scattering based vibrational spectroscopic analysis to directly characterize topographic, electronic, and chemical properties of molecules confined in the local area of M3 junction to elucidate the molecular level behavior of molecular junction electronic devices. In the introduction, the characterization of molecular electronic devices with different types of metal-molecule-metal (M3) structures based upon self-assembled monolayers (SAMs) is reviewed. A background of the characterization methods I use in this dissertation, conducting probe atomic force microscopy (cp-AFM) and surface enhanced Raman spectroscopy (SERS), is provided in chapter 1. Several attempts are performed to create the ideal top metal contacts on SAMs by metal vapor phase deposition in order to prevent the metal penetration inducing critical defects of the molecular electronic devices. The scanning probe microscopy (SPM), such as cp-AFM, contact mode (c-) AFM and non-contact mode (nc-) AFM, in ultra high vacuum conditions are utilized to study the process of the metal-SAM interface construction in terms of the correlation between the morphological and electrical properties including the metal nucleation and filament generation as a function of the functionalization of long-chain alkane thiolate SAMs on Au. In chapter 2, the nascent condensation process of vapor phase Al deposition on inert and reactive SAMs are studied by SPM. The results of top deposition, penetration, and filament generation of deposited Al are discussed and compared to the results previously observed by spectroscopic measurements. Cp-AFM was shown to provide new insights into Al filament formation which has not been observed by conventional spectroscopic analysis. Additionally, the electronic characteristics of individual Al filaments are measured. Chapter 3 reveals SPM characterization of Au deposition onto --COOH terminated SAMs utilized with strong surface dipole-dipole intermolecular interaction based on hydrogen bonding and ionic bonding potentially preventing the metal penetration. The observed results are discussed with kinetic paths of metal atoms on each SAM including temporal vacancies controlled by the intermolecular interactions in SAM upon the comparison with the spectroscopic results previously reported. The results in chapter 2 and 3 strongly suggests that AFM based characterization technique is powerful tool especially for detecting molecular-size local phenomena in vapor phase metal deposition process, especially, the electric short-circuit filaments growing through SAMs, which may induce critical misinterpretation of M3 junction device properties. In Chapter 4, an altered metal deposition process on inert SAM with using a buffer layer is performed to diminish the kinetic energy of impinging metal atoms. SPM characterization reveals an abrupt metal-SAM interface without any metal penetration. Examined electric characteristics also revealed typical non-resonant tunneling characteristics of long chain alkane thiolate SAMs. In chapter 5, the buffer layer assisted growth process is used to prepare a nano particles-SAM pristine interface on SAMs to control the metal-SAM interaction in order to study the fundamental issue of chemical enhancement mechanism of SERS. Identical Au nanoparticles-SAM-Au M3 structures with different Au-SAM interactions reveal a large discrepancy of enhancement factors of ˜100 attributed to the chemical interaction. In chapter 6, Raman spectroscopy of M3 junction is applied to the characterization of molecular electronics devices. A crossed nanowire junction (X-nWJ) device is employed for in-situ electronic-spectroscopic simultaneous characterization using Raman spectroscopy. A detailed study reveals the multi-probe capability of X-nWJ for in-situ Raman and in-elastic electron tunneling spectroscopy (IETS) as vibrational spectroscopies to diagnose molecular electronic devices. In chapter 7, aniline oligomer (OAn) based redox SAMs are characterized by spectroscopic and microscopic methods under different chemical redox states by reflection absorption infrared spectroscopy (RAIRS), Raman, x-ray photoelectron spectroscopy (XPS), and AFM in order to elucidate the mechanism of electric switching molecular junctions previously reported. Obtained results are discussed in terms of the chemical and geometrical conformations of molecules in closely packed SAM domains. In chapter 8, in-situ Raman spectroscopy and cp-AFM microscopic techniques are applied to study the electric switching characteristics of X-nWJ incorporating OAn based SAM. The results of tunneling current and in-situ Raman spectroscopy are discussed with the conformational change of OAn component. The conductance switching mechanism associated with domain conformation change of OAn SAM is proposed and evaluated based on the results.

Organic-inorganic hybrid materials as semiconducting channels in thin-film field-effect transistors

PubMed

Kagan; Mitzi; Dimitrakopoulos

1999-10-29

Organic-inorganic hybrid materials promise both the superior carrier mobility of inorganic semiconductors and the processability of organic materials. A thin-film field-effect transistor having an organic-inorganic hybrid material as the semiconducting channel was demonstrated. Hybrids based on the perovskite structure crystallize from solution to form oriented molecular-scale composites of alternating organic and inorganic sheets. Spin-coated thin films of the semiconducting perovskite (C(6)H(5)C(2)H(4)NH(3))(2)SnI(4) form the conducting channel, with field-effect mobilities of 0.6 square centimeters per volt-second and current modulation greater than 10(4). Molecular engineering of the organic and inorganic components of the hybrids is expected to further improve device performance for low-cost thin-film transistors.

Doping of free-standing zinc-blende GaN layers grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Novikov, S. V.; Powell, R. E. L.; Staddon, C. R.; Kent, A. J.; Foxon, C. T.

2014-10-01

Currently there is high level of interest in developing of vertical device structures based on the group III nitrides. We have studied n- and p-doping of free-standing zinc-blende GaN grown by plasma-assisted molecular beam epitaxy (PA-MBE). Si was used as the n-dopant and Mg as the p-dopant for zinc-blende GaN. Controllable levels of doping with Si and Mg in free-standing zinc-blende GaN have been achieved by PA-MBE. The Si and Mg doping depth uniformity through the zinc-blende GaN layers have been confirmed by secondary ion mass spectrometry (SIMS). Controllable Si and Mg doping makes PA-MBE a promising method for the growth of conducting group III-nitrides bulk crystals.

Epidemiology of Enterocytozoon bieneusi Infection in Humans.

PubMed

Matos, Olga; Lobo, Maria Luisa; Xiao, Lihua

2012-01-01

A review was conducted to examine published works that focus on the complex epidemiology of Enterocytozoon bieneusi infection in humans. Studies on the prevalence of these emerging microsporidian pathogens in humans, in developed and developing countries, the different clinical spectra of E. bieneusi intestinal infection in children, in different settings, and the risk factors associated with E. bieneusi infection have been reviewed. This paper also analyses the impact of the recent application of PCR-based molecular methods for species-specific identification and genotype differentiation has had in increasing the knowledge of the molecular epidemiology of E. bieneusi in humans. The advances in the epidemiology of E. bieneusi, in the last two decades, emphasize the importance of epidemiological control and prevention of E. bieneusi infections, from both the veterinary and human medical perspectives.

Conductive Photo-Activated Porphyrin-ZnO Nanostructured Gas Sensor Array.

PubMed

Magna, Gabriele; Catini, Alexandro; Kumar, Raj; Palmacci, Massimo; Martinelli, Eugenio; Paolesse, Roberto; di Natale, Corrado

2017-04-01

Chemoresistors working at room temperature are attractive for low-consumption integrated sensors. Previous studies show that this feature can be obtained with photoconductive porphyrins-coated ZnO nanostructures. Furthermore, variations of the porphyrin molecular structure alter both the chemical sensitivity and the photoconductivity, and can be used to define the sensor characteristics. Based on these assumptions, we investigated the properties of an array of four sensors made of a layer of ZnO nanoparticles coated with porphyrins with the same molecular framework but different metal atoms. The array was tested with five volatile organic compounds (VOCs), each measured at different concentrations. Results confirm that the features of individual porphyrins influence the sensor behavior, and the differences among sensors are enough to enable the discrimination of volatile compounds disregarding their concentration.

Inelastic electron tunneling spectroscopy of difurylethene-based photochromic single-molecule junctions

PubMed Central

Sysoiev, Dmytro; Huhn, Thomas; Pauly, Fabian

2017-01-01

Diarylethene-derived molecules alter their electronic structure upon transformation between the open and closed forms of the diarylethene core, when exposed to ultraviolet (UV) or visible light. This transformation results in a significant variation of electrical conductance and vibrational properties of corresponding molecular junctions. We report here a combined experimental and theoretical analysis of charge transport through diarylethene-derived single-molecule devices, which are created using the mechanically controlled break-junction technique. Inelastic electron tunneling (IET) spectroscopy measurements performed at 4.2 K are compared with first-principles calculations in the two distinct forms of diarylethenes connected to gold electrodes. The combined approach clearly demonstrates that the IET spectra of single-molecule junctions show specific vibrational features that can be used to identify different isomeric molecular states by transport experiments. PMID:29259875

Ionotropic GABA receptor antagonism-induced adverse outcome pathways for potential neurotoxicity biomarkers.

PubMed

Gong, Ping; Hong, Huixiao; Perkins, Edward J

2015-01-01

Antagonism of ionotropic GABA receptors (iGABARs) can occur at three distinct types of receptor binding sites causing chemically induced epileptic seizures. Here we review three adverse outcome pathways, each characterized by a specific molecular initiating event where an antagonist competitively binds to active sites, negatively modulates allosteric sites or noncompetitively blocks ion channel on the iGABAR. This leads to decreased chloride conductance, followed by depolarization of affected neurons, epilepsy-related death and ultimately decreased population. Supporting evidence for causal linkages from the molecular to population levels is presented and differential sensitivity to iGABAR antagonists in different GABA receptors and organisms discussed. Adverse outcome pathways are poised to become important tools for linking mechanism-based biomarkers to regulated outcomes in next-generation risk assessment.

FAST TRACK COMMUNICATION: Conformation dependence of molecular conductance: chemistry versus geometry

NASA Astrophysics Data System (ADS)

Finch, Christopher M.; Sirichantaropass, Skon; Bailey, Steven W.; Grace, Iain M.; García-Suárez, Víctor M.; Lambert, Colin J.

2008-01-01

Recent experiments by Venkataraman et al (2006 Nature 442 904) on a series of molecular wires with varying chemical compositions revealed a linear dependence of the conductance on cos2 θ, where θ is the angle of twist between neighbouring aromatic rings. To investigate whether or not this dependence has a more general applicability, we present a first-principles theoretical study of the transport properties of this family of molecules as a function of the chemical composition, conformation and the contact atom and geometry. If the Fermi energy EF lies within the HOMO-LUMO (highest occupied molecular orbital-lowest unoccupied molecular orbital) gap, then we reproduce the above experimental results. More generally, however, if EF is located within either the LUMO or the HOMO states, the presence of resonances destroys the linear dependence of the conductance on cos2 θ and gives rise to non-monotonic behaviour associated with the level structure of the different molecules. Our results suggest that the above experiments provide a novel method for extracting spectroscopic information about molecules contacted to electrodes.

Thermal conductivity of Bi2(SexTe1-x)3 alloy films grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Yoo, Taehee; Lee, Eungkyu; Dong, Sining; Li, Xiang; Liu, Xinyu; Furdyna, Jacek K.; Dobrowolska, Margaret; Luo, Tengfei

2017-06-01

We studied the thermal conductivity of Bi2Se3, Bi2Te3, and their alloy Bi2(SexTe1-x)3 at room temperature using time-domain thermoreflectance measurements. The Bi2(SexTe1-x)3 films with various concentrations of Se and Te prepared by molecular beam epitaxy on GaAs substrates were investigated to study the dependence of thermal conductivity on film composition. We observed that the Bi2(SexTe1-x)3 ternary alloys can have much lower thermal conductivity values compared to those of Bi2Se3 and Bi2Te3. These results may provide useful information for developing and engineering low thermal conductivity materials for thermoelectric applications.

Behavior of stem cells under outer-space microgravity and ground-based microgravity simulation.

PubMed

Zhang, Cui; Li, Liang; Chen, Jianling; Wang, Jinfu

2015-06-01

With rapid development of space engineering, research on life sciences in space is being conducted extensively, especially cellular and molecular studies on space medicine. Stem cells, undifferentiated cells that can differentiate into specialized cells, are considered a key resource for regenerative medicine. Research on stem cells under conditions of microgravity during a space flight or a ground-based simulation has generated several excellent findings. To help readers understand the effects of outer space and ground-based simulation conditions on stem cells, we reviewed recent studies on the effects of microgravity (as an obvious environmental factor in space) on morphology, proliferation, migration, and differentiation of stem cells. © 2015 International Federation for Cell Biology.

Fatigue Resistant Bioinspired Composite from Synergistic Two-Dimensional Nanocomponents.

PubMed

Wan, Sijie; Zhang, Qi; Zhou, Xiaohang; Li, Dechang; Ji, Baohua; Jiang, Lei; Cheng, Qunfeng

2017-07-25

Portable and wearable electronics require much more flexible graphene-based electrode with high fatigue life, which could repeatedly bend, fold, or stretch without sacrificing its mechanical properties and electrical conductivity. Herein, a kind of ultrahigh fatigue resistant graphene-based nanocomposite via tungsten disulfide (WS 2 ) nanosheets is synthesized by introducing a synergistic effect with covalently cross-linking inspired by the orderly layered structure and abundant interfacial interactions of nacre. The fatigue life of resultant graphene-based nanocomposites is more than one million times at the stress level of 270 MPa, and the electrical conductivity can be kept as high as 197.1 S/cm after 1.0 × 10 5 tensile testing cycles. These outstanding properties are attributed to the synergistic effect from lubrication of WS 2 nanosheets for deflecting crack propagation, and covalent bonding between adjacent GO nanosheets for bridging crack, which is verified by the molecular dynamics (MD) simulations. The WS 2 induced synergistic effect with covalent bonding offers a guidance for constructing graphene-based nanocomposites with high fatigue life, which have great potential for applications in flexible and wearable electronic devices, etc.

Atomistic simulations of thermal transport in Si and SiGe based materials: From bulk to nanostructures

NASA Astrophysics Data System (ADS)

Savic, Ivana; Mingo, Natalio; Donadio, Davide; Galli, Giulia

2010-03-01

It has been recently proposed that Si and SiGe based nanostructured materials may exhibit low thermal conductivity and overall promising properties for thermoelectric applications. Hence there is a considerable interest in developing accurate theoretical and computational methods which can help interpret recent measurements, identify the physical origin of the reduced thermal conductivity, as well as shed light on the interplay between disorder and nanostructuring in determining a high figure of merit. In this work, we investigate the capability of an atomistic Green's function method [1] to describe phonon transport in several types of Si and SiGe based systems: amorphous Si, SiGe alloys, planar and nanodot Si/SiGe multilayers. We compare our results with experimental data [2,3], and with the findings of molecular dynamics simulations and calculations based on the Boltzmann transport equation. [1] I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008). [2] S.-M. Lee, D. G. Cahill, and R. Venkatasubramanian, Appl. Phys. Lett. 70, 2957 (1997). [3] G. Pernot et al., submitted.

Ultrasensitive molecular detection using thermal conductance of a hydrophobic gold-water interface.

PubMed

Green, Andrew J; Alaulamie, Arwa A; Baral, Susil; Richardson, Hugh H

2013-09-11

The thermal conductance from a hydrophobic gold aqueous interface is measured with increasing solute concentration. A small amount of aqueous solute molecules (1 solute molecule in 550 water molecules) dramatically increases the heat dissipation into the surrounding liquid. This result is consistent with a thermal conductance that is limited by an interface interaction where minority aqueous components significantly alter the surface properties and heat transport through the interface. The increase in heat dissipation can be used to make an extremely sensitive molecular detector that can be scaled to give single molecule detection without amplification or utilizing fluorescence labels.

Compact ion accelerator source

DOEpatents

Schenkel, Thomas; Persaud, Arun; Kapadia, Rehan; Javey, Ali

2014-04-29

An ion source includes a conductive substrate, the substrate including a plurality of conductive nanostructures with free-standing tips formed on the substrate. A conductive catalytic coating is formed on the nanostructures and substrate for dissociation of a molecular species into an atomic species, the molecular species being brought in contact with the catalytic coating. A target electrode placed apart from the substrate, the target electrode being biased relative to the substrate with a first bias voltage to ionize the atomic species in proximity to the free-standing tips and attract the ionized atomic species from the substrate in the direction of the target electrode.

