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Journal of Self-Assembly and Molecular Electronics

Open Access

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: 6   Issue: Continuous Article Publication

Published In:   2018

Publication Frequency: Continuous Article Publication

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

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Methods of Synthesis and Characterization of Conductive DNA Nanowires Based on Metal Ion-Mediated Base Pairing for Single-Molecule Electronics

doi: https://doi.org/10.13052/jsame2245-4551.6.004
Simon Vecchioni1, Mark C. Capece2, Emily Toomey3, Lynn Rothschild4 and Shalom J.Wind5

1Department of Biomedical Engineering at Columbia University, New York, NY 10027, USA
2Department of Chemistry, Stanford University, Stanford, CA 94305, USA
3Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4NASA Ames Research Center, Space Science and Astrobiology Division, Moffett Field, CA 94035, USA
5Department of Applied Physics and Applied Mathematics at Columbia University, New York, NY 10027, USA

Abstract: [+]    |    Download File [ 689KB ]    |   Read Article Online    |   Supplementary Information

Abstract: Advances in the field of molecular electronics have made possible the direct measurement of charge transport across single molecules. In particular, work on DNA oligomers has demonstrated that this weakly-conducting biomolecule can be functionalized through metal-mediated nucleobase pairing in order to significantly increase electron mobility across the molecule. The introduction of interacting stacks of single metal ions inside the DNA helix is an attractive platform for assay and optimization; for this reason we present a protocol for the production and processing of nanowires with a metal base pair for single-molecule applications. In particular, we describe the construction of DNA duplex wires with a cytosine-Ag+-cytosine base pair (dC:Ag+:dC). A thorough investigation of buffer components suggests the use of divalent magnesium counterions to stabilize highly mismatched oligonucleotides in solution. We further analyse cleaning and processing of thin gold films for batch-fabrication of conductive imaging substrates for use in conductive scanning probe assays of single-molecule conductivity. With a clear path to electrical assays, we suggest that the C:Ag+:C orthogonal nucleotide pair and other similar chemistries may provide a foundation for molecular electronic components in integrated devices.

Keywords: Molecular electronics, DNA nanowire, nanomaterials, cytosine mismatch, methods.

Salt Bridges Regulate in Silico Dimers Formation for β2-Microglobulin Amyloidogenic Variants

doi: https://doi.org/10.13052/jsame2245-4551.6.003
Maria Celeste Maschio1,2, Giorgia Brancolini2, and Stefano Corni2,3

1Department of Physics, University of Modena and Reggio Emilia, Via Campi 213/a, 41125 Modena, Italy
2Center S3, CNR-NANO Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
3Department of Chemical Science, University of Padova, Via Marzolo 1, 35131 Padova, Italy

Abstract: [+]    |    Download File [ 2045KB ]    |   Read Article Online

Abstract: dialysis-related amyloidosis, a disease associated to long-term hemodialyzed patients and characterized by accumulation of amyloid deposits in the osteoarticular tissues. In the early stages of amyloid fibril formation, β2-microglobulin associates into dimers and higher oligomers, but clarifications are still needed for the triggering conditions, mechanisms and specificity of dimer formation. To characterize the dimeric association process, the protein-protein interactions between three different species are investigated: namely, the native protein and the two amyloidogenic variants ΔN6 and D76N. The dimerization process is rationalized relying on state of the art computational methods. A comparative mechanism for how different mutations in the three variants can affect protein dimerization and thus fibril formation is proposed. The number of salt bridges involved at the protein-protein interface correlates with the degree of amyloidogenicity of each individual species. The findings can offer possible strategies in controlling the dimerization mechanism based on different β2-microglobulin protein mutations, which have significant roles in the fibrillogenical process.

Keywords: amyloidosis, molecular dynamics, protein aggregation, β2-microglobulin.

