River Publishers: Journal of Self-Assembly and Molecular Electronics

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Journal of Self-Assembly and Molecular Electronics

Editors-in-Chief:
Baoquan Ding, National Center for Nanoscience and Technology, China
Peter Fojan, Aalborg University, Denmark
Leonid Gurevich, Aalborg University, Denmark

ISSN: 2245-4551 (Print Version),

ISSN: 2245-8824 (Online Version)
Vol: 3 Issue: Continuous Article Publication

Published In: 2015

Publication Frequency: Continuous Article Publication

Search Available Volume and Issue for Journal of Self-Assembly and Molecular Electronics

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AFM study on amyloid peptide - graphene oxide assembly and its interaction with liposome
doi: https://doi.org/10.13052/jsame2245-4551.312
Yunpeng Cao,^1,2 Liguo Tao,³ Jie Wang¹ Hüsnü Aslan,⁴ Lei Liu¹ and Mingdong Dong⁴

¹Institue for Advanced Materials, Jiangsu University, China
²School of Materials Science and Engineering, Jiangsu University, China
³School of Food and Biological Engineering, Jiangsu University, China
⁴Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark)

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Abstract: The interaction between amyloid peptides and membrane is a broad research topic due to the variety of biological events occurring, such as the membrane disruption related pathogenesis of amyloid diseases or the toxicity of peptide materials. Amyloid peptides have many structural forms, it is therefore important to explore the interactions between the membrane and assemblies of amyloid peptides, and to find ways to control these interactions. Herein, we utilized atomic force microscopy (AFM) and circular dichroism spectra to explore the modulating effect of Graphene Oxide (GO) on amyloid peptide assembly. In addition, the interaction between liposome samples and amyloid peptide assembly modulated by GO was investigated. It is achieved that the membrane disruption of amyloid peptide aggregates can be fine-tuned by tweaking the GO concentration. The findings in this work provide a better understanding of amyloid peptide and membrane interactions and how it can be tuned.

Keywords: Enzyme Mediated Encapsulation of Gold Nanoparticles by Polyaniline Nanoshell

Enzyme Mediated Encapsulation of Gold Nanoparticles by Polyaniline Nanoshell
doi: https://doi.org/10.13052/jsame2245-4551.311
R. Sfez,^1,2 E. Natan, ¹ Y. Bardavid, ¹ M. Ikbal, ¹ E. Arbeli, ³ S. Arkin³, I. Popov⁴ and Shlomo Yitzchaik^1,4

¹ Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel,
² Azrieli, College of Engineering, Jerusalem, Israel,
³ Department of Biochemistry
⁴ The HU Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel

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Abstract: In this contribution we describe the formation of gold nanoparticles (AuNP) and polyaniline (PANI) AuNP-PANI nanocomposite via in-situ enzymatic polymerization. The method consists of electrostatic adsorption of anilinium monomers on AuNPs citrate stabilized surface of 50 nm diameters, followed by oxidation with horseradish peroxidase (HRP) enzyme and its cofactor H2O2. All reaction steps were monitored by UV-Vis-NIR spectroscopy including in-situ detection of the polymerization process. UV-Vis-NIR, Cyclic voltammetry (CV) and surface enhanced Raman scattering (SERS) measurements supported the formation of a nanoshell of PANI on the AuNP core. Two templates for anilinium assembly were compared revealing a strong dependence of the enzymatic kinetics on the template. The kinetic study had shown that the rigid template of the AuNP contributes to higher reaction rate on the AuNP compared with the more flexible polyanion template. The mild reaction’ condition enables an easy and precise method for obtaining PANI nano-shell on anionic templates for advanced bioelectronic applications.

Keywords: Au-nanoparticles (AuNP), enzymatic polymerization, HRP enzyme, polyaniline, nano-shell.

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Thematic Issue

"Molecular Self-Assembly: Synergy of Modelling and Experiment"
Guest Editor: Giorgia Brancolini
CNR-NANO S3, Institute of Nanoscience, via Campi 213/A, 41100 Modena, Italy

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Sensitization of ZnO surface through cyanidin functionalization
doi: https://doi.org/10.13052/jsame2245-4551.2015003

Arrigo Calzolari
CNR-NANO Istituto Nanoscienze, Centro S3, via campi 213A I-41125 Modena, Italy; and Physics Departmet, University of North Texas, Denton TX, USA

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Abstract: By using simulations from first principles, we investigate the electronic and optical properties of the hybrid interface resulting from the functionalization of the non-polar ZnO(101 0) surface due to the adsorption of cyanidin dye. This system has been proposed as metal-free active elements for dye sensitized solar cell applications. However, despite the intense sensitization activity, the resulting solar cells provided extremely low conversion efficiency. Our results elucidate the microscopic mechanisms that regulate the light harvesting and the photocharge injection/ricombination at the interface, and provide an explanation of the dramatically low efficiency reported by the experiments.