Electron transport through a spin crossover junction. Perspectives from a wavefunction-based approach

NASA Astrophysics Data System (ADS)

Vela, Sergi; Verot, Martin; Fromager, Emmanuel; Robert, Vincent

2017-02-01

The present paper reports the application of a computational framework, based on the quantum master equation, the Fermi's golden Rule, and conventional wavefunction-based methods, to describe electron transport through a spin crossover molecular junction (Fe(bapbpy) (NCS)2, 1, bapbpy = N-(6-(6-(Pyridin-2-ylamino)pyridin-2-yl)pyridin-2-yl)-pyridin-2-amine). This scheme is an alternative to the standard approaches based on the relative position and nature of the frontier orbitals, as it evaluates the junction's Green's function by means of accurate state energies and wavefunctions. In the present work, those elements are calculated for the relevant states of the high- and low-spin species of 1, and they are used to evaluate the output conductance within a given range of bias- and gate-voltages. The contribution of the ground and low-lying excited states to the current is analyzed, and inspected in terms of their 2S + 1 Ms-states. In doing so, it is shown the relevance of treating not only the ground state in its maximum-Ms projection, as usually done in most computational-chemistry packages, but the whole spectrum of low-energy states of the molecule. Such improved representation of the junction has a notable impact on the total conductivity and, more importantly, it restores the equivalence between alpha and beta transport, which means that no spin polarization is observed in the absence of Zeeman splitting. Finally, this work inspects the strong- and weak-points of the suggested theoretical framework to understand electron transport through molecular switchable materials, identifies a pathway for future improvement, and offers a new insight into concepts that play a key role in spintronics.

The interplay of ion crosslinking, free ion content, and polymer mobility in PEO-based single-ion conductors

NASA Astrophysics Data System (ADS)

Lin, Kan-Ju; Maranas, Janna

2010-03-01

We use molecular dynamics simulation to study ion clustering and dynamics in ion containing polymers. This PEO based single-ion conducting ionomer serves as a model system for understanding cation transport in solid state polymer electrolytes (SPEs). Although small-angle x-ray scattering does not show an ionomer peak, we observer various cation-anion complexes in the simulation, suggesting ionomer backbones are crosslinked through ion complexes. These crosslinks reduce the adjacent PEO mobility resulting in a symmetric mobility gradient along the PEO chain. We vary the cation-anion interaction in the simulation to observe the interplay of cation-anion association, polymer mobility and cation motion. Cation-anion association controls the number of free ions, which is important in ionic conductivity when these materials are used as SPEs. Polymer mobility controls how fast the free ions are able to move through the SPE. High conductivity requires both a high free ion content and fast polymer motion. To understand the connection between the two, we ``tune'' the force field in order to manipulate the free ion content and observe the influence on PEO dynamics.

Rhizoma Dioscoreae extract protects against alveolar bone loss by regulating the cell cycle: A predictive study based on the protein‑protein interaction network.

PubMed

Zhang, Zhi-Guo; Song, Chang-Heng; Zhang, Fang-Zhen; Chen, Yan-Jing; Xiang, Li-Hua; Xiao, Gary Guishan; Ju, Da-Hong

2016-06-01

Rhizoma Dioscoreae extract (RDE) exhibits a protective effect on alveolar bone loss in ovariectomized (OVX) rats. The aim of this study was to predict the pathways or targets that are regulated by RDE, by re‑assessing our previously reported data and conducting a protein‑protein interaction (PPI) network analysis. In total, 383 differentially expressed genes (≥3‑fold) between alveolar bone samples from the RDE and OVX group rats were identified, and a PPI network was constructed based on these genes. Furthermore, four molecular clusters (A‑D) in the PPI network with the smallest P‑values were detected by molecular complex detection (MCODE) algorithm. Using Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA) tools, two molecular clusters (A and B) were enriched for biological process in Gene Ontology (GO). Only cluster A was associated with biological pathways in the IPA database. GO and pathway analysis results showed that cluster A, associated with cell cycle regulation, was the most important molecular cluster in the PPI network. In addition, cyclin‑dependent kinase 1 (CDK1) may be a key molecule achieving the cell‑cycle‑regulatory function of cluster A. From the PPI network analysis, it was predicted that delayed cell cycle progression in excessive alveolar bone remodeling via downregulation of CDK1 may be another mechanism underling the anti‑osteopenic effect of RDE on alveolar bone.

Single-molecule designs for electric switches and rectifiers.

PubMed

Kornilovitch, Pavel; Bratkovsky, Alexander; Williams, Stanley

2003-12-01

A design for molecular rectifiers is proposed. Current rectification is based on the spatial asymmetry of a molecule and requires only one resonant conducting molecular orbital. Rectification is caused by asymmetric coupling of the orbital to the electrodes, which results in asymmetric movement of the two Fermi levels with respect to the orbital under external bias. Results from numerical studies of the family of suggested molecular rectifiers, HS-(CH(2))(n)-C(6)H(4)(CH(2))(m)SH, are presented. Current rectification ratios in excess of 100 are achievable for n = 2 and m > 6. A class of bistable stator-rotor molecules is proposed. The stationary part connects the two electrodes and facilitates electron transport between them. The rotary part, which has a large dipole moment, is attached to an atom of the stator via a single sigma bond. Electrostatic bonds formed between the oxygen atom of the rotor and hydrogen atoms of the stator make the symmetric orientation of the dipole unstable. The rotor has two potential minima with equal energy for rotation about the sigma bond. The dipole can be flipped between the two states by an external electric field. Both rotor-orientation states have asymmetric current-voltage characteristics that are the reverse of each other, so they are distinguishable electrically. Theoretical results on conformation, energy barriers, retention times, switching voltages, and current-voltage characteristics are presented for a particular stator-rotor molecule. Such molecules could be the base for single-molecule switches, reversible diodes, and other molecular electronic devices.

Investigation of miscellaneous hERG inhibition in large diverse compound collection using automated patch-clamp assay

PubMed Central

Yu, Hai-bo; Zou, Bei-yan; Wang, Xiao-liang; Li, Min

2016-01-01

Aim: hERG potassium channels display miscellaneous interactions with diverse chemical scaffolds. In this study we assessed the hERG inhibition in a large compound library of diverse chemical entities and provided data for better understanding of the mechanisms underlying promiscuity of hERG inhibition. Methods: Approximately 300 000 compounds contained in Molecular Library Small Molecular Repository (MLSMR) library were tested. Compound profiling was conducted on hERG-CHO cells using the automated patch-clamp platform–IonWorks Quattro™. Results: The compound library was tested at 1 and 10 μmol/L. IC50 values were predicted using a modified 4-parameter logistic model. Inhibitor hits were binned into three groups based on their potency: high (IC50<1 μmol/L), intermediate (1 μmol/L< IC50<10 μmol/L), and low (IC50>10 μmol/L) with hit rates of 1.64%, 9.17% and 16.63%, respectively. Six physiochemical properties of each compound were acquired and calculated using ACD software to evaluate the correlation between hERG inhibition and the properties: hERG inhibition was positively correlative to the physiochemical properties ALogP, molecular weight and RTB, and negatively correlative to TPSA. Conclusion: Based on a large diverse compound collection, this study provides experimental evidence to understand the promiscuity of hERG inhibition. This study further demonstrates that hERG liability compounds tend to be more hydrophobic, high-molecular, flexible and polarizable. PMID:26725739

Highly conductive and anticorrosion Ag/CNTs/NDs hybrid films on molecular-grafted PET substrate for flexible electrodes

NASA Astrophysics Data System (ADS)

Zhang, Yang; Kang, Zhixin

2018-01-01

We reported an approach of preparing highly conductive, anticorrosion, flexible Ag hybrid films enhanced by multi-walled carbon nanotubes (CNTs) and nanodaimonds (NDs) on molecular-grafted PET substrate by spin-spray for flexible electronics. we studied in this paper and found that even an outstanding enhancement on conductivity of Ag films, CNTs have a negative effect on anticorrosion property. Meanwhile, NDs decreased the conductivity of Ag/CNTs hybrids, but it remained a relatively high conductivity property and even was affirmed a distinctly boost improvement on anticorrosion, microhardness and tensile strength, which meant a better mechanical chemical stabilization and practicability in real flexible electronics. To obtain the strong adhesive strength of films/substrate, molecular-grafting technology was applied, which was affirmed by XPS and cross-cut test. What's more, we evaluated anticorrosion property by electrochemistry test, including Tafel measurements and electrochemical impedance spectroscopy measurements, proving the positive effect of NDs on Ag/CNTs hybrid films. For practical application, a flexible light-emitting diode (LED) circuit was successfully structured and remained steady under bending, folding and twisting. Besides, after 1000000 cycles inner/outer bending deformation, the hybrid films showed a mechanical compliance, fatigue stability and practicability in real flexible electronics.

TCNQ molecular semiconductor of the Cu(II)TAAB macrocycle: Optical and electrical properties.

PubMed

Sánchez Vergara, M E; Salcedo, R; Molina, Bertha; Carrera-Téllez, R; Álvarez-Bada, J R; Hernández-García, A; Gómez-Vidales, V

2018-07-05

The present study reports the doping of a semiconducting molecular material through the formation of hydrogen bonds between the macrocycle Cu(II)(TAAB) and the electronic acceptor TCNQ. According to density functional theory (DFT) calculations and electron paramagnetic resonance (EPR) analysis, the doped compound has the shape of a distorted square pyramid, with four nitrogen atoms in the equatorial position and the apical oxygen atom from the water ligands. These water molecules can generate strong hydrogen bonds with TCNQ and the TAAB metallic complex. Thin films of copper molecular material were obtained through high vacuum evaporation and were structurally characterized by IR spectroscopy, EPR and scanning electron microscopy (SEM). Additionally, the absorption coefficient (α) and photon energy (hν) were calculated from UV-vis spectroscopy and used to determine the optical activation energy in each film, from which its semiconducting behavior was established. An important aspect to consider is that the presence of hydrogen bonds is essential to establish the semiconducting nature of these species; this chemical behavior, as well as the resulting electronic mobility, have been studied by DFT theoretical calculations, which reinforce the experimental conclusion of a relationship between Cu(II)TAAB and TCNQ moieties generated by a weak bond. Finally, I-V characteristics have been obtained from a glass/ITO/doped molecular semiconductor/Ag device using Ag and ITO electrodes. Results for the copper-based device show that, at low voltages, the conduction process is of an ohmic nature while, at higher voltages, space-charge-limited current (SCLC) is found. It is highly probable that the doping effect in TCNQ favors electronic transport due to the formation of conduction channels caused by dopant-favored anisotropy. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular transport through nanoporous silicon nitride membranes produced from self-assembling block copolymers.

PubMed

Montagne, Franck; Blondiaux, Nicolas; Bojko, Alexandre; Pugin, Raphaël

2012-09-28

To achieve fast and selective molecular filtration, membrane materials must ideally exhibit a thin porous skin and a high density of pores with a narrow size distribution. Here, we report the fabrication of nanoporous silicon nitride membranes (NSiMs) at the full wafer scale using a versatile process combining block copolymer (BCP) self-assembly and conventional photolithography/etching techniques. In our method, self-assembled BCP micelles are used as templates for creating sub-100 nm nanopores in a thin low-stress silicon nitride layer, which is then released from the underlying silicon wafer by etching. The process yields 100 nm thick free-standing NSiMs of various lateral dimensions (up to a few mm(2)). We show that the membranes exhibit a high pore density, while still retaining excellent mechanical strength. Permeation experiments reveal that the molecular transport rate across NSiMs is up to 16-fold faster than that of commercial polymeric membranes. Moreover, using dextran molecules of various molecular weights, we also demonstrate that size-based separation can be achieved with a very good selectivity. These new silicon nanosieves offer a relevant technological alternative to commercially available ultra- and microfiltration membranes for conducting high resolution biomolecular separations at small scales.

Habitat segregation and cryptic adaptation of species of Periophthalmus (Gobioidei: Gobiidae).

PubMed

Polgar, G; Zaccara, S; Babbucci, M; Fonzi, F; Antognazza, C M; Ishak, N; Sulaiman, Z; Crosa, G

2017-05-01

A study was conducted on the habitat distribution of four sympatric species of Periophthalmus (the silver-lined mudskipper Periophthalmus argentilineatus, the slender mudskipper Periophthalmus gracilis, the kalolo mudskipper Periophthalmus kalolo and the Malacca mudskipper Periophthalmus malaccensis) from northern Sulawesi. Molecular phylogenetic reconstructions based on one mtDNA marker (16S) were used to validate the morphological taxa, identifying five molecular clades. Periophthalmus argentilineatus includes two molecular species, which are named Periophthalmus argentilineatus clades F and K. Multivariate direct gradient analysis show that these species form three distinct ecological guilds, with the two molecular species occurring in different guilds. Periophthalmus clade F is ecologically eurytypic; Periophthalmus clade K and P. kalolo are prevalent in ecosystems isolated by strong oceanic currents and at shorter distances from the sea; P. gracilis plus P. malaccensis are prevalent in ecosystems connected by shallow coastal waters, in vegetated habitats at larger distances from the sea. This indicates for the first time that mudskipper species exhibit a range of adaptations to semiterrestrialism not only within genera, but even within morphospecies, delineating a much more complex adaptive scenario than previously assumed. © 2017 The Fisheries Society of the British Isles.

The equally wonderful field: Ernst Mayr and organismic biology.

PubMed

Milam, Erika Lorraine

2010-01-01

Biologists in the 1960s witnessed a period of intense intra-disciplinary negotiations, especially the positioning of organismic biologists relative to molecular biologists. The perceived valorization of the physical sciences by "molecular" biologists became a catalyst creating a unified front of "organismic" biology that incorporated not just evolutionary biologists, but also students of animal behavior, ecology, systematics, botany - in short, almost any biological community that predominantly conducted their research in the field or museum and whose practitioners felt the pinch of the prestige and funding accruing to molecular biologists and biochemists. Ernst Mayr, Theodosius Dobzhansky, and George Gaylord Simpson took leading roles in defending alternatives to what they categorized as the mechanistic approach of chemistry and physics applied to living systems - the "equally wonderful field of organismic biology." Thus, it was through increasingly tense relations with molecular biology that organismic biologists cohered into a distinct community, with their own philosophical grounding, institutional security, and historical identity. Because this identity was based in large part on a fundamental rejection of the physical sciences as a desirable model within biology, organismic biologists succeeded in protecting the future of their field by emphasizing deep divisions that ran through the biological sciences as a whole.