In Situ Atomic Force Microscopy Studies of the Effect of Indolicidin on E.coli Cells

doi: https://doi.org/10.13052/jsame2245-4551.6.002
Hans Jakob Askou, Rasmus Neergaard Jakobsen and Peter Fojan

Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, 9220 Aalborg, Denmark

Abstract: [+]    |    Download File [ 459KB ]    |   Read Article Online

Abstract: E.coli cells were succesfully attached to both gelatin coated surfaces and polylactic acid honeycomb patterned mica surfaces as determined by in situ atomic force microscopy. The gelatin coated surfaces provided a softer support onto which the E.coli cells were capable of slightly submerging leading to a better adhesion compared to the harder surfaces consisting of polylactic acid polymer surfaces. After continuous scanning in liquid media, the E.coli cells remained rod shaped and smooth. Indolicidin, a 13-AA linear antimicrobial peptide, was injected in order to visualize the peptide-membrane interactions in real time. Instantly after the injection of the peptides, the bacterial membranes were observed to be distorted and seemed to melt proceeding as a function of time. In conclusion, these experiments proved that the E.coli cells were not ruptured as could be expected due to pore formation and disruption of the osmotic pressure. This indicates a possible intracellular target killing mechanism of indolicidin interacting with E.coli cells.

Keywords: Atomic force microscopy, indolicidin, antimicrobial peptides, E.coli cells, gelatin, honeycomb pattern, PLA, intracellular killing mechanism.

Gas-phase Ion Spectroscopy of Flexible and Nonflexible Nitrophenolates: Effect of Locking the Two Phenyl Units in 4’-nitro-[1,1’-biphenyl]-4-olate by a Bridging Atom

doi: https://doi.org/10.13052/jsame2245-4551.6.001
Bjarke Møller Pedersen and Steen Brøndsted Nielsen

Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark

Abstract: [+]    |    Download File [ 3321KB ]    |   Read Article Online

Abstract: Nitrophenolates (NPs) are molecular anions that can undergo charge-transfer (CT) transitions determined by the degree of electron delocalization between the phenolate oxygen (donor group) and the nitro group (acceptor). Here we have studied four different NPs: 4’-nitro-[1,1’-biphenyl]-4-olate (1), 7-nitro-9H-carbazol-2-olate (NH linker, 2), 7-nitrodibenzo[b,d]furan-3- olate (oxygen linker, 3), and 7-nitrodibenzo[b,d]thiophen-3-olate (sulphur linker, 4), and recorded their electronic absorption spectra when isolated in vacuo to determine the effect of locking the biphenyl spacer group between the donor and acceptor on transition energies. Absorption was identified from ion dissociation (action spectroscopy) using a homebuilt setup (sector mass spectrometer combined with pulsed laser). We find that the absorption is broad in the visible region for all four NPs with significant vibronic features. The lowest energy peak is at 601 ± 4 nm, 606 ± 4 nm, 615 ± 4 nm, and 620 ± 4 nm, for 3, 4, 2, and 1, respectively. NP 1 is flexible, and its lowest energy structure is nonplanar while the other three NPs are planar according to density functional theory calculations. Hence in the case of 1 the electronic transition has a higher degree of CT than for the other three, accounting for its absorption furthest to the red. Our work demonstrates that oxygen and sulphur are best at conveying the electronic coupling between the donor and acceptor sites as 3 and 4 absorb furthest to the blue (i.e., the degree of CT is lowest for these two NPs). Based on the average spacing between the peaks in the vibrational progressions, coupling occurs to skeleton vibrational modes with frequencies of 649±69 cm-1 (3), 655±49 cm-1 (4), and 697±52 cm-1 (2).

Keywords: Intrinsic electronic absorption, charge transfer, nitrophenolates, mass spectroscopy.