Keywords: photovoltaics, anthocyanidin, ZnO, DFT, DSSC.

Robustness of DFT predictions of the charge transfer mechanism for self-assembled monolayers modied with Ferrocene on Au(111)
doi: https://doi.org/10.13052/jsame2245-4551.2015004

Filipe C. D. A. Lima, Arrigo Calzolari, Helena M. Petrilli, and Marilia J. Caldas
Departamento de Física dos Materiais e Mecâanica, Instituto de Física, Universidade de São Paulo, 05508-090, São Paulo, SP, Brasil, and CNR-NANO Istituto Nanoscienze S3 National Center, I-41100, Modena, Italia

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Abstract: The charge transfer mechanism of ferrocene-modied monolayers is a controversial topic in the literature. Recently, theoretical results of the ferrocenyl-glycyl-cystamine (Fc-Gly-CSA) on Au(111) have shown evidences of electronic tunneling from the ferrocene center to the electrode. Here we study the Fc-Gly-CSA molecule using the Density Functional Theory with the Perdew-Burke-Ernzerhof (PBE) and hybrid-PBE (PBEh) functionals in order to investigate the robustness of the electronic structure to the inherent Kohn-Sham scheme approximations. For PBEh, we tested dierent values for the Hartree-Fock exact exchange (Exx). Our results show that as the Exx increases, the Highest Occupied Molecular Orbital(HOMO)- Lowest Unoccupied Molecular Orbital( LUMO) energy dierence also increase. Nevertheless, the states located over the Gly-CSA always remained at least 1 eV below the HOMO in all cases here investigated. These results indicate that the evidences of electronic tunneling charge transfer mechanism for the Fc-Gly-CSA/Au(111) are robust concerning the exchange correlation functionals.

Keywords: Electronic Structure, DFT, Exact Exchange, Self-Assembled Monolayers (SAMs), Molecular Electronics, Ferrocene.

Self assembly of ionic liquids at the air/water interface
doi: https://doi.org/10.13052/jsame2245-4551.2015005

Babak Minofar^1,2
¹ Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
² Faculty of Science, University of South Bohemia Branisovska 31, Českė Budějovice, Czech Republic

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Abstract: and biology. Understanding phenomena at the interface is a challenging subject in both experimental and theoretical research. The behavior of ions at the air/water interface is of special interest since it is relevant for many surface chemical reactions. Ionic liquids are liquid organic salts that are generally composed of a bulky hydrophobic cationic partner and a smaller but generally multi-atomic and more hydrophilic anionic partner. The propensity of the constituent hydrophobic and hydrophilic ions of ionic liquids for the air/water interface raises many questions regarding the self-assembly of these ions and their interactions with water molecules. How do these ions interact with water? How do hydrogen-bonding networks of water change when ions have strong propensity to the surface? Are water-anion interactions stronger than water-cation or water-water interactions? How are those interactions affected at different concentrations of ionic liquids? How does the nature of these cations and anions influence surface properties and orientation of ions at the interface? How do ionic liquids make self-assemblies at the interface, and which are the dominant forces for this process? This minireview aims to answer these questions.

Keywords: onic liquids, air/water interface, self assembly, ion-water interaction, ion-ion interaction.

Molecular Scale Simulations of the Self-Assembly of Amphiphilic Molecules: Current State-of-the-Art and Future Directions
doi: https://doi.org/10.13052/jsame2245-4551.2015006

Daniel T. Allen and Christian D. Lorenz
Theory & Simulation of Condensed Matter Group, Department of Physics, Strand Campus, King's College London, Strand, London WC2R 2LS, UK,

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Abstract: Gaining an understanding of the self-assembly of amphiphilic molecules has been a goal for experimental, theoretical and computational research in the field of soft matter for approximately a century. In the field of materials modelling, understanding the self-assembly of amphiphilic molecules at experimental conditions has proven to be a challenging problem and has led to several developments that have driven the entire field of computational materials science forward. In this review, we present the current-state-ofthe- art in terms of applying all-atom and coarse-grain molecular dynamics simulations in order to study the self-assembly process and the structure that results. Additionally, we present a few of the challenges that still exist with some ideas as to future directions that may be used to overcome them.