PREFACE: Transport phenomena in proton conducting media Transport phenomena in proton conducting media

NASA Astrophysics Data System (ADS)

Eikerling, Michael

2011-06-01

Proton transport phenomena are of paramount importance for acid-base chemistry, energy transduction in biological organisms, corrosion processes, and energy conversion in electrochemical systems such as polymer electrolyte fuel cells. The relevance for such a plethora of materials and systems, and the ever-lasting fascination with the highly concerted nature of underlying processes drive research across disciplines in chemistry, biology, physics and chemical engineering. A proton never travels alone. Proton motion is strongly correlated with its environment, usually comprised of an electrolyte and a solid or soft host material. For the transport in nature's most benign proton solvent and shuttle, water that is, insights from ab initio simulations, matured over the last 15 years, have furnished molecular details of the structural diffusion mechanism of protons. Excess proton movement in water consists of sequences of Eigen-Zundel-Eigen transitions, triggered by hydrogen bond breaking and making in the surrounding water network. Nowadays, there is little debate about the validity of this mechanism in water, which bears a stunning resemblance to the basic mechanistic picture put forward by de Grotthuss in 1806. While strong coupling of an excess proton with degrees of freedom of solvent and host materials facilitates proton motion, this coupling also creates negative synergies. In general, proton mobility in biomaterials and electrochemical proton conducting media is highly sensitive to the abundance and structure of the proton solvent. In polymer electrolyte membranes, in which protons are bound to move in nano-sized water-channels, evaporation of water or local membrane dehydration due to electro-osmotic coupling are well-known phenomena that could dramatically diminish proton conductivity. Contributions in this special issue address various vital aspects of the concerted nature of proton motion and they elucidate important structural and dynamic effects of solvent, charge-bearing species at interfaces and porous host materials on proton transport properties. As a common thread, articles in this special issue contribute to understanding the functionality provided by complex materials, beyond hydrogen bond fluctuations in water. The first group of articles (Smirnov et al, Henry et al, Medvedev and Stuchebrukhov) elucidates various aspects of the impact of local structural fluctuations, hydrogen bonding and long-range electrostatic forces on proton transfer across and at the surface of mitochondrial membranes. The second group of articles (Ilhan and Spohr, Allahyarov et al and Idupulapati et al) employ molecular dynamics simulations to rationalize vital dependencies of proton transport mechanisms in aqueous-based polymer electrolyte membranes on the nanoporous, phase-separated ionomer morphology, and on the level of hydration. The articles by Gebel et al, Boillat et al, and Aleksandrova et al employ small angle neutron scattering, neutron radiography, and electrochemical atomic force microscopy, respectively, to obtain detailed insights into the kinetics of water sorption, water distribution, water transport properties, as well as spatial maps of proton conductivity in fuel cell membranes. The contribution of Paschos et al provides a comprehensive review of phosphate-based solid state protonic conductors for intermediate temperature fuel cells. The topic of proton conductive materials for high-temperature, water-free operation of fuel cells is continued in the article of Verbraeken et al which addresses synthesis and characterization of a proton conducting perovskite. The guest editor wishes to acknowledge and thank all contributing authors for their commitment to this special issue. Moreover, I would like to thank the staff at IOP Publishing for coordinating submission and refereeing processes. Finally, for the readers, I hope that this special issue will be a valuable and stimulating source of insights into the versatile and eminently important field of transport phenomena in proton conducting media. Complex dynamics of fluids in disordered and crowded environments contents Electrostatic models of electron-driven proton transfer across a lipid membrane Anatoly Yu Smirnov, Lev G Mourokh and Franco Nori Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase Rowan M Henry, David Caplan, Elisa Fadda and Régis Pomès Proton diffusion along biological membranes E S Medvedev and A A Stuchebrukhov Ab initio molecular dynamics of proton networks in narrow polymer electrolyte pores Mehmet A Ilhan and Eckhard Spohr A simulation study of field-induced proton-conduction pathways in dry ionomers Elshad Allahyarov, Philip L Taylor and Hartmut Löwen Molecular structure and transport dynamics in perfluoro sulfonyl imide membranes Nagesh Idupulapati, Ram Devanathan and Michel Dupuis The kinetics of water sorption in Nafion membranes: a small-angle neutron scattering study Gérard Gebel, Sandrine Lyonnard, Hakima Mendil-Jakani and Arnaud Morin Using 2H labeling with neutron radiography for the study of solid polymer electrolyte water transport properties P Boillat, P Oberholzer, B C Seyfang, A Kästner, R Perego, G G Scherer, E H Lehmann and A Wokaun Spatial distribution and dynamics of proton conductivity in fuel cell membranes: potential and limitations of electrochemical atomic force microscopy measurements E Aleksandrova, S Hink, R Hiesgen and E Roduner A review on phosphate based, solid state, protonic conductors for intermediate temperature fuel cells O Paschos, J Kunze, U Stimming and F Maglia A structural study of the proton conducting B-site ordered perovskite Ba3Ca1.18Ta1.82O8.73 Maarten C Verbraeken, Hermenegildo A L Viana, Philip Wormald and John T S Irvine

Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions

NASA Astrophysics Data System (ADS)

Hoy, Erik P.; Mazziotti, David A.; Seideman, Tamar

2017-11-01

Can an electronic device be constructed using only a single molecule? Since this question was first asked by Aviram and Ratner in the 1970s [Chem. Phys. Lett. 29, 277 (1974)], the field of molecular electronics has exploded with significant experimental advancements in the understanding of the charge transport properties of single molecule devices. Efforts to explain the results of these experiments and identify promising new candidate molecules for molecular devices have led to the development of numerous new theoretical methods including the current standard theoretical approach for studying single molecule charge transport, i.e., the non-equilibrium Green's function formalism (NEGF). By pairing this formalism with density functional theory (DFT), a wide variety of transport problems in molecular junctions have been successfully treated. For some systems though, the conductance and current-voltage curves predicted by common DFT functionals can be several orders of magnitude above experimental results. In addition, since density functional theory relies on approximations to the exact exchange-correlation functional, the predicted transport properties can show significant variation depending on the functional chosen. As a first step to addressing this issue, the authors have replaced density functional theory in the NEGF formalism with a 2-electron reduced density matrix (2-RDM) method, creating a new approach known as the NEGF-RDM method. 2-RDM methods provide a more accurate description of electron correlation compared to density functional theory, and they have lower computational scaling compared to wavefunction based methods of similar accuracy. Additionally, 2-RDM methods are capable of capturing static electron correlation which is untreatable by existing NEGF-DFT methods. When studying dithiol alkane chains and dithiol benzene in model junctions, the authors found that the NEGF-RDM predicts conductances and currents that are 1-2 orders of magnitude below those of B3LYP and M06 DFT functionals. This suggests that the NEGF-RDM method could be a viable alternative to NEGF-DFT for molecular junction calculations.

Understanding transport mechanisms in ionic liquid/carbonate solvent electrolyte blends.

PubMed

Oldiges, K; Diddens, D; Ebrahiminia, M; Hooper, J B; Cekic-Laskovic, I; Heuer, A; Bedrov, D; Winter, M; Brunklaus, G

2018-06-20

To unravel mechanistic details of the ion transport in liquid electrolytes, blends of the ionic liquid (IL) 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (Pyr14TFSI), ethylene carbonate (EC) and dimethyl carbonate (DMC) with the conducting salts lithium hexafluorophosphate (LiPF6) and lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) were investigated as a function of the IL concentration. Electrochemical impedance, Pulsed Field Gradient Nuclear Magnetic Resonance (PFG NMR) and Raman spectroscopy supported by Molecular Dynamics (MD) simulations allowed the structural and dynamic correlations of the ion motions to be probed. Remarkably, we identified that though the individual correlations among different ion types exhibit a clear concentration dependence, their net effect is nearly constant throughout the entire concentration range, resulting in approximately equal transport and transference numbers, despite a monitored cross-over from carbonate-based lithium coordination to a TFSI-based ion coordination. In addition, though dynamical ion correlation could be found, the absolute values of the ionic conductivity are essentially determined by the overall viscosity of the electrolyte. The IL/carbonate blends with a Pyr14TFSI fraction of ∼10 wt% are found to be promising electrolyte solvents, with ionic conductivities and lithium ion transference numbers comparable to those of standard carbonate-based electrolytes while the thermal and electrochemical stabilities are considerably improved. In contrast, the choice of the conducting salt only marginally affects the transport properties.

Molecular Astrophysics from Space: the Physical and Chemical Effects of Star Formation and the Destruction of Planetary Systems around Evolved Stars

NASA Technical Reports Server (NTRS)

Neufeld, David

2005-01-01

The research conducted during the reporting period is grouped into three sections: 1) Warm molecular gas in the interstellar medium (ISM); 2) Absorption line studies of "cold" molecular clouds; 3) Vaporization of comets around the AGB star IRC+10216.

The prevalence of X-linked hypohidrotic ectodermal dysplasia (XLHED) in Denmark, 1995-2010.

PubMed

Nguyen-Nielsen, Mary; Skovbo, Stine; Svaneby, Dea; Pedersen, Lars; Fryzek, Jon

2013-05-01

X-linked hypohidrotic ectodermal dysplasia (XLHED) is characterised by hypohidrosis, sparse hair, and teeth abnormalities. Infants with XLHED have an increased risk of death by hyperpyrexia. XLHED is the most common form of hypohidrotic ectodermal dysplasia (HED); however, no population-based prevalence estimates are available. We aimed to: 1) estimate the prevalence of XLHED in the Danish population per January 1, 2011; 2) identify the most frequent age at time of diagnosis; and 3) quantify the most frequent clinical feature associated with XLHED. We conducted a nationwide cross-sectional study (1995-2010). We leveraged national medical registries and data from clinical departments to categorise XLHED cases into three groups: 1) Molecularly-confirmed XLHED; 2) Clinically-diagnosed HED (registered with ICD-10 Q 82.4); and 3) Possible HED (registered with sufficient clinical features based on a clinical algorithm that we designed). We identified 90 molecularly-confirmed XLHED, 146 clinically-diagnosed HED, and 988 possible HED cases between 1995 and 2010 (total n = 1224). The prevalence was 21.9 per 100,000 overall and 1.6 per 100,000 when restricting to molecularly-confirmed XLHED cases. The most frequent age at time of XLHED diagnosis occurred between the ages of 11 and 18 years. Teeth abnormalities occurred in 79% of all cases and 52% of molecularly-confirmed cases as a primary clinical marker. We present the first ever population-based prevalence estimates of XLHED and suggest that the prevalence of XLHED may be higher than previously estimated. Diagnosis occurs most frequently during adolescence and teeth abnormalities were the most frequent clinical marker of XLHED. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Long-Range Charge Transport in Adenine-Stacked RNA:DNA Hybrids.

PubMed

Li, Yuanhui; Artés, Juan M; Hihath, Joshua

2016-01-27

An extremely important biological component, RNA:DNA can also be used to design nanoscale structures such as molecular wires. The conductance of single adenine-stacked RNA:DNA hybrids is rapidly and reproducibly measured using the break junction approach. The conductance decreases slightly over a large range of molecular lengths, suggesting that RNA:DNA can be used as an oligonucleotide wire. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding glass formation and ion transport in polymeric ionic liquids using computer simulations

NASA Astrophysics Data System (ADS)

Patra, Tarak; Yang, Junhong; Cheng, Yiz; Simmons, David

Polymeric ionic liquids (PILs) are very promising materials to enable more environmentally stable high density energy storage devices. Realization of PILs providing high environmental and mechanical stability while maximizing ion conductivity would be accelerated by an improved molecular level understanding of their structure and dynamics. Extensive evidence suggests that both mechanical properties and ion conductivity in anhydrous PILs are intimately related to the PIL's glass formation behavior. This represents a major challenge to the rational design of these materials, given that the basic nature of glass formation and its connection to molecular properties remains a substantial open question in polymer and condensed matter physics. Here we describe coarse-grained and atomistic molecular dynamics simulations probing the relationship between PIL architecture and interactions, glass formation behavior, and ion transport characteristics. These studies provide guidance towards the design of PILs with improved stability and ion conductivity for future energy applications.

Conduction mechanism of nitronyl-nitroxide molecular magnetic compounds

NASA Astrophysics Data System (ADS)

Dotti, N.; Heintze, E.; Slota, M.; Hübner, R.; Wang, F.; Nuss, J.; Dressel, M.; Bogani, L.

2016-04-01

We investigate the conduction mechanisms of nitronyl-nitroxide (NIT) molecular radicals, as useful for the creation of nanoscopic molecular spintronic devices, finding that it does not correspond to standard Mott behavior, as previously postulated. We provide a complete investigation using transport measurements, low-energy, sub-THz spectroscopy and introducing differently substituted phenyl appendages. We show that a nontrivial surface-charge-limited regime is present in addition to the standard low-voltage Ohmic conductance. Scaling analysis allows one to determine all the main transport parameters for the compounds and highlights the presence of charge-trapping effects. Comparison among the different compounds shows the relevance of intermolecular stacking between the aromatic ring of the phenyl appendix and the NIT motif in the creation of useful electron transport channels. The importance of intermolecular pathways is further highlighted by electronic structure calculations, which clarify the nature of the electronic channels and their effect on the Mott character of the compounds.

Graphene as a Promising Electrode for Low-Current Attenuation in Nonsymmetric Molecular Junctions.

PubMed

Zhang, Qian; Liu, Longlong; Tao, Shuhui; Wang, Congyi; Zhao, Cezhou; González, César; Dappe, Yannick J; Nichols, Richard J; Yang, Li

2016-10-12

We have measured the single-molecule conductance of 1,n-alkanedithiol molecular bridges (n = 4, 6, 8, 10, 12) on a graphene substrate using scanning tunneling microscopy (STM)-formed electrical junctions. The conductance values of this homologous series ranged from 2.3 nS (n = 12) to 53 nS (n = 4), with a decay constant β n of 0.40 per methylene (-CH 2 ) group. This result is explained by a combination of density functional theory (DFT) and Keldysh-Green function calculations. The obtained decay, which is much lower than the one obtained for symmetric gold junctions, is related to the weak coupling at the molecule-graphene interface and the electronic structure of graphene. As a consequence, we show that using graphene nonsymmetric junctions and appropriate anchoring groups may lead to a much-lower decay constant and more-conductive molecular junctions at longer lengths.

Structural Characterization of Two Pore-Forming Peptides: Consequences of Introducing a C-Terminal Tryptophan

PubMed Central

Herrera, Alvaro I.; Al-Rawi, Ahlam; Cook, Gabriel A.; Gao, Jian; Iwamoto, Takeo; Prakash, Om; Tomich, John M.; Chen, Jianhan

2010-01-01

Synthetic channel-forming peptides that can restore chloride conductance across epithelial membranes could provide a novel treatment of channelopathies such as cystic fibrosis. Among series of 22-residue peptides derived from the second transmembrane segment of the glycine receptor α1-subunit (M2GlyR), p22-S22W (KKKKP ARVGL GITTV LTMTT QW) is particularly promising with robust membrane insertion and assembly. The concentration to reach one-half maximal short circuit current is reduced to 45±6 μM from that of 210±70 μM of peptide p22 (KKKKP ARVGL GITTV LTMTT QS). However, this is accompanied with nearly 50% reduction in conductance. Towards obtaining a molecular level understanding of the channel activities, we combine information from solution NMR, existing biophysical data, and molecular modeling to construct atomistic models of the putative pentameric channels of p22 and p22-S22W. Simulations in membrane bilayers demonstrate that these structural models, even though highly flexible, are stable and remain adequately open for ion conductance. The membrane-anchoring tryptophan residues not only rigidify the whole channel, suggesting increased stability, but also lead to global changes in the pore profile. Specifically, the p22-S22W pore has a smaller opening on average, consistent with lower measured conductance. Direct observation of several incidences of chloride transport suggests several qualitative features of how these channels might selectively conduct anions. The current study thus helps to rationalize the functional consequences of introducing a single C-terminal tryptophan. Availability of these structural models also paves the way for future work to rationally modify and improve M2GlyR-derived peptides toward potential peptide-based channel replacement therapy. PMID:20544961

New insights into the thermal behaviour of organic ionic plastic crystals: magnetic resonance imaging of polycrystalline morphology alterations induced by solid-solid phase transitions.

PubMed

Romanenko, Konstantin; Pringle, Jennifer M; O'Dell, Luke A; Forsyth, Maria

2015-07-15

Organic ionic plastic crystals (OIPCs) show strong potential as solid-state electrolytes for lithium battery applications, demonstrating promising electrochemical performance and eliminating the need for a volatile and flammable liquid electrolyte. The ionic conductivity (σ) in these systems has recently been shown to depend strongly on polycrystalline morphology, which is largely determined by the sample's thermal history. [K. Romanenko et al., J. Am. Chem. Soc., 2014, 136, 15638]. Tailoring this morphology could lead to conductivities sufficiently high for battery applications, so a more complete understanding of how phenomena such as solid-solid phase transitions can affect the sample morphology is of significant interest. Anisotropic relaxation of nuclear spin magnetisation provides a new MRI based approach for studies of polycrystalline materials at both a macroscopic and molecular level. In this contribution, morphology alterations induced by solid-solid phase transitions in triisobutyl(methyl)phosphonium bis(fluorosulfonyl)imide (P1444FSI) and diethyl(methyl)(isobutyl)phosphonium hexafluorophosphate (P1224PF6) are examined using magnetic resonance imaging (MRI), alongside nuclear magnetic resonance (NMR) spectroscopy, diffusion measurements and conductivity data. These observations are linked to molecular dynamics and structural behaviour crucial for the conductive properties of OIPCs. A distinct correlation is established between the conductivity at a given temperature, σ(T), and the intensity of the narrow NMR signal that is attributed to a mobile fraction, fm(T), of ions in the OIPC. To explain these findings we propose an analogy with the well-studied relationship between permeability (k) and void fraction (θ) in porous media, with k(θ) commonly quantified by a power-law dependence that can also be employed to describe σ(fm).