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Vol. 6, Supplement 1

"Abstracts of the 4th International Conference on Self Assembly and Molecular Electronics"



Mono-dispersed multi-doped LiFePO4/C nanoparticles as a cathode material for lithium-ion batteries

doi: https://doi.org/10.13052/jsame2245-4551.2018032
Wanmin Liu1,2, Zhengjun Fang1,2, Ru Zhang1,2, Qiang Tao1,2,
Bianling Zhang1, Donghong Yu2 and Yuanzheng Yue2

1College of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
2Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark

Abstract: [+]    |    Download File [ 693KB ]    |   Read Article Online

Abstract: Ni-Co-Mn doped LiFePO4/C has been prepared from the spent electroless nickel plating bath, ferrous oxalate and lithium carbonate. A plausible formation mechanism of the multi-doped LiFePO4/C is proposed. XRD and Rietveld refinement confirm that Ni, Co and Mn have been successfully incorporated in the LiFePO4/C crystal. SEM and laser particle size analyses verify that the material synthesized at 700C for 10 h consists of narrow-distribution mono-dispersed grape-like nanoparticles. The charge-discharge tests demonstrate that the material delivers initial discharge specific capacities of 167.5, 152.3 and 116.8 mAh⋅g-1 at 0.2 C, with the capacity retentions of 99.7%, 99.0% and 98.9% after 50 cycles at 25, 0 and -20C, respectively.

Screening for functional peptide based SsGPRC6A to recognize L-amino acids specifically by molecular docking and dynamics simulation

doi: https://doi.org/10.13052/jsame2245-4551.2018031
Ru Zhang1,2, Zhengjun Fang1,2, Wanmin Liu1,2, Bianling Zhang1, Qiang Tao1,2, and Donghong Yu2,3

1College of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
2Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
3Sino-Danish Center for Education and Research (SDC), Aarhus, 8000, Denmark

Abstract: [+]    |    Download File [ 91KB ]    |   Read Article Online

Abstract: One of the most important function of G protein-coupled receptors family C subtype 6A (GPRC6A) recognizes and responds to L-amino acids as its principal physiological ligand. In this study, homology modeling, molecular docking and molecular dynamics simulation were performed to explore structural features and binding mechanism of L-amino acids on SsGPRC6A of Sus scrofa, and to construct model containing the binding domain of the ligands for searching functional and special polypeptide to recognize the L-amino acids respectively. The homology model of SsGPRC6A was constructed using the crystal structure of the extracellular region of the group II metabotropic glutamate receptor (2E4U) at 2.35 Ã… resolution as template.

Effects of Remote Substituents on Electrochemical Reduction of X-PhCH=NPhCH=CHPh-Y

doi: https://doi.org/10.13052/jsame2245-4551.2018030
Zhengjun Fang1,2, Ru Zhang1,2, Wanmin Liu1,2, Qiang Tao1,2, Bianlin Zhang1 and Donghong Yu2,3

1Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
2Department of Chemistry and Bioscience, Aalborg University,
Aalborg 9220, Denmark
3Sino-Danish Center for Education and Research (SDC), Aarhus, 8000, Denmark

Abstract: [+]    |    Download File [ 148KB ]    |   Read Article Online

Abstract: Schiff-bases have prospective applications in functional technologies such as organic photovoltaic [1] and other molecular electronic devices [2]. Therefore, for the design of molecular optoelectronic devices of high efficiency, it is hence of great interest and significance to understand the relationship between structure and electrochemical property of Schiff bases in the molecular level [3]. However, Schiff base displays a high degree of complexity that makes it difficult and expensive to elaborate this in a large scale. Consequently, quantitative structure-property relationship (QSPR) focusing on simple, costeffective and easily scalable Schiff bases has emerged [4].

Colloidal lithography approaches to study plasmon coupling and plasmonic devices

doi: https://doi.org/10.13052/jsame2245-4551.2018029
Duncan S. Sutherland1,∗, Hans Dyrnesli1, Gunnar Klös1, Maria G. D. R. H. Salazar1, Kasper R. Okholm1 and Vladimir E. Bochenkov2

1Aarhus University, Aarhus, Denmark
2Lomonosov Moscow State University, Moscow, Russia

Abstract: [+]    |    Download File [ 101KB ]    |   Read Article Online

Abstract: In the last two decades a wide range of nanofabrication approaches have been developed based on top down lithography or bottom up self assembly. Here approaches based on colloidal monolayer masks combined with cleanroom processing such as Sparse Colloidal Lithography (SCL) [1] and Hole Mask Colloidal Lithography (HMCL) [2] will be presented. Traditionally these approaches have given arrays of circularly symmetric structures such as disks [3], holes [4], rings [5] and cones [2]. More recent approaches have allowed postmodification of the masks to change their size [6] or their shape. Colloidal lithography approaches have proven appropriate to allow arrays of novel plasmonic structures to be fabricated to study plasmon coupling [7], refractive index sensitivity [8] and chiral properties of arrays [9].