Keywords: colloids, polymers, self-assembly, molecular dynamics, all-atom, coarse-grain, implicit solvent models.

Thermoelectric properties of functionalized graphene grain boundaries
doi: https://doi.org/10.13052/jsame2245-4551.2015007

Leonardo Medrano Sandonas^1,2,3, Rafael Gutierrez^1,3, Alessandro Pecchia⁴, Arezoo Dianat^1,3 and Giovanni Cuniberti^1,3,5
¹Institute for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany
²Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
³Dresden Center for Computational Materials Science (DCCMS), TU Dresden, 01062 Dresden, Germany
⁴Consiglio Nazionale delle Ricerche, ISMN, Via Salaria km 29.6, 00017 Monterotondo, Rome, Italy
⁵Center for Advancing Electronics Dresden, TU Dresden, 01062 Dresden, Germany

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Abstract: Thermoelectric effect enables direct conversion between thermal and electrical energy and provide an alternative route for power generation and refrigeration. Hereby it is important to find materials with a high thermoelectric performance. In this sense, in the present work, we study the behavior of the thermoelectric properties of functionalized graphene grain boundaries by employing non-equilibrium Green�s Functions formalism combined with density functional tight-binding theory (NEGF-DFTB) approach. Our results show that H and O ad-atoms affect the phonon and electron transport properties of the grain boundaries but the thermoelectric figure of merit is slightly reduced. However, grain boundaries functionalized with nitrophenyl molecules improve the thermoelectric behavior. We have also found that physisorbed molecules do not alter their transport properties. We expect our results to shed light on the potential of 2D materials for engineering highly efficient nanoscale thermoelectric devices.

Keywords: thermoelectric properties, graphene grain boundaries, functionalization, quantum transport.

Same-spin dynamical correlation effects on the electron localization
doi: https://doi.org/10.13052/jsame2245-4551.2015008

Stefano Pittalis¹, Alain Delgado^1,2, and Carlo Andrea Rozzi¹
¹CNR - Istituto Nanoscienze, Via Campi 213a, 41125 Modena, Italy
²Department of Physics, University of Ottawa, Ottawa, ON K1N 6N5, Canada
³Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, Calle 30 \# 502, 11300 La Habana, Cuba.

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Abstract: The Electron Localization Function (ELF) - as proposed originally by Becke and Edgecombe - has been widely adopted as a descriptor of atomic shells and covalent bonds. The ELF takes into account the antisymmetry of Fermions but it neglects the multi-reference character of a truly interacting many-electron state. Electron-electron interactions induce, schematically, different kind of correlations: non-dynamical correlations mostly affect stretched molecules and strongly correlated systems; dynamical correlations dominate in weakly correlated systems. Here, within an affordable computational effort, we estimate the effects of same-spin dynamical correlations on the electron localization by means of a simple modification of the ELF.

Keywords: Electron Localization Function (ELF)

Docking of DNA duplexes on a gold surface
doi: https://doi.org/10.13052/jsame2245-4551.2015009

Marta Rosa^1,2 Daria B. Kokh³, Stefano Corni², Rebecca Wade^3,4,5 and Rosa Di Felice^2,6
¹Department of Physics, University of Modena and Reggio Emilia, Modena, Italy
²Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
³Heidelberg Institute for Theoretical Studies (HITS)
³Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
⁴Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
⁵Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
⁶Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA

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Abstract: Understanding the interaction of DNA molecules with hard substrates is a crucial step both for the study of DNA and for the development of new nanotechnology applications, as the adsorption on hard surfaces strongly influences the shape and properties of DNA itself. We developed a multiscale approach based on electronic structure calculations and molecular simulations, able to investigate the interaction of DNA molecules with a hard inorganic surface and to describe the adsorption configurations. Here we present our approach and we discuss preliminary results obtained with docking calculations of the adsorption of DNA molecules on Au(111). We obtained two main adsorption configurations, with DNA oligomers adsorbed parallel or tilted with respect to the surface. Our results evidence the importance of an accurate description of Lennard-Jones interactions between nucleobases and gold atoms in the DNA adsorption process.

Keywords: DNA

River Publishers: Journal of Self-Assembly and Molecular Electronics