Thermal conductivity of ternary III-V semiconductor alloys: The role of mass difference and long-range order

NASA Astrophysics Data System (ADS)

Mei, S.; Knezevic, I.

2018-03-01

Thermal transport in bulk ternary III-V arsenide (III-As) semiconductor alloys was investigated using equilibrium molecular dynamics with optimized Albe-Tersoff empirical interatomic potentials. Existing potentials for binary AlAs, GaAs, and InAs were optimized to match experimentally obtained acoustic-phonon dispersions and temperature-dependent thermal conductivity. Calculations of thermal transport in ternary III-Vs commonly employ the virtual-crystal approximation (VCA), where the structure is assumed to be a random alloy and all group-III atoms (cations) are treated as if they have an effective weighted-average mass. Here, we showed that it is critical to treat atomic masses explicitly and that the thermal conductivity obtained with explicit atomic masses differs considerably from the value obtained with the average VCA cation mass. The larger the difference between the cation masses, the poorer the VCA prediction for thermal conductivity. The random-alloy assumption in the VCA is also challenged because X-ray diffraction and transmission electron microscopy show order in InGaAs, InAlAs, and GaAlAs epilayers. We calculated thermal conductivity for three common types of order (CuPt-B, CuAu-I, and triple-period-A) and showed that the experimental results for In0.53Ga0.47As and In0.52Al0.48As, which are lattice matched to the InP substrate, can be reproduced in molecular dynamics simulation with 2% and 8% of random disorder, respectively. Based on our results, thermal transport in ternary III-As alloys appears to be governed by the competition between mass-difference scattering, which is much more pronounced than the VCA suggests, and the long-range order that these alloys support.

The multiple roles of computational chemistry in fragment-based drug design

NASA Astrophysics Data System (ADS)

Law, Richard; Barker, Oliver; Barker, John J.; Hesterkamp, Thomas; Godemann, Robert; Andersen, Ole; Fryatt, Tara; Courtney, Steve; Hallett, Dave; Whittaker, Mark

2009-08-01

Fragment-based drug discovery (FBDD) represents a change in strategy from the screening of molecules with higher molecular weights and physical properties more akin to fully drug-like compounds, to the screening of smaller, less complex molecules. This is because it has been recognised that fragment hit molecules can be efficiently grown and optimised into leads, particularly after the binding mode to the target protein has been first determined by 3D structural elucidation, e.g. by NMR or X-ray crystallography. Several studies have shown that medicinal chemistry optimisation of an already drug-like hit or lead compound can result in a final compound with too high molecular weight and lipophilicity. The evolution of a lower molecular weight fragment hit therefore represents an attractive alternative approach to optimisation as it allows better control of compound properties. Computational chemistry can play an important role both prior to a fragment screen, in producing a target focussed fragment library, and post-screening in the evolution of a drug-like molecule from a fragment hit, both with and without the available fragment-target co-complex structure. We will review many of the current developments in the area and illustrate with some recent examples from successful FBDD discovery projects that we have conducted.

Block Copolymer-Based Supramolecular Elastomers with High Extensibility and Large Stress Generation Capability

NASA Astrophysics Data System (ADS)

Noro, Atsushi; Hayashi, Mikihiro

We prepared block copolymer-based supramolecular elastomers with high extensibility and large stress generation capability. Reversible addition fragmentation chain transfer polymerizations were conducted under normal pressure and high pressure to synthesize several large molecular weight polystyrene-b-[poly(butyl acrylate)-co-polyacrylamide]-b-polystyrene (S-Ba-S) block copolymers. Tensile tests revealed that the largest S-Ba-S with middle block molecular weight of 3140k achieved a breaking elongation of over 2000% with a maximum tensile stress of 3.6 MPa and a toughness of 28 MJ/m3 while the reference sample without any middle block hydrogen bonds, polystyrene-b-poly(butyl acrylate)-b-polystyrene with almost the same molecular weight, was merely viscous and not self-standing. Hence, incorporation of hydrogen bonds into a long soft middle block was found to be beneficial to attain high extensibility and large stress generation capability probably due to concerted combination of entropic changes and internal potential energy changes originaing from the dissociation of multiple hydrogen bonds by elongation. This work was supported by JSPS KAKENHI Grant Numbers 13J02357, 24685035, 15K13785, and 23655213 for M.H. and A.N. A.N. also expresses his gratitude for Tanaka Rubber Science & Technology Award by Enokagaku-Shinko Foundation, Japan.

Characteristics of the mixing volume model with the interactions among spatially distributed particles for Lagrangian simulations of turbulent mixing

NASA Astrophysics Data System (ADS)

Watanabe, Tomoaki; Nagata, Koji

2016-11-01

The mixing volume model (MVM), which is a mixing model for molecular diffusion in Lagrangian simulations of turbulent mixing problems, is proposed based on the interactions among spatially distributed particles in a finite volume. The mixing timescale in the MVM is derived by comparison between the model and the subgrid scale scalar variance equation. A-priori test of the MVM is conducted based on the direct numerical simulations of planar jets. The MVM is shown to predict well the mean effects of the molecular diffusion under various conditions. However, a predicted value of the molecular diffusion term is positively correlated to the exact value in the DNS only when the number of the mixing particles is larger than two. Furthermore, the MVM is tested in the hybrid implicit large-eddy-simulation/Lagrangian-particle-simulation (ILES/LPS). The ILES/LPS with the present mixing model predicts well the decay of the scalar variance in planar jets. This work was supported by JSPS KAKENHI Nos. 25289030 and 16K18013. The numerical simulations presented in this manuscript were carried out on the high performance computing system (NEC SX-ACE) in the Japan Agency for Marine-Earth Science and Technology.

Physical chemistry: Molecular motion watched

NASA Astrophysics Data System (ADS)

Siwick, Bradley; Collet, Eric

2013-04-01

A laser pulse can switch certain crystals from an insulating phase to a highly conducting phase. The ultrafast molecular motions that drive the transition have been directly observed using electron diffraction. See Letter p.343

An electrically actuated molecular toggle switch

NASA Astrophysics Data System (ADS)

Gerhard, Lukas; Edelmann, Kevin; Homberg, Jan; Valášek, Michal; Bahoosh, Safa G.; Lukas, Maya; Pauly, Fabian; Mayor, Marcel; Wulfhekel, Wulf

2017-03-01

Molecular electronics is considered a promising approach for future nanoelectronic devices. In order that molecular junctions can be used as electrical switches or even memory devices, they need to be actuated between two distinct conductance states in a controlled and reproducible manner by external stimuli. Here we present a tripodal platform with a cantilever arm and a nitrile group at its end that is lifted from the surface. The formation of a coordinative bond between the nitrile nitrogen and the gold tip of a scanning tunnelling microscope can be controlled by both electrical and mechanical means, and leads to a hysteretic switching of the conductance of the junction by more than two orders of magnitude. This toggle switch can be actuated with high reproducibility so that the forces involved in the mechanical deformation of the molecular cantilever can be determined precisely with scanning tunnelling microscopy.

Quantum transport in alkane molecular wires: Effects of binding modes and anchoring groups

NASA Astrophysics Data System (ADS)

Sheng, W.; Li, Z. Y.; Ning, Z. Y.; Zhang, Z. H.; Yang, Z. Q.; Guo, H.

2009-12-01

Effects of binding modes and anchoring groups on nonequilibrium electronic transport properties of alkane molecular wires are investigated from atomic first-principles based on density functional theory and nonequilibrium Green's function formalism. Four typical binding modes, top, bridge, hcp-hollow, and fcc-hollow, are considered at one of the two contacts. For wires with three different anchoring groups, dithiol, diamine, or dicarboxylic acid, the low bias conductances resulting from the four binding modes are all found to have either a high or a low value, well consistent with recent experimental observations. The trend can be rationalized by the behavior of electrode-induced gap states at small bias. When bias increases to higher values, states from the anchoring groups enter into the bias window and contribute significantly to the tunneling process so that transport properties become more complicated for the four binding modes. Other low bias behaviors including the values of the inverse length scale for tunneling characteristic, contact resistance, and the ratios of the high/low conductance values are also calculated and compared to experimental results. The conducting capabilities of the three anchoring groups are found to decrease from dithiol, diamine to dicarboxylic-acid, largely owing to a decrease in binding strength to the electrodes. Our results give a clear microscopic picture to the transport physics and provide reasonable qualitative explanations for the corresponding experimental data.

Treatment Algorithms Based on Tumor Molecular Profiling: The Essence of Precision Medicine Trials.

PubMed

Le Tourneau, Christophe; Kamal, Maud; Tsimberidou, Apostolia-Maria; Bedard, Philippe; Pierron, Gaëlle; Callens, Céline; Rouleau, Etienne; Vincent-Salomon, Anne; Servant, Nicolas; Alt, Marie; Rouzier, Roman; Paoletti, Xavier; Delattre, Olivier; Bièche, Ivan

2016-04-01

With the advent of high-throughput molecular technologies, several precision medicine (PM) studies are currently ongoing that include molecular screening programs and PM clinical trials. Molecular profiling programs establish the molecular profile of patients' tumors with the aim to guide therapy based on identified molecular alterations. The aim of prospective PM clinical trials is to assess the clinical utility of tumor molecular profiling and to determine whether treatment selection based on molecular alterations produces superior outcomes compared with unselected treatment. These trials use treatment algorithms to assign patients to specific targeted therapies based on tumor molecular alterations. These algorithms should be governed by fixed rules to ensure standardization and reproducibility. Here, we summarize key molecular, biological, and technical criteria that, in our view, should be addressed when establishing treatment algorithms based on tumor molecular profiling for PM trials. © The Author 2015. Published by Oxford University Press.

The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages.

PubMed

Soares, André E R; Schrago, Carlos G

2015-01-07

Although taxon sampling is commonly considered an important issue in phylogenetic inference, it is rarely considered in the Bayesian estimation of divergence times. In fact, the studies conducted to date have presented ambiguous results, and the relevance of taxon sampling for molecular dating remains unclear. In this study, we developed a series of simulations that, after six hundred Bayesian molecular dating analyses, allowed us to evaluate the impact of taxon sampling on chronological estimates under three scenarios of among-lineage rate heterogeneity. The first scenario allowed us to examine the influence of the number of terminals on the age estimates based on a strict molecular clock. The second scenario imposed an extreme example of lineage specific rate variation, and the third scenario permitted extensive rate variation distributed along the branches. We also analyzed empirical data on selected mitochondrial genomes of mammals. Our results showed that in the strict molecular-clock scenario (Case I), taxon sampling had a minor impact on the accuracy of the time estimates, although the precision of the estimates was greater with an increased number of terminals. The effect was similar in the scenario (Case III) based on rate variation distributed among the branches. Only under intensive rate variation among lineages (Case II) taxon sampling did result in biased estimates. The results of an empirical analysis corroborated the simulation findings. We demonstrate that taxonomic sampling affected divergence time inference but that its impact was significant if the rates deviated from those derived for the strict molecular clock. Increased taxon sampling improved the precision and accuracy of the divergence time estimates, but the impact on precision is more relevant. On average, biased estimates were obtained only if lineage rate variation was pronounced. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evidence in Gabon for an intrafamilial clustering with mother-to-child and sexual transmission of a new molecular variant of human T-lymphotropic virus type-II subtype B.

PubMed

Tuppin, P; Gessain, A; Kazanji, M; Mahieux, R; Cosnefroy, J Y; Tekaia, F; Georges-Courbot, M C; Georges, A; de Thé, G

1996-01-01

Following the observation of an HTLV-II seropositive 60-year-old woman living in Gabon (Central Africa), a serologic and molecular study of her family members was conducted in an attempt to determine the duration of the HTLV-II infection and the modes of transmission of the virus. Among 41 family members, five were HTLV-I seropositive and 7 exhibited specific HTLV-II antibodies in their sera as demonstrated by high immunofluorescence titers on C19 cells and/or specific Western-blot pattern. The second husband of the index case and two of his sisters were infected by the virus, suggesting the presence of HTLV-II in this family over two generations. Sequence analysis of an amplified fragment of 172 nucleotides within the gp21 of the env region (6469-6640) of four HTLV-II infected individuals revealed a new HTLV-II molecular variant of the subtype b diverging from the prototypes NRA and G12 by seven (4.1%) and five (2.9%) bases substitutions, respectively. Molecular analysis of the total env gene (1462 bp) and fragments of the pol and pX regions confirmed that this new African variant was the most divergent HTLV-II subtype b yet described, exhibiting 2.3% of nucleotide substitutions in the env gene (33 bases) as compared to the two HTLV-II b prototypes. These data demonstrate, for the first time in Africa, intrafamilial both mother-to-child transmission and sexual transmission between spouses of an HTLV-II b molecular variant, and also suggest that this virus has been present in Gabon for a long period of time.

The principle of respect for autonomy – Concordant with the experience of oncology physicians and molecular biologists in their daily work?

PubMed Central

Ebbesen, Mette; Pedersen, Birthe D

2008-01-01

Background This article presents results from a qualitative empirical investigation of how Danish oncology physicians and Danish molecular biologists experience the principle of respect for autonomy in their daily work. Methods This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. Results We found that that molecular biologists consider the principle of respect for autonomy as a negative obligation, where the informed consent of patients or research subjects should be respected. Furthermore, molecular biologists believe that very sick patients are constraint by the circumstances to a certain choice. However, in contrast to molecular biologists, oncology physicians experience the principle of respect for autonomy as a positive obligation, where the physician in dialogue with the patient performs a medical prognosis based on the patient's wishes and ideas, mutual understanding and respect. Oncology physicians believe that they have a positive obligation to adjust to the level of the patient when providing information making sure that the patient understands. Oncology physicians experience situations where the principle of respect for autonomy does not apply because the patient is in a difficult situation. Conclusion In this study we explore the moral views and attitudes of oncology physicians and molecular biologists and compare these views with bioethical theories of the American bioethicists Tom L. Beauchamp & James F. Childress and the Danish philosophers Jakob Rendtorff & Peter Kemp. This study shows that essential parts of the two bioethical theories are reflected in the daily work of Danish oncology physicians and Danish molecular biologists. However, the study also explores dimensions where the theories can be developed further to be concordant with biomedical practice. The hope is that this study enhances the understanding of the principle of respect for autonomy and the way it is practiced. PMID:18366749

Ultra-low Thermal Conductivity in Si/Ge Hierarchical Superlattice Nanowire.

PubMed

Mu, Xin; Wang, Lili; Yang, Xueming; Zhang, Pu; To, Albert C; Luo, Tengfei

2015-11-16

Due to interfacial phonon scattering and nanoscale size effect, silicon/germanium (Si/Ge) superlattice nanowire (SNW) can have very low thermal conductivity, which is very attractive for thermoelectrics. In this paper, we demonstrate using molecular dynamics simulations that the already low thermal conductivity of Si/Ge SNW can be further reduced by introducing hierarchical structure to form Si/Ge hierarchical superlattice nanowire (H-SNW). The structural hierarchy introduces defects to disrupt the periodicity of regular SNW and scatters coherent phonons, which are the key contributors to thermal transport in regular SNW. Our simulation results show that periodically arranged defects in Si/Ge H-SNW lead to a ~38% reduction of the already low thermal conductivity of regular Si/Ge SNW. By randomizing the arrangement of defects and imposing additional surface complexities to enhance phonon scattering, further reduction in thermal conductivity can be achieved. Compared to pure Si nanowire, the thermal conductivity reduction of Si/Ge H-SNW can be as large as ~95%. It is concluded that the hierarchical structuring is an effective way of reducing thermal conductivity significantly in SNW, which can be a promising path for improving the efficiency of Si/Ge-based SNW thermoelectrics.