Molecular Dynamics Simulations of CRISPR/Cas9

doi: https://doi.org/10.13052/jsame2245-4551.2018028
Angana Ray and Rosa Di Felice

University of Southern California, Los Angeles, USA

Abstract: [+]    |    Download File [ 189KB ]    |   Read Article Online

Abstract: Class 2 CRISPR (clustered regularly interspaced short palindromic repeats) systems offer a unique protocol for genome editing in eukaryotic cells and has already been validated in many organisms [1]. In genome editing through CRISPR, the target DNA is first recognized by a complementary RNA bound to an endonuclease. The RNA-guided DNA unwinding leads to formation of a RNA-DNA hybrid duplex and a displaced DNA strand (Figure 1) . Thereafter, the nuclease portion of the Cas9 protein closest to the DNA cleavage site attains a conformation essential for concerted DNA cutting.

Preparation of Protein materials for applications in photonics and bioelectronics

doi: https://doi.org/10.13052/jsame2245-4551.2018027
Niclas Solin

Department of Physics, Chemistry, and Biology (IFM), Biomolecular and Organic Electronics, Linköping University, 581 83 Linköping, Sweden.

Abstract: [+]    |    Download File [ 78KB ]    |   Read Article Online

Abstract: Natural materials often display hierarchical organization of nano-structures, lending unique properties to the macroscopic material. Many proteins are able to self-assemble into ordered nano/micro-structures, and it is interesting to investigate applications of such structures in materials science. However, for many applications it is desirable to have additional functionality, not present in the original protein. It is therefore desirable to develop methodology for functionalization of protein materials. We have developed novel techniques for preparation of functionalized protein materials. One extremely flexible and facile method involves co-grinding of a protein with a hydrophobic material. Upon exposure to appropriate stimuli the composite undergoes self-assembly into functionalized fibrils. The process can be performed simply with mortar and pestle [1-3] or with automated milling equipment [4]. These fibrils can then be induced to undergo colloidal assembly into materials. In this presentation will be given examples of such materials preparation, and applications of the materials in photonics and bioelectronics will be presented.

Luminescence Spectroscopy of Rhodamine Homodimer Dications in Vacuo

doi: https://doi.org/10.13052/jsame2245-4551.2018026
Steen Brøndsted Nielsen

Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark

Abstract: [+]    |    Download File [ 110KB ]    |   Read Article Online

Abstract: The photophysics of dyes strongly depends on their microenvironment, either solvent molecules or nearby charges. Also interactions with other dyes affect the spectroscopical properties. For ionic dyes it can be difficult to quantify the interactions due to solvent screening and/or nearby counter ions. To shed light on intrinsic properties, it is advantageous to perform luminescence experiments in the gas phase, which, however, requires specialized apparatus. In Aarhus we have constructed the LUNA setup, LUminescence iNstrument in Aarhus (Figure 1) [1] that allows us to measure fluorescence from larger ions produced by electrospray ionization. We used this setup to study rhodamine monomer cations as well as homodimers where the two dye cations are separated by methylene linkers, (CH2)n. I will present the results and compare to spectra measured in solution. Indeed, in the gas phase, we measure significant redshifted emission when there is a nearby charge while in solution solvent screening reduces this effect to almost nothing. The impact of nearby charges may have implications for gas-phase Förster Resonance Energy Transfer experiments where the aim is to reveal the structures of biomolecular ions in the gas phase.