Ultra-low Thermal Conductivity in Si/Ge Hierarchical Superlattice Nanowire

PubMed Central

Mu, Xin; Wang, Lili; Yang, Xueming; Zhang, Pu; To, Albert C.; Luo, Tengfei

2015-01-01

Due to interfacial phonon scattering and nanoscale size effect, silicon/germanium (Si/Ge) superlattice nanowire (SNW) can have very low thermal conductivity, which is very attractive for thermoelectrics. In this paper, we demonstrate using molecular dynamics simulations that the already low thermal conductivity of Si/Ge SNW can be further reduced by introducing hierarchical structure to form Si/Ge hierarchical superlattice nanowire (H-SNW). The structural hierarchy introduces defects to disrupt the periodicity of regular SNW and scatters coherent phonons, which are the key contributors to thermal transport in regular SNW. Our simulation results show that periodically arranged defects in Si/Ge H-SNW lead to a ~38% reduction of the already low thermal conductivity of regular Si/Ge SNW. By randomizing the arrangement of defects and imposing additional surface complexities to enhance phonon scattering, further reduction in thermal conductivity can be achieved. Compared to pure Si nanowire, the thermal conductivity reduction of Si/Ge H-SNW can be as large as ~95%. It is concluded that the hierarchical structuring is an effective way of reducing thermal conductivity significantly in SNW, which can be a promising path for improving the efficiency of Si/Ge-based SNW thermoelectrics. PMID:26568511

Unconventional Current Scaling and Edge Effects for Charge Transport through Molecular Clusters

PubMed Central

2017-01-01

Metal–molecule–metal junctions are the key components of molecular electronics circuits. Gaining a microscopic understanding of their conducting properties is central to advancing the field. In the present contribution, we highlight the fundamental differences between single-molecule and ensemble junctions focusing on the fundamentals of transport through molecular clusters. In this way, we elucidate the collective behavior of parallel molecular wires, bridging the gap between single molecule and large-area monolayer electronics, where even in the latter case transport is usually dominated by finite-size islands. On the basis of first-principles charge-transport simulations, we explain why the scaling of the conductivity of a junction has to be distinctly nonlinear in the number of molecules it contains. Moreover, transport through molecular clusters is found to be highly inhomogeneous with pronounced edge effects determined by molecules in locally different electrostatic environments. These effects are most pronounced for comparably small clusters, but electrostatic considerations show that they prevail also for more extended systems. PMID:29043825

Atomistic characterisation of Li+ mobility and conductivity in Li(7-x)PS(6-x)Ix argyrodites from molecular dynamics simulations, solid-state NMR, and impedance spectroscopy.

PubMed

Pecher, Oliver; Kong, Shiao-Tong; Goebel, Thorsten; Nickel, Vera; Weichert, Katja; Reiner, Christof; Deiseroth, Hans-Jörg; Maier, Joachim; Haarmann, Frank; Zahn, Dirk

2010-07-26

The atomistic mechanisms of Li(+) ion mobility/conductivity in Li(7-x)PS(6-x)I(x) argyrodites are explored from both experimental and theoretical viewpoints. Ionic conductivity in the title compound is associated with a solid-solid phase transition, which was characterised by low-temperature differential scanning calorimetry, (7)Li and (127)I NMR investigations, impedance measurements and molecular dynamics simulations. The NMR signals of both isotopes are dominated by anisotropic interactions at low temperatures. A significant narrowing of the NMR signal indicates a motional averaging of the anisotropic interactions above 177+/-2 K. The activation energy to ionic conductivity was assessed from both impedance spectroscopy and molecular dynamics simulations. The latter revealed that a series of interstitial sites become accessible to the Li(+) ions, whilst the remaining ions stay at their respective sites in the argyrodite lattice. The interstitial positions each correspond to the centres of tetrahedra of S/I atoms, and differ only in terms of their common corners, edges, or faces with adjacent PS(4) tetrahedra. From connectivity analyses and free-energy rankings, a specific tetrahedron is identified as the key restriction to ionic conductivity, and is clearly differentiated from local mobility, which follows a different mechanism with much lower activation energy. Interpolation of the lattice parameters as derived from X-ray diffraction experiments indicates a homogeneity range for Li(7-x)PS(6-x)I(x) with 0.97 < or = x < or = 1.00. Within this range, molecular dynamics simulations predict Li(+) conductivity at ambient conditions to vary considerably.

Studies on Molecular and Ion Transport in Silicalite Membranes and Applications as Ion Separator for Redox Flow Battery

NASA Astrophysics Data System (ADS)

Yang, Ruidong

Microporous zeolite membranes have been widely studied for molecular separations based on size exclusion or preferential adsorption-diffusion mechanisms. The MFI-type zeolite membranes were also demonstrated for brine water desalination by molecular sieving effect. In this research, the pure silica MFI-type zeolite (i.e. silicalite) membrane has been for the first time demonstrated for selective permeation of hydrated proton (i.e. H3O+) in acidic electrolyte solutions. The silicalite membrane allows for permeation of H 3O+ ions, but is inaccessible to the large hydrated multivalent vanadium ions due to steric effect. The silicalite membrane has been further demonstrated as an effective ion separator in the all-vanadium redox flow battery (RFB).The silicalite is nonionic and its proton conductivity relies on the electric field-driven H3O+ transport through the sub nanometer-sized pores under the RFB operation conditions. The silicalite membrane displayed a significantly reduced self-discharge rate because of its high proton-to-vanadium ion transport selectivity. However, the nonionic nature of the silicalite membrane and very small diffusion channel size render low proton conductivity and is therefore inefficient as ion exchange membranes (IEMs) for practical applications. The proton transport efficiency may be improved by reducing the membrane thickness. However, the zeolite thin films are extremely fragile and must be supported on mechanically strong and rigid porous substrates. In this work, silicalite-Nafion composite membranes were synthesized to achieve a colloidal silicalite skin on the Nafion thin film base. The "colloidal zeolite-ionic polymer" layered composite membrane combines the advantages of high proton-selectivity of the zeolite layer and the mechanical flexibility and low proton transport resistance of the ionic polymer membrane. The composite membrane exhibited higher proton/vanadium ion separation selectivity and lower electrical resistance than the commercial Nafion 117 membrane. The high proton transport selectivity is a result of the molecular sieving effect between the H3O+ and multivalent vanadium ions by the zeolitic pores; thus the zeolite particles significantly reduced the effective membrane surface area for vanadium ion permeation. The low resistance of the composite membrane can be attributed to the reduced thickness of the Nafion base film and the thinness of the colloidal silicalite top layer. The composite membrane outperformed the Nafion 117 membrane in the vanadium RFB operation in terms of the overall charge-discharge energy efficiency. Efforts have been made in further investigation of ion and molecular transport diffusivity in the polycrystalline silicalite film using zeolite-coated optical fiber interferometers. A physical model has been established for analyzing the molecular diffusivity in the zeolite layer based on the temporal responses of the optical interferometric signals during the transient process of molecular sorption. Experiments were first carried out to study the diffusivity of isobutane to evaluate the effectiveness of the proposed optical method. The isobutane diffusivities in silicalite measured by this method were in good agreement with the values reported in literature. The zeolite coated fiber optic interferometer was however ineffective in monitoring ion sorption or ion exchange in the silicalite films. It is suggested that more sensitive fiber optic devices are needed for studying the ion diffusion.

Evaluation of electrical conductivity and equations of state of non-ideal plasma through microsecond timescale underwater electrical wire explosion

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

Sheftman, D.; Krasik, Ya. E.

2011-09-15

Experimental and simulation results of underwater electrical Cu, Al, and W wire explosions in the microsecond timescale are presented. It was shown that the electrical conductivity results for Cu and Al agree well with modified Lee-More and quantum molecular dynamic models for temperatures above 10 kK. The equation of state (EOS) values based on SESAME tables for Cu and Al were slightly modified for intermediate temperatures in order to obtain fitting between experimental and simulated exploding wire radial expansion. Also, it was shown that the electrical conductivity results and the EOS evaluation differ significantly from the results obtained in nanosecondmore » timescale experiments. Finally, it was found that underwater electrical W wire explosion is characterized by the appearance of non-uniformities along the z-axis of the wire. This phenomena adds uncertainty to the possibility of applying this type of experiments for evaluation of the electrical conductivity and EOS of W.« less

Crucial role of decoherence for electronic transport in molecular wires: Polyaniline as a case study

NASA Astrophysics Data System (ADS)

Cattena, Carlos J.; Bustos-Marún, Raúl A.; Pastawski, Horacio M.

2010-10-01

In this work we attempt to elucidate the nature of conductivity in polymers by taking the acid-base doped polyaniline (PAni) polymer. We evaluate the PAni conductance by using realistic ab initio parameters and including decoherent processes within the minimal parametrization model of D’Amato-Pastawski. In contrast to general wisdom, which associates the conducting state with coherent propagation in a periodic polaronic lattice, we show that decoherence can account for high conductance in the strongly disordered bipolaronic lattice. Hence, according to our results, there is no need of considering a mix model of “conducting” polaronic lattice islands separated by “insulating” bipolaronic lattice strands as is usually assumed for PAni. We find that without dephasing events, even very short strands of bipolaronic lattices are not able to sustain electronic transport. We also include a discussion of specific mechanisms that should be involved in decoherence rates of PAni and relate them with Marcus-Hush theory of electron transfer.

Atomic and Molecular Layer Deposition for Enhanced Lithium Ion Battery Electrodes and Development of Conductive Metal Oxide/Carbon Composites

NASA Astrophysics Data System (ADS)

Travis, Jonathan

The performance and safety of lithium-ion batteries (LIBs) are dependent on interfacial processes at the positive and negative electrodes. For example, the surface layers that form on cathodes and anodes are known to affect the kinetics and capacity of LIBs. Interfacial reactions between the electrolyte and the electrodes are also known to initiate electrolyte combustion during thermal runaway events that compromise battery safety. Atomic layer deposition (ALD) and molecular layer deposition (MLD) are thin film deposition techniques based on sequential, self-limiting surface reactions. ALD and MLD can deposit ultrathin and conformal films on high aspect ratio and porous substrates such as composite particulate electrodes in lithium-ion batteries. The effects of electrode surface modification via ALD and MLD are studied using a variety of techniques. It was found that sub-nm thick coatings of Al2O 3 deposited via ALD have beneficial effects on the stability of LIB anodes and cathodes. These same Al2O3 ALD films were found to improve the safety of graphite based anodes through prevention of exothermic solid electrolyte interface (SEI) degradation at elevated temperatures. Ultrathin and conformal metal alkoxide polymer films known as "metalcones" were grown utilizing MLD techniques with trimethylaluminum (TMA) or titanium tetrachloride (TiCl4) and organic diols or triols, such as ethylene glycol (EG), glycerol (GL) or hydroquinone (HQ), as the reactants. Pyrolysis of these metalcone films under inert gas conditions led to the development of conductive metal oxide/carbon composites. The composites were found to contain sp2 carbon using micro-Raman spectroscopy in the pyrolyzed films with pyrolysis temperatures ≥ 600°C. Four point probe measurements demonstrated that the graphitic sp2 carbon domains in the metalcone films grown using GL and HQ led to significant conductivity. The pyrolysis of conformal MLD films to obtain conductive metal oxide/carbon composite films is presented as a method for enabling non-conductive, but possibly electrochemically active materials, to be used for electrochemical applications.

Assessment of knowledge of participants on basic molecular biology techniques after 5-day intensive molecular biology training workshops in Nigeria.

PubMed

Yisau, J I; Adagbada, A O; Bamidele, T; Fowora, M; Brai, B I C; Adebesin, O; Bamidele, M; Fesobi, T; Nwaokorie, F O; Ajayi, A; Smith, S I

2017-07-08

The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of Medical Research (NIMR), to improve the knowledge and skills of laboratory personnel and academics in health, research, and educational facilities. Five-day molecular biology workshops were conducted annually between 2011 and 2014, with participants drawn from health, research facilities, and the academia. The courses consisted of theoretical and practical sessions. The impact of the workshops on knowledge and skill acquisition was evaluated by pre- and post-tests which consisted of 25 multiple choice and other questions. Sixty-five participants took part in the workshops. The mean knowledge of molecular biology as evaluated by the pre- and post-test assessments were 8.4 (95% CI 7.6-9.1) and 13.0 (95 CI 11.9-14.1), respectively. The mean post-test score was significantly greater than the mean pre-test score (p < 0.0001). The five-day molecular biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):313-317, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Expression and permeation properties of the K(+) channel Kir7.1 in the retinal pigment epithelium.

PubMed

Shimura, M; Yuan, Y; Chang, J T; Zhang, S; Campochiaro, P A; Zack, D J; Hughes, B A

2001-03-01

Bovine Kir7.1 clones were obtained from a retinal pigment epithelium (RPE)-subtracted cDNA library. Human RPE cDNA library screening resulted in clones encoding full-length human Kir7.1. Northern blot analysis indicated that bovine Kir7.1 is highly expressed in the RPE. Human Kir7.1 channels were expressed in Xenopus oocytes and studied using the two-electrode voltage-clamp technique. The macroscopic Kir7.1 conductance exhibited mild inward rectification and an inverse dependence on extracellular K+ concentration ([K+]o). The selectivity sequence based on permeability ratios was K+ (1.0) approximately Rb+ (0.89) > Cs+ (0.013) > Na+ (0.003) approximately Li+ (0.001) and the sequence based on conductance ratios was Rb+ (9.5) > K+ (1.0) > Na+ (0.458) > Cs+ (0.331) > Li+ (0.139). Non-stationary noise analysis of Rb+ currents in cell-attached patches yielded a unitary conductance for Kir7.1 of approximately 2 pS. In whole-cell recordings from freshly isolated bovine RPE cells, the predominant current was a mild inwardly rectifying K+ current that exhibited an inverse dependence of conductance on [K+]o. The selectivity sequence based on permeability ratios was K+ (1.0) approximately Rb+ (0.89) > Cs+ (0.021) > Na+ (0.003) approximately Li+ (0.002) and the sequence based on conductance ratios was Rb+ (8.9) > K+ (1.0) > Na+ (0.59) > Cs+ (0.23) > Li+ (0.08). In cell-attached recordings with Rb+ in the pipette, inwardly rectifying currents were observed in nine of 12 patches of RPE apical membrane but in only one of 13 basolateral membrane patches. Non-stationary noise analysis of Rb+ currents in cell-attached apical membrane patches yielded a unitary conductance for RPE Kir of approximately 2 pS. On the basis of this molecular and electrophysiological evidence, we conclude that Kir7.1 channel subunits comprise the K+ conductance of the RPE apical membrane.

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

Takaki, Hirokazu; Kobayashi, Kazuaki; Shimono, Masato

We present the thermoelectric properties of TiN/MgO superlattices employing first-principles calculation techniques. The Seebeck coefficients, the electrical conductances, the thermal conductances, and the figure of merit are investigated employing electrical and thermal transport calculations based on density functional theory combined with the nonequilibrium Green's function and nonequilibrium molecular dynamics simulation methods. The TiN/MgO superlattices with a small lattice mismatch at the interfaces are ideal systems to study the way for an enhancement of thermoelectric properties in artificial nanostructures. We find that the interfacial scattering between the two materials in the metal/insulator superlattices causes the electrical conductance to change rapidly, whichmore » enhances the Seebeck coefficient significantly. We show that the figure of merit for the artificial superlattice nanostructures has a much larger value compared with that of the bulk material and changes drastically with the superlattice configurations at the atomistic level.« less

Spatial resolution of the electrical conductance of ionic fluids using a Green-Kubo method.

PubMed

Jones, R E; Ward, D K; Templeton, J A

2014-11-14

We present a Green-Kubo method to spatially resolve transport coefficients in compositionally heterogeneous mixtures. We develop the underlying theory based on well-known results from mixture theory, Irving-Kirkwood field estimation, and linear response theory. Then, using standard molecular dynamics techniques, we apply the methodology to representative systems. With a homogeneous salt water system, where the expectation of the distribution of conductivity is clear, we demonstrate the sensitivities of the method to system size, and other physical and algorithmic parameters. Then we present a simple model of an electrochemical double layer where we explore the resolution limit of the method. In this system, we observe significant anisotropy in the wall-normal vs. transverse ionic conductances, as well as near wall effects. Finally, we discuss extensions and applications to more realistic systems such as batteries where detailed understanding of the transport properties in the vicinity of the electrodes is of technological importance.

Dynamic superconcentration at critical-point double-layer gates of conducting nanoporous granules due to asymmetric tangential fluxes

PubMed Central

Wang, Shau-Chun; Wei, Hsien-Hung; Chen, Hsiao-Ping; Tsai, Min-Hsuan; Yu, Chun-Ching; Chang, Hsueh-Chia

2008-01-01

A transient 106-fold concentration of double-layer counterions by a high-intensity electric field is demonstrated at the exit pole of a millimeter-sized conducting nanoporous granule that permits ion permeation. The phenomenon is attributed to a unique counterion screening dynamics that transforms half of the surface field into a converging one toward the ejecting pole. The resulting surface conduction flux then funnels a large upstream electro-osmotic convective counterion flux into the injecting hemisphere toward the zero-dimensional gate of the ejecting hemisphere to produce the superconcentration. As the concentrated counterion is ejected into the electroneutral bulk electrolyte, it attracts co-ions and produce a corresponding concentration of the co-ions. This mechanism is also shown to trap and concentrate co-ion microcolloids of micron sizes too (macroions) and hence has potential application in bead-based molecular assays. PMID:19693364

Neisseria gonorrhoeae molecular typing for understanding sexual networks and antimicrobial resistance transmission: A systematic review.

PubMed

Town, Katy; Bolt, Hikaru; Croxford, Sara; Cole, Michelle; Harris, Simon; Field, Nigel; Hughes, Gwenda

2018-06-01

Neisseria gonorrhoeae (NG) is a significant global public health concern due to rising diagnoses rates and antimicrobial resistance. Molecular combined with epidemiological data have been used to understand the distribution and spread of NG, as well as relationships between cases in sexual networks, but the public health value gained from these studies is unclear. We conducted a systematic review to examine how molecular epidemiological studies have informed understanding of sexual networks and NG transmission, and subsequent public health interventions. Five research databases were systematically searched up to 31st March 2017 for studies that used sequence-based DNA typing methods, including whole genome sequencing, and linked molecular data to patient-level epidemiological data. Data were extracted and summarised to identify common themes. Of the 49 studies included, 82% used NG Multi-antigen Sequence Typing. Gender and sexual orientation were commonly used to characterise sexual networks that were inferred using molecular clusters; clusters predominantly of one patient group often contained a small number of isolates from other patient groups. Suggested public health applications included using these data to target interventions at specific populations, confirm outbreaks, and inform partner management, but these were mainly untested. Combining molecular and epidemiological data has provided insight into sexual mixing patterns, and dissemination of NG, but few studies have applied these findings to design or evaluate public health interventions. Future studies should focus on the application of molecular epidemiology in public health practice to provide evidence for how to prevent and control NG. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Thermoelectricity in fullerene-metal heterojunctions.

PubMed

Yee, Shannon K; Malen, Jonathan A; Majumdar, Arun; Segalman, Rachel A

2011-10-12

Thermoelectricty in heterojunctions, where a single-molecule is trapped between metal electrodes, has been used to understand transport properties at organic-inorganic interfaces. (1) The transport in these systems is highly dependent on the energy level alignment between the molecular orbitals and the Fermi level (or work function) of the metal contacts. To date, the majority of single-molecule measurements have focused on simple small molecules where transport is dominated through the highest occupied molecular orbital. (2, 3) In these systems, energy level alignment is limited by the absence of electrode materials with low Fermi levels (i.e., large work functions). Alternatively, more controllable alignment between molecular orbitals and the Fermi level can be achieved with molecules whose transport is dominated by the lowest unoccupied molecular orbital (LUMO) because of readily available metals with lower work functions. Herein, we report molecular junction thermoelectric measurements of fullerene molecules (i.e., C(60), PCBM, and C(70)) trapped between metallic electrodes (i.e., Pt, Au, Ag). Fullerene junctions demonstrate the first strongly n-type molecular thermopower corresponding to transport through the LUMO, and the highest measured magnitude of molecular thermopower to date. While the electronic conductance of fullerenes is highly variable, due to fullerene's variable bonding geometries with the electrodes, the thermopower shows predictable trends based on the alignment of the LUMO with the work function of the electrodes. Both the magnitude and trend of the thermopower suggest that heterostructuring organic and inorganic materials at the nanoscale can further enhance thermoelectric performance, therein providing a new pathway for designing thermoelectric materials.

Car and Parrinello meet Green and Kubo: simulating atomic heat transport from equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Baroni, Stefano

Modern simulation methods based on electronic-structure theory have long been deemed unfit to compute heat transport coefficients within the Green-Kubo formalism. This is so because the quantum-mechanical energy density from which the heat flux is derived is inherently ill defined, thus allegedly hampering the use of the Green-Kubo formula. While this objection would actually apply to classical systems as well, I will demonstrate that the thermal conductivity is indeed independent of the specific microscopic expression for the energy density and current from which it is derived. This fact results from a kind of gauge invariance stemming from energy conservation and extensivity, which I will illustrate numerically for a classical Lennard-Jones fluid. I will then introduce an expression for the adiabatic energy flux, derived within density-functional theory, that allows simulating atomic heat transport using equilibrium ab initio molecular dynamics. The resulting methodology is demonstrated by comparing results from ab-initio and classical molecular-dynamics simulations of a model liquid-Argon system, for which accurate inter-atomic potentials are derived by the force-matching method, and applied to compute the thermal conductivity of heavy water at ambient conditions. The problem of evaluating transport coefficients along with their accuracy from relatively short trajectories is finally addressed and discussed with a few representative examples. Partially funded by the European Union through the MaX Centre of Excellence (Grant No. 676598).

Effects of polarizability on the structural and thermodynamics properties of [C{sub n}mim][Gly] ionic liquids (n = 1–4) using EEM/MM molecular dynamic simulations

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

Wu, Yang; Hu, Na; Yue, Lili

2015-02-14

An extended electronegativity equalization method/molecular mechanics (EEM/MM) model for ionic liquids is used to investigate the structures and properties of 1-alkyl-3-methylimidazolium glycine ionic liquids [C{sub n}mim][Gly] (n = 1–4) with alkyl substituents of different lengths. The EEM/MM model describes the electrostatic interactions of atoms and their changes in different ambient environments. This property is the most outstanding characteristic of the model. EEM parameters (i.e., valence electronegativities and valence hardness parameters) are calibrated using linear regression and least-squares methods, which can accurately predict the gas-phase properties of [C{sub n}mim]{sup +}, [Gly]{sup −}, and [C{sub n}mim][Gly] ion pairs. We utilize the EEM/MMmore » force field to systematically investigate the effects of polarizability on the accuracy of [C{sub n}mim][Gly] properties predicted through the molecular dynamic simulations. EEM/MM explicitly describes the atom-based polarizability of [C{sub n}mim][Gly]; thus, the densities, enthalpies of vaporization, self-diffusion coefficients, and conductivities of the [C{sub n}mim][Gly] are consistent with the experimental values. The calculated radial distribution functions provide a mechanistic understanding of the effects of polarizability on ionic aggregations in amino acid ionic liquids. The effects of alkyl chain length on the diffusion coefficient and conductivity are also discussed.« less

Challenges in initiating and conducting personalized cancer therapy trials: perspectives from WINTHER, a Worldwide Innovative Network (WIN) Consortium trial

PubMed Central

Rodon, J.; Soria, J. C.; Berger, R.; Batist, G.; Tsimberidou, A.; Bresson, C.; Lee, J. J.; Rubin, E.; Onn, A.; Schilsky, R. L.; Miller, W. H.; Eggermont, A. M.; Mendelsohn, J.; Lazar, V.; Kurzrock, R.

2015-01-01

Advances in ‘omics’ technology and targeted therapeutic molecules are together driving the incorporation of molecular-based diagnostics into the care of patients with cancer. There is an urgent need to assess the efficacy of therapy determined by molecular matching of patients with particular targeted therapies. WINTHER is a clinical trial that uses cutting edge genomic and transcriptomic assays to guide treatment decisions. Through the lens of this ambitious multinational trial (five countries, six sites) coordinated by the Worldwide Innovative Networking Consortium for personalized cancer therapy, we discovered key challenges in initiation and conduct of a prospective, omically driven study. To date, the time from study concept to activation has varied between 19 months at Gustave Roussy Cancer Campus in France to 30 months at the Segal Cancer Center, McGill University (Canada). It took 3+ years to be able to activate US sites due to national regulatory hurdles. Access to medications proposed by the molecular analysis remains a major challenge, since their availability through active clinical trials is highly variable over time within sites and across the network. Rules regarding the off-label use of drugs, or drugs not yet approved at all in some countries, pose a further challenge, and many biopharmaceutical companies lack a simple internal mechanism to supply the drugs even if they wish to do so. These various obstacles should be addressed to test and then implement precision medicine in cancer. PMID:25908602

Effect of point defects on the thermal conductivity of UO2: molecular dynamics simulations

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

Liu, Xiang-Yang; Stanek, Christopher Richard; Andersson, Anders David Ragnar

2015-07-21

The thermal conductivity of uranium dioxide (UO 2) fuel is an important materials property that affects fuel performance since it is a key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. [1] The thermal conductivity of UO 2 nuclear fuel is also affected by fission gas, fission products, defects, and microstructural features such as grain boundaries. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of irradiation induced point defects on the thermal conductivity of UO 2, as a function of defectmore » concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel [2].« less

Thermal Conductivity of Twisted Bilayer Graphene Nanoribbons from Non-equilibrium Molecular Dynamics Study.

NASA Astrophysics Data System (ADS)

Li, Chenyang; Su, Shanshan; Ge, Supeng; Lake, Roger

Misorientation of the two layers of bilayer graphene affects both the electronic properties and the vibrational modes or phonons. The phonon density of modes is little affected by misorientation, however, zone-folding can allow new Umklapp scattering processes that could affect the phonon transport and thermal conductivity. To investigate this, we use NEMD molecular dynamics simulations as implemented in LAMMPS to study the thermal conductivity of the misoriented graphene bilayers. Seven commensurate misorientation angles varying from 6.01º to 48.36º have modeled and analyzed to understand how the misorientation angle affects the thermal conductivity of relatively wide ( 10 nm) misoriented bilayer graphene nanoribbons (m-BLGNRs). Within numerical accuracy, we find that the thermal conductivity of the m-BLGNRs for all of the simulated commensurate angles have the same thermal conductivity with AB stacked and AA stacked BLGNRs. These results indicate that neither the misorientation angle nor the stacking order affect the thermal conductivity of BLGNRs. This work was supported as part by the NSF #1307671.

Negative Differential Conductance in Polyporphyrin Oligomers with Nonlinear Backbones.

PubMed

Kuang, Guowen; Chen, Shi Zhang; Yan, Linghao; Chen, Ke Qiu; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2018-01-17

We study negative differential conductance (NDC) effects in polyporphyrin oligomers with nonlinear backbones. Using a low-temperature scanning tunneling microscope, we selectively controlled the charge transport path in single oligomer wires. We observed robust NDC when charge passed through a T-shape junction, bistable NDC when charge passed through a 90° kink and no NDC when charge passed through a 120° kink. Aided by density functional theory with nonequilibrium Green's functions simulations, we attributed this backbone-dependent NDC to bias-modulated hybridization of the electrode states with the resonant transport molecular orbital. We argue this mechanism is generic in molecular systems, which opens a new route of designing molecular NDC devices.

Distinguishing Lead and Molecule States in Graphene-Based Single-Electron Transistors

PubMed Central

2017-01-01

Graphene provides a two-dimensional platform for contacting individual molecules, which enables transport spectroscopy of molecular orbital, spin, and vibrational states. Here we report single-electron tunneling through a molecule that has been anchored to two graphene leads. Quantum interference within the graphene leads gives rise to an energy-dependent transmission and fluctuations in the sequential tunnel-rates. The lead states are electrostatically tuned by a global back-gate, resulting in a distinct pattern of varying intensity in the measured conductance maps. This pattern could potentially obscure transport features that are intrinsic to the molecule under investigation. Using ensemble averaged magneto-conductance measurements, lead and molecule states are disentangled, enabling spectroscopic investigation of the single molecule. PMID:28423272

Effect of molecular weight on polymer processability

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

Karg, R.F.

1983-01-01

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

Lessons learned from implementing a wet laboratory molecular training workshop for beach water quality monitoring.

PubMed

Verhougstraete, Marc Paul; Brothers, Sydney; Litaker, Wayne; Blackwood, A Denene; Noble, Rachel

2015-01-01

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods.

Lessons Learned from Implementing a Wet Laboratory Molecular Training Workshop for Beach Water Quality Monitoring

PubMed Central

Verhougstraete, Marc Paul; Brothers, Sydney; Litaker, Wayne; Blackwood, A. Denene; Noble, Rachel

2015-01-01

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods. PMID:25822486

Development of a molecular diagnostic test for Retinitis Pigmentosa in the Japanese population.

PubMed

Maeda, Akiko; Yoshida, Akiko; Kawai, Kanako; Arai, Yuki; Akiba, Ryutaro; Inaba, Akira; Takagi, Seiji; Fujiki, Ryoji; Hirami, Yasuhiko; Kurimoto, Yasuo; Ohara, Osamu; Takahashi, Masayo

2018-05-21

Retinitis Pigmentosa (RP) is the most common form of inherited retinal dystrophy caused by different genetic variants. More than 60 causative genes have been identified to date. The establishment of cost-effective molecular diagnostic tests with high sensitivity and specificity can be beneficial for patients and clinicians. Here, we developed a clinical diagnostic test for RP in the Japanese population. Evaluation of diagnostic technology, Prospective, Clinical and experimental study. A panel of 39 genes reported to cause RP in Japanese patients was established. Next generation sequence (NGS) technology was applied for the analyses of 94 probands with RP and RP-related diseases. After interpretation of detected genetic variants, molecular diagnosis based on a study of the genetic variants and a clinical phenotype was made by a multidisciplinary team including clinicians, researchers and genetic counselors. NGS analyses found 14,343 variants from 94 probands. Among them, 189 variants in 83 probands (88.3% of all cases) were selected as pathogenic variants and 64 probands (68.1%) have variants which can cause diseases. After the deliberation of these 64 cases, molecular diagnosis was made in 43 probands (45.7%). The final molecular diagnostic rate with the current system combining supplemental Sanger sequencing was 47.9% (45 of 94 cases). The RP panel provides the significant advantage of detecting genetic variants with a high molecular diagnostic rate. This type of race-specific high-throughput genotyping allows us to conduct a cost-effective and clinically useful genetic diagnostic test.

Physiological and molecular characterization of an IRK-type inward rectifier K+ channel in a tumour mast cell line.

PubMed

Wischmeyer, E; Lentes, K U; Karschin, A

1995-04-01

The basophilic leucaemia cell line RBL-2H3 exhibits a robust inwardly rectifying potassium current, IKIR, which is likely to be modulated by G proteins. We examined the physiological and molecular properties of this KIR conductance to define the nature of the underlying channel species. The macroscopic conductance revealed characteristics typical of classical K+ inward rectifiers of the IRK type. Channel gating was rapid, first order (tau approximately 1 ms at -100 mV) and steeply voltage dependent. Both activation potential and slope conductance were dependent on extracellular K+ concentration ([K+]o) and inward rectification persisted in the absence of internal Mg2+. The current was susceptible to a concentration- and voltage-dependent block by extracellular Na+, Cs+ and Ba2+. Initial IKIR whole-cell amplitudes as well as current rundown were dependent on the presence of 1 mM internal ATP. Perfusion of intracellular guanosine 5'-Q-(3-thiotriphosphate) (GTP[gamma S]) suppressed IKIR with an average half-time of decline of approximately 400 s. It was demonstrated that the dominant IRK-type 25 pS conductance channel was indeed suppressed by 100 microM preloaded GTP[gamma S]. Reverse transcriptase-polymerase chain reactions (RT-PCR) with RBL cell poly(A)+ RNA identified a full length K+ inward rectifier with 94% base pair homology to the recently cloned mouse IRK1 channel. It is concluded that RBL cells express a classical voltage-dependent IRK-type K+ inward rectifier RBL-IRK1 which is negatively controlled by G proteins.

Water-Stable Nanoporous Polymer Films with Excellent Proton Conductivity.

PubMed

Wang, Zhengbang; Liang, Cong; Tang, Haolin; Grosjean, Sylvain; Shahnas, Artak; Lahann, Joerg; Bräse, Stefan; Wöll, Christof

2018-03-01

Achieving high values for proton conductivity in a material critically depends on providing hopping sites arranged in a regular fashion. Record values reported for regular, molecular crystals cannot yet be reached by technologically relevant systems, and the best values measured for polymer membranes suited for integration into devices are almost two orders of magnitude lower. Here, an alternative polymer membrane synthesis strategy based on the chemical modification of surface-mounted, monolithic, crystalline metal-organic framework thin films is demonstrated. Due to chemical crosslinking and subsequent removal of metal ions, these surface-mounted gels (SURGELs) are found to exhibit high proton conductivity (0.1 S cm -1 at 30 °C and 100% RH (relative humidity). These record values are attributed to the highly ordered polymer network structure containing regularly spaced carboxylic acid side groups. These covalently bound organic frameworks outperform conventional, ion-conductive polymers with regard to ion conductivity and water stability. Pronounced water-induced swelling, which causes severe mechanical instabilities in commercial membranes, is not observed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding Nanoscale Thermal Conduction an Mechanical Strength Correlation in High Temperature Ceramics with Improved Thermal Shock Resistance for Aerospace Applications

DTIC Science & Technology

2012-08-08

simulation data is available on this system. Molecular simulation , ab initio simulations , thermal conductivity, biomimetic materials, phase transformation...MOLECULAR SIMULATIONS …………….. 28 §2.2.1 THERMAL CONDUCTION ANALYSES IN SUPERLATTICES AS A FUNCTION OF STRAIN……………………………………………………………. 29 §2.2.2...analyses also focus on Si-Ge interfaces and nanocomposites, as a lot of simulation data is available on this system. In terms of modeling the required

Self-diffusion and conductivity in an ultracold strongly coupled plasma: Calculation by the method of molecular dynamics

NASA Astrophysics Data System (ADS)

Zelener, B. B.; Zelener, B. V.; Manykin, E. A.; Bronin, S. Ya; Bobrov, A. A.; Khikhlukha, D. R.

2018-01-01

We present results of calculations by the method of molecular dynamics of self-diffusion and conductivity of electron and ion components of ultracold plasma in a comparison with available theoretical and experimental data. For the ion self-diffusion coefficient, good agreement was obtained with experiments on ultracold plasma. The results of the calculation of self-diffusion also agree well with other calculations performed for the same values of the coupling parameter, but at high temperatures. The difference in the results of the conductivity calculations on the basis of the current autocorrelation function and on the basis of the diffusion coefficient is discussed.

Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore

PubMed Central

Zhou, Wenchang; Marinelli, Fabrizio; Nief, Corrine; Faraldo-Gómez, José D

2017-01-01

Pathological metabolic conditions such as ischemia induce the rupture of the mitochondrial envelope and the release of pro-apoptotic proteins, leading to cell death. At the onset of this process, the inner mitochondrial membrane becomes depolarized and permeable to osmolytes, proposedly due to the opening of a non-selective protein channel of unknown molecular identity. A recent study purports that this channel, referred to as Mitochondrial Permeability Transition Pore (MPTP), is formed within the c-subunit ring of the ATP synthase, upon its dissociation from the catalytic domain of the enzyme. Here, we examine this claim for two c-rings of different lumen width, through calculations of their ion conductance and selectivity based on all-atom molecular dynamics simulations. We also quantify the likelihood that the lumen of these c-rings is in a hydrated, potentially conducting state rather than empty or blocked by lipid molecules. These calculations demonstrate that the structure and biophysical properties of a correctly assembled c-ring are inconsistent with those attributed to the MPTP. DOI: http://dx.doi.org/10.7554/eLife.23781.001 PMID:28186490

Adsorption properties of chloropicrin on pristine and borazine-doped nanographenes: A theoretical study

NASA Astrophysics Data System (ADS)

Hosseinian, Akram; Vessally, Esmail; Babazadeh, Mirzaagha; Edjlali, Ladan; Es'haghi, Moosa

2018-04-01

Recently, nanographenes were introduced as definite segments of graphene where their end atoms are saturated with hydrogens. In this study, we explored the reactivity and electronic sensitivity of a hexa-peri-hexabenzocoronene (HBC) and newly synthesized borazine-like ring-doped nanographenes (BNG) to the chloropicrin molecule based on density functional theory. We found that chloropicrin is preferentially adsorbed via its N atoms on both HBC and BNG nanographenes. The electronic properties of HBC were predicted to be sensitive to chloropicrin but the adsorption capacity is low because of the small adsorption energy (-7.1 kcal/mol). However, chloropicrin is adsorbed somewhat more strongly on BNG, with an adsorption energy of about -29.9 kcal/mol. After the adsorption of chloropicrin, the lowest unoccupied molecular orbital (LUMO) level of BNG stabilizes and the highest occupied molecular orbital-LUMO gap is decreased by about 85.9%. Thus, BNG converts from a semiconductor into a semimetal with a higher electrical conductivity. The change in electrical conductivity can generate an electrical signal, which is helpful for detecting chloropicrin. In addition, we predicted a short recovery time of 14.6 s at 350 K for this sensor.

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

Kadoura, Ahmad, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Sun, Shuyu, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Siripatana, Adil, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa

In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercriticalmore » isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH{sub 4}, N{sub 2}, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO{sub 2} and C{sub 2} H{sub 6}.« less

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.

Phase Transition of Single-Layer Molybdenum Disulfide Nanosheets under Mechanical Loading Based on Molecular Dynamics Simulations.

PubMed

Pang, Haosheng; Li, Minglin; Gao, Chenghui; Huang, Haili; Zhuo, Weirong; Hu, Jianyue; Wan, Yaling; Luo, Jing; Wang, Weidong

2018-03-27

The single-layer molybdenum disulfide (SLMoS2) nanosheets have been experimentally discovered to exist in two different polymorphs, which exhibit different electrical properties, metallic or semiconducting. Herein, molecular dynamics (MD) simulations of nanoindentation and uniaxial compression were conducted to investigate the phase transition of SLMoS2 nanosheets. Typical load-deflection curves, stress-strain curves, and local atomic structures were obtained. The loading force decreases sharply and then increases again at a critical deflection under the nanoindentation, which is inferred to the phase transition. In addition to the layer thickness, some related bond lengths and bond angles were also found to suddenly change as the phase transition occurs. A bell-like hollow, so-called residual deformation, was found to form, mainly due to the lattice distortion around the waist of the bell. The effect of indenter size on the residual hollow was also analyzed. Under the uniaxial compression along the armchair direction, a different phase transition, a uniformly quadrilateral structure, was observed when the strain is greater than 27.7%. The quadrilateral structure was found to be stable and exhibit metallic conductivity in view of the first-principle calculation.

The Effects of the Organic-Inorganic Interactions on the Thermal Transport Properties of CH3NH3PbI3.

PubMed

Hata, Tomoyuki; Giorgi, Giacomo; Yamashita, Koichi

2016-04-13

Methylammonium lead iodide perovskite (CH3NH3PbI3), the most investigated hybrid organic-inorganic halide perovskite, is characterized by a quite low thermal conductivity. The rotational motion of methylammonium cations is considered responsible for phonon transport suppression; however, to date, the specific mechanism of the process has not been clarified. In this study, we elucidate the role of rotations in thermal properties based on molecular dynamics simulations. To do it, we developed an empirical potential for CH3NH3PbI3 by fitting to ab initio calculations and evaluated its thermal conductivity by means of nonequilibrium molecular dynamics. Results are compared with model systems that include different embedded cations, and this comparison shows a dominant suppression effect provided by rotational motions. We also checked the temperature dependence of the vibrational density of states and specified the energy range in which anharmonic couplings occur. By means of phonon dispersion analysis, we were able to fully elucidate the suppression mechanism: the rotations are coupled with translational motions of cations, via which inorganic lattice vibrations are coupled and scatter each other.

Molecular Testing for miRNA, mRNA, and DNA on Fine-Needle Aspiration Improves the Preoperative Diagnosis of Thyroid Nodules With Indeterminate Cytology.

PubMed

Labourier, Emmanuel; Shifrin, Alexander; Busseniers, Anne E; Lupo, Mark A; Manganelli, Monique L; Andruss, Bernard; Wylie, Dennis; Beaudenon-Huibregtse, Sylvie

2015-07-01

Molecular testing for oncogenic mutations or gene expression in fine-needle aspirations (FNAs) from thyroid nodules with indeterminate cytology identifies a subset of benign or malignant lesions with high predictive value. This study aimed to evaluate a novel diagnostic algorithm combining mutation detection and miRNA expression to improve the diagnostic yield of molecular cytology. Surgical specimens and preoperative FNAs (n = 638) were tested for 17 validated gene alterations using the miRInform Thyroid test and with a 10-miRNA gene expression classifier generating positive (malignant) or negative (benign) results. Cross-sectional sampling of thyroid nodules with atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS) or follicular neoplasm/suspicious for a follicular neoplasm (FN/SFN) cytology (n = 109) was conducted at 12 endocrinology centers across the United States. Qualitative molecular results were compared with surgical histopathology to determine diagnostic performance and model clinical effect. Mutations were detected in 69% of nodules with malignant outcome. Among mutation-negative specimens, miRNA testing correctly identified 64% of malignant cases and 98% of benign cases. The diagnostic sensitivity and specificity of the combined algorithm was 89% (95% confidence interval [CI], 73-97%) and 85% (95% CI, 75-92%), respectively. At 32% cancer prevalence, 61% of the molecular results were benign with a negative predictive value of 94% (95% CI, 85-98%). Independently of variations in cancer prevalence, the test increased the yield of true benign results by 65% relative to mRNA-based gene expression classification and decreased the rate of avoidable diagnostic surgeries by 69%. Multiplatform testing for DNA, mRNA, and miRNA can accurately classify benign and malignant thyroid nodules, increase the diagnostic yield of molecular cytology, and further improve the preoperative risk-based management of benign nodules with AUS/FLUS or FN/SFN cytology.

Electronic Transport through Self Assembled Thiol Molecules: Effect of Monolayer Order, Dynamics and Temperature

NASA Technical Reports Server (NTRS)

Dholakia, Geetha; Fan, Wendy; Meyyappan, M.

2005-01-01

We present the charge transport and tunneling conductance of self assembled organic thiol molecules and discuss the influence of order and dynamics in the monolayer on the transport behavior and the effect of temperature. Conjugated thiol molecular wires and organometals such as terpyridine metal complexes provide a new platform for molecular electronic devices and we study their self assembly on Au(111) substrates by the scanning tunneling microscope. Determining the organization of the molecule and the ability to control the nature of its interface with the substrate is important for reliable performance of the molecular electronic devices. By concurrent scanning tunneling microscopy and spectroscopy studies on SAMs formed from oligo (phenelyne ethynelyne) monolayers with and without molecular order, we show that packing and order determine the response of a self assembled monolayer (SAM) to competing interactions. Molecular resolution STM imaging in vacuum shows that the OPES adopt an imcommensurate SAM structure on Au(111) with a rectangular unit cell. Tunneling spectroscopic measurements were performed on the SAM as a function of junction resistance. STS results show that the I-Vs are non linear and asymmetric due to the inherent asymmetry in the molecular structure, with larger currents at negative sample biases. The asymmetry increases with increasing junction resistance due to the asymmetry in the coupling to the leads. This is brought out clearly in the differential conductance, which also shows a gap at the Fermi level. We also studied the effect of order and dynamics in the monolayer on the charge transport and found that competing forces between the electric field, intermolecular interactions, tip-molecule physisorption and substrate-molecule chemisorption impact the transport measurements and its reliability and that the presence of molecular order is very important for reproducible transport measurements. Thus while developing new electronic platforms based on molecules, it is important to have a good control of the molecule-substrate interface, for the devices to perform reliably. While such a control would minimize fluctuations and dynamics in the ensemble, the real challenge is to develop device architectures that are tolerant to fluctuations, since they cannot be totally eliminated in these low dimensional soft systems. Results of temperature dependent STS measurements will also be discussed.

Molecular confocal laser endomicroscopy: a novel technique for in vivo cellular characterization of gastrointestinal lesions.

PubMed

Karstensen, John Gásdal; Klausen, Pia Helene; Saftoiu, Adrian; Vilmann, Peter

2014-06-28

While flexible endoscopy is essential for macroscopic evaluation, confocal laser endomicroscopy (CLE) has recently emerged as an endoscopic method enabling visualization at a cellular level. Two systems are currently available, one based on miniprobes that can be inserted via a conventional endoscope or via a needle guided by endoscopic ultrasound. The second system has a confocal microscope integrated into the distal part of an endoscope. By adding molecular probes like fluorescein conjugated antibodies or fluorescent peptides to this procedure (either topically or systemically administered during on-going endoscopy), a novel world of molecular evaluation opens up. The method of molecular CLE could potentially be used for estimating the expression of important receptors in carcinomas, subsequently resulting in immediate individualization of treatment regimens, but also for improving the diagnostic accuracy of endoscopic procedures by identifying otherwise invisible mucosal lesions. Furthermore, studies have shown that fluorescein labelled drugs can be used to estimate the affinity of the drug to a target organ, which probably can be correlated to the efficacy of the drug. However, several of the studies in this research field have been conducted in animal facilities or in vitro, while only a limited number of trials have actually been carried out in vivo. Therefore, safety issues still needs further evaluations. This review will present an overview of the implications and pitfalls, as well as future challenges of molecular CLE in gastrointestinal diseases.

A RAD-based phylogenetics for Orestias fishes from Lake Titicaca.

PubMed

Takahashi, Tetsumi; Moreno, Edmundo

2015-12-01

The fish genus Orestias is endemic to the Andes highlands, and Lake Titicaca is the centre of the species diversity of the genus. Previous phylogenetic studies based on a single locus of mitochondrial and nuclear DNA strongly support the monophyly of a group composed of many of species endemic to the Lake Titicaca basin (the Lake Titicaca radiation), but the relationships among the species in the radiation remain unclear. Recently, restriction site-associated DNA (RAD) sequencing, which can produce a vast number of short sequences from various loci of nuclear DNA, has emerged as a useful way to resolve complex phylogenetic problems. To propose a new phylogenetic hypothesis of Orestias fishes of the Lake Titicaca radiation, we conducted a cluster analysis based on morphological similarities among fish samples and a molecular phylogenetic analysis based on RAD sequencing. From a morphological cluster analysis, we recognised four species groups in the radiation, and three of the four groups were resolved as monophyletic groups in maximum-likelihood trees based on RAD sequencing data. The other morphology-based group was not resolved as a monophyletic group in molecular phylogenies, and some members of the group were diverged from its sister group close to the root of the Lake Titicaca radiation. The evolution of these fishes is discussed from the phylogenetic relationships. Copyright © 2015 Elsevier Inc. All rights reserved.

Pressure effect on phonon frequencies in some transition metals: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Kazanc, S.; Ozgen, S.

2005-08-01

It is important to determine the atomic lattice vibrations of metallic materials, under high-pressure conditions, due to its effects on material properties such as thermal, electrical and optical conductions. In this work, we have investigated the changes of acoustic phonon frequencies with hydrostatic pressure for Cu, Ni, Al, Ag and Au transition metals, using molecular dynamics (MD) simulations based on embedded atom method (EAM). For this aim, we have adopted the embedded atom potential proposed by Sutton and Chen. The phonon frequencies have been calculated from the dynamical matrix for [1 0 0], [1 1 0] and [1 1 1] high symmetry directions of the Brillouin zone. The obtained results show that the hydrostatic pressure causes an increment in phonon frequencies, and this rising do not depend linearly on the increasing pressure.

From "seahorse" to "molecular Recording"

NASA Astrophysics Data System (ADS)

Gao, Hong-Jun

2002-08-01

We will first present unique dendritic "seahorse" patterns observed when we study structural features in functional C60-TCNQ complex thin films, and their formation mechanism. Then we report a new process for ultrahigh density, erasable data storage, based on the molecular electrical bistability of an organic charge transfer complex, 3-nitrobenzal malononitrile and 1,4-phenylenediamine (NBMN-pDA). Switched by a voltage pulse from a scanning tunneling microscope (STM), we demonstrate a data density exceeding 1013 bits/cm2. The experiment results and theoretical ab initio calculations show the writing and erasing mechanism to be a conductance transition of the organic compound due to a structural change from crystalline to noncrystalline. The ultimate bit density appears limited only by the size of the organic complex, less than 1 nm in our case, corresponding to 1014 bits/cm2.

Molecular transport through large-diameter DNA nanopores

NASA Astrophysics Data System (ADS)

Krishnan, Swati; Ziegler, Daniela; Arnaut, Vera; Martin, Thomas G.; Kapsner, Korbinian; Henneberg, Katharina; Bausch, Andreas R.; Dietz, Hendrik; Simmel, Friedrich C.

2016-09-01

DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ~4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ~3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration.

Experimental and theoretical analysis of nanofluids based on high temperature-heat transfer fluid with enhanced thermal properties

NASA Astrophysics Data System (ADS)

Navas, Javier; Sánchez-Coronilla, Antonio; Martín, Elisa I.; Gómez-Villarejo, Roberto; Teruel, Miriam; Gallardo, Juan Jesús; Aguilar, Teresa; Alcántara, Rodrigo; Fernández-Lorenzo, Concha; Martín-Calleja, Joaquín

2017-04-01

In this work, nanofluids were prepared using commercial Cu nanoparticles and a commercial high temperature-heat transfer Fluid (eutectic mixture of diphenyl oxide and biphenyl) as the base fluid, which is used in concentrating solar power (CSP) plants. Different properties such as density, viscosity, heat capacity and thermal conductivity were characterized. Nanofluids showed enhanced heat transfer efficiency. In detail, the incorporation of Cu nanoparticles led to an increase of the heat capacity up to 14%. Also, thermal conductivity was increased up to 13%. Finally, the performance of the nanofluids prepared increased up to 11% according to the Dittus-Boelter correlation. On the other hand, equilibrium molecular dynamics simulation was used to model the experimental nanofluid system studied. Thermodynamic properties such as heat capacity and thermal conductivity were calculated and the results were compared with experimental data. The analysis of the radial function distributions (RDFs) and the inspection of the spatial distribution functions (SDFs) indicate the important role that plays the metal-oxygen interaction in the system. Dynamic properties such as the diffusion coefficients of base fluid and nanofluid were computed according to Einstein relation by computing the mean square displacement (MSD). Supplementary online material is available in electronic form at http://www.epjap.org

Two orders of magnitude reduction in silicon membrane thermal conductivity by resonance hybridizations

NASA Astrophysics Data System (ADS)

Honarvar, Hossein; Hussein, Mahmoud I.

2018-05-01

The thermal conductivity of a freestanding single-crystal silicon membrane may be reduced significantly by attaching nanoscale pillars on one or both surfaces. Atomic resonances of the nanopillars form vibrons that intrinsically couple with the base membrane phonons causing mode hybridization and flattening at each coupling location in the phonon band structure. This in turn causes group velocity reductions of existing phonons, in addition to introducing new modes that get excited but are localized and do not transport energy. The nanopillars also reduce the phonon lifetimes at and around the hybridization zones. These three effects, which in principle may be tuned to take place across silicon's full spectrum, lead to a lowering of the in-plane thermal conductivity in the base membrane. Using equilibrium molecular dynamics simulations, and utilizing the concept of vibrons compensation, we report a staggering two orders of magnitude reduction in the thermal conductivity at room temperature by this mechanism. Specifically, a reduction of a factor of 130 is demonstrated for a roughly 10-nm-thick pillared membrane compared to a corresponding unpillared membrane. This amounts to a record reduction of a factor of 481 compared to bulk crystalline silicon and nearly a factor of 2 compared to bulk amorphous silicon. These results are obtained while providing a path for preserving performance with upscaling.

On the structural and impedance characteristics of Li- doped PEO, using n-butyl lithium in hexane as dopant

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

Anand, P. B., E-mail: anandputhirath@gmail.com, E-mail: jayalekshmi@cusat.ac.in; Jayalekshmi, S., E-mail: anandputhirath@gmail.com, E-mail: jayalekshmi@cusat.ac.in

2014-01-28

Nowadays polymer based solid state electrolytes for applications in rechargeable battery systems are highly sought after materials, pursued extensively by various research groups worldwide. Numerous methods are discussed in literature to improve the fundamental properties like electrical conductivity, mechanical stability and interfacial stability of polymer based electrolytes. The application of these electrolytes in Li-ion cells is still in the amateur state, due to low ionic conductivity, low lithium transport number and the processing difficulties. The present work is an attempt to study the effects of Li doping on the structural and transport properties of the polymer electrolyte, poly-ethelene oxide (PEO)more » (Molecular weight: 200,000). Li doped PEO was obtained by treating PEO with n-Butyllithium in hexane for different doping concentrations. Structural characterization of the samples was done by XRD and FTIR techniques. Impedance measurements were carried out to estimate the ionic conductivity of Li doped PEO samples. It is seen that, the crystallinity of the doped PEO decreases on increasing the doping concentration. XRD and FTIR studies support this observation. It is inferred that, ionic conductivity of the sample is increasing on increasing the doping concentration since less crystallinity permits more ionic transport. Impedance measurements confirm the results quantitatively.« less

Experimental and modeling study on charge storage/transfer mechanism of graphene-based supercapacitors

NASA Astrophysics Data System (ADS)

Ban, Shuai; Jing, Xie; Zhou, Hongjun; Zhang, Lei; Zhang, Jiujun

2014-12-01

A symmetrical graphene-based supercapacitor is constructed for studying the charge-transfer mechanism within the graphene-based electrodes using both experiment measurements and molecular simulation. The in-house synthesized graphene is characterized by XRD, SEM and BET measurements for morphology and surface area. It is observed that the electric capacity of graphene electrode can be reduced by both high internal resistance and limited mass transfer. Computer modeling is conducted at the molecular level to characterize the diffusion behavior of electrolyte ions to the interior of electrode with emphasis on the unique 2D confinement imposed by graphene layers. Although graphene powder poses a moderate internal surface of 400 m2 g-1, the capacitance performance of graphene electrode can be as good as that of commercial activated carbon which has an overwhelming surface area of 1700 m2 g-1. An explanation to this abnormal correlation is that graphene material has an intrinsic capability of adaptively reorganizing its microporous structure in response to intercalation of ions and immergence of electrolyte solvent. The accessible surface of graphene is believed to be dramatically enlarged for ion adsorption during the charging process of capacitor.

High carrier concentration p-type transparent conducting oxide films

DOEpatents

Yan, Yanfa; Zhang, Shengbai

2005-06-21

A p-type transparent conducting oxide film is provided which is consisting essentially of, the transparent conducting oxide and a molecular doping source, the oxide and doping source grown under conditions sufficient to deliver the doping source intact onto the oxide.

Evolution of plant conducting cells: perspectives from key regulators of vascular cell differentiation.

PubMed

Ohtani, Misato; Akiyoshi, Nobuhiro; Takenaka, Yuto; Sano, Ryosuke; Demura, Taku

2017-01-01

One crucial problem that plants faced during their evolution, particularly during the transition to growth on land, was how to transport water, nutrients, metabolites, and small signaling molecules within a large, multicellular body. As a solution to this problem, land plants developed specific tissues for conducting molecules, called water-conducting cells (WCCs) and food-conducting cells (FCCs). The well-developed WCCs and FCCs in extant plants are the tracheary elements and sieve elements, respectively, which are found in vascular plants. Recent molecular genetic studies revealed that transcriptional networks regulate the differentiation of tracheary and sieve elements, and that the networks governing WCC differentiation are largely conserved among land plant species. In this review, we discuss the molecular evolution of plant conducting cells. By focusing on the evolution of the key transcription factors that regulate vascular cell differentiation, the NAC transcription factor VASCULAR-RELATED NAC-DOMAIN for WCCs and the MYB-coiled-coil (CC)-type transcription factor ALTERED PHLOEM DEVELOPMENT for sieve elements, we describe how land plants evolved molecular systems to produce the specialized cells that function as WCCs and FCCs. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Molecular dynamics of alamethicin transmembrane channels from open-channel current noise analysis.

PubMed

Mak, D O; Webb, W W

1995-12-01

Conductance noise measurement of the open states of alamethicin transmembrane channels reveals excess noise attributable to cooperative low-frequency molecular dynamics that can generate fluctuations approximately 1 A rms in the effective channel pore radius. Single-channel currents through both persistent and nonpersistent channels with multiple conductance states formed by purified polypeptide alamethicin in artificial phospholipid bilayers isolated onto micropipettes with gigaohm seals were recorded using a voltage-clamp technique with low background noise (rms noise < 3 pA up to 20 kHz). Current noise power spectra between 100 Hz and 20 kHz of each open channel state showed little frequency dependence. Noise from undetected conductance state transitions was insignificant. Johnson and shot noises were evaluated. Current noise caused by electrolyte concentration fluctuation via diffusion was isolated by its dependence on buffer concentration. After removing these contributions, significant current noise remains in all persistent channel states and increases in higher conductance states. In nonpersistent channels, remaining noise occurs primarily in the lowest two states. These fluctuations of channel conductance are attributed to thermal oscillations of the channel molecular conformation and are modeled as a Langevin translational oscillation of alamethicin molecules moving radially from the channel pore, damped mostly by lipid bilayer viscosity.

The low-bias conducting mechanism of single-molecule junctions constructed with methylsulfide linker groups and gold electrodes

NASA Astrophysics Data System (ADS)

Wang, Minglang; Wang, Yongfeng; Sanvito, Stefano; Hou, Shimin

2017-08-01

The atomic structure and electronic transport properties of two types of molecular junctions, in which a series of saturated and conjugated molecules are symmetrically connected to gold electrodes through methylsulfide groups, are investigated using the non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that the low-bias junction conductance is determined by the electronic tunneling between the two Au-S donor-acceptor bonds formed at the molecule-electrode interfaces. For alkanes with 4, 6, and 8 carbon atoms in the chain, the Au-S bonds moderately couple with the σ-type frontier molecular orbitals of the alkane backbone and thus prefer to be coplanar with the alkane backbone in the junction. This results in an exponential decrease of the junction conductance as a function of the number of methylene groups. In contrast, the Au-S bonds couple strongly with the π-type orbitals of the 1,4'-bis(methylsulfide)benzene and 4,4'-bis(methylsulfide)biphenyl molecules and thus tend to be perpendicular to the neighboring benzene rings, leading to the rather large junction conductance. Our findings contribute to the understanding of the low-bias conducting mechanism and facilitate the design of molecular electronic devices with methylsulfide groups and gold electrodes.

Raman Scattering at Plasmonic Junctions Shorted by Conductive Molecular Bridges

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

El-Khoury, Patrick Z.; Hu, Dehong; Apkarian, V. Ara

2013-04-10

Intensity spikes in Raman scattering, accompanied by switching between line spectra and band spectra, can be assigned to shorting the junction plasmon through molecular conductive bridges. This is demonstrated through Raman trajectories recorded at a plasmonic junction formed by a gold AFM tip in contact with a silver surface coated either with biphenyl-4,4’-dithiol or biphenyl-4-thiol. The fluctuations are absent in the monothiol. In effect, the making and breaking of chemical bonds is tracked.

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

DOE PAGES

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu; ...

2016-06-30

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

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

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Conductance manipulation at the molecular level

NASA Astrophysics Data System (ADS)

Paulsson, Magnus; Stafström, Sven

1999-05-01

Using a tight-binding model we have studied the electronic transmission through a C60 molecule sandwiched between a metal surface and a metal (scanning tunnelling microscope) tip. By simulating compression of C60 we have interpreted an experimental study of the variation of the conductance through a C60 molecule with an applied external pressure. We found that the observed increase in conductance cannot be explained in terms of the changes in the electronic structure of the C60 molecule alone. Effects related to the metal/molecule contact, i.e. the strength of the metal/C60 interaction and the shape of the molecular orbitals in the tip, are in fact more important for the conductance. In view of this we discuss the importance of interference effects in the tip/molecule coupling.

Thermal conductance of interfaces with molecular layers - low temperature transient absorption study on gold nanorods supported on self assembled monolayers

NASA Astrophysics Data System (ADS)

Wang, Wei; Huang, Jingyu; Murphy, Catherine; Cahill, David; University of Illinois At Urbana Champaign, Department of Materials Science; Engineering Team; Department Collaboration

2011-03-01

While heat transfer via phonons across solid-solid boundary has been a core field in condense matter physics for many years, vibrational energy transport across molecular layers has been less well elucidated. We heat rectangular-shaped gold nanocrystals (nanorods) with Ti-sapphire femtosecond pulsed laser at their longitudinal surface plasmon absorption wavelength to watch how their temperature evolves in picoseconds transient. We observed single exponential decay behavior, which suggests that the heat dissipation is only governed by a single interfacial conductance value. The ``RC'' time constant was 300ps, corresponding to a conductance value of 95MW/ m 2 K. This interfacial conductance value is also a function of ambient temperature since at temperatures as low as 80K, which are below the Debye temperature of organic layers, several phonon modes were quenched, which shut down the dominating channels that conduct heat at room temperature.

Characterization of Pathogenic Human MSH2 Missense Mutations Using Yeast as a Model System: A Laboratory Course in Molecular Biology

ERIC Educational Resources Information Center

Gammie, Alison E.; Erdeniz, Naz

2004-01-01

This work describes the project for an advanced undergraduate laboratory course in cell and molecular biology. One objective of the course is to teach students a variety of cellular and molecular techniques while conducting original research. A second objective is to provide instruction in science writing and data presentation by requiring…

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

PubMed

Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

2013-01-01

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework

PubMed Central

Chen, Xi; Cui, Qiang; Tang, Yuye; Yoo, Jejoong; Yethiraj, Arun

2008-01-01

A hierarchical simulation framework that integrates information from molecular dynamics (MD) simulations into a continuum model is established to study the mechanical response of mechanosensitive channel of large-conductance (MscL) using the finite element method (FEM). The proposed MD-decorated FEM (MDeFEM) approach is used to explore the detailed gating mechanisms of the MscL in Escherichia coli embedded in a palmitoyloleoylphosphatidylethanolamine lipid bilayer. In Part I of this study, the framework of MDeFEM is established. The transmembrane and cytoplasmic helices are taken to be elastic rods, the loops are modeled as springs, and the lipid bilayer is approximated by a three-layer sheet. The mechanical properties of the continuum components, as well as their interactions, are derived from molecular simulations based on atomic force fields. In addition, analytical closed-form continuum model and elastic network model are established to complement the MDeFEM approach and to capture the most essential features of gating. In Part II of this study, the detailed gating mechanisms of E. coli-MscL under various types of loading are presented and compared with experiments, structural model, and all-atom simulations, as well as the analytical models established in Part I. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction. PMID:18390626