Kinetics of a Solid-Solid Charge Transfer Reaction

doi: https://doi.org/10.13052/jsame2245-4551.2018025
Ying Pan1, Dimos Poulikakos2, Nate Cira1 and Ye Tao1

1Rowland Institute at Harvard, Cambridge MA, USA
2ETH Zurich, Zurich, Switzerland

Abstract: [+]    |    Download File [ 239KB ]    |   Read Article Online

Abstract: We present a detailed analysis of the kinetics of electron transfer at a solid-solid interface. The study was enabled by measuring the conductance of ultra-thin (< 50 nm), fully suspended single-crystalline silicon nanowires with several well-defined surface chemistries [1]. The measurement had a dynamic range across 7 orders of magnitude with a detection sensitivity of order single event over a 103 μm2 reaction area. We find that classic, first-order process [2, 3] is unable to capture the reaction progress and propose a new kinetic model based on a continuum of reactant geometries inherently present at typical solid-solid interfaces. The new model captures the kinetic manifestation of heterogeneity in a single, global rate constant. Quantitative agreement with data and an analysis of the parameters suggest that this model may be generally applicable to charge transfer at solid-solid interfaces.

Large-area molecular electronic devices from self-assembled monolayers

doi: https://doi.org/10.13052/jsame2245-4551.2018024
Kasper Nørgaard

Nano-Science Center & Department of Chemistry, University of Copenhagen, Denmark

Abstract: [+]    |    Download File [ 344KB ]    |   Read Article Online

Abstract: A central goal in molecular electronics is to understand charge transport properties of single molecules and their ensembles. This fundamental knowledge may ultimately pave the way for electronic components constructed from tailor-made molecular building-blocks that can overcome some limits of conventional silicon-based microelectronics. The formation of robust and reproducible contact between molecule and electrode is a key challenge. At the single-molecule level, we have recently explored the use of parallel self-assembly strategies towards the formation of multiple single-molecule junctions, wherein the molecule-electrode interface is controlled with atomic precision [1]. However, the use of self-assembled monolayers (SAMs) offer a complementary approach for fabricating molecular electronic devices that are more amenable to device integration and up-scaling.

Optical resonances and field-enhancement in 3D metal nanorods

doi: https://doi.org/10.13052/jsame2245-4551.2018023
Thomas M. Søndergaard

Department of materials and production, Aalborg University, Aalborg East, Denmark

Abstract: [+]    |    Download File [ 171KB ]    |   Read Article Online

Abstract: In this paper the optics of single and coupled 3D metal nanorods in solution is considered theoretically using the Electric-Field Integral Equation (EFIE) [1]. The extinction, scattering, and absorption cross section spectra, and field enhancement distributions, will be presented at the conference for a range of single rod geometries, and for configurations of rods with e.g. varying lengths and separation.

Gold Nanostar Assays for Oncology and Virology

doi: https://doi.org/10.13052/jsame2245-4551.2018022
Manjari Bhamidipati, Kholud Dardir, Hao Wang and Laura Fabris

Rutgers university, Piscataway, United States

Abstract: [+]    |    Download File [ 1510KB ]    |   Read Article Online

Abstract: Plasmonic nanostructures are well-known as effective substrates for applications in which near field enhancements are sought. In particular, we have shown that gold nanoparticles can be employed to carry out identification of U87 glioblastoma cells with surface enhanced Raman spectroscopy (SERS), by targeting overexpressed aVb3 integrins via RGD peptides [1]. However, gold nanostars have been shown to lead to much higher field enhancements, owing to their uniquely sharp protruding spikes. In particular, we have shown how they can be employed to build sensing platforms for the direct identification of small molecule analytes by SERS achieving femtomolar limits of detection [2]. We have also demonstrated how gold nanostars can be tethered to rigid substrates and conjugated in situ to aptamers for targeting and recognition of prostate cancer cells and enable the quantification of cancer cell biomarkers at the single cell level [3]. In this talk I will also present how SERS-based quantification of prostate specific membrane antigen (PSMA), a promising biomarker for prostate cancer diagnosis, enables discrete patient stratification, and how gold nanostars can be uniquely employed for the identification of influenza virus mutations at the single cell level with no interference from protein corona.

Sense and sensitivity: SERS-based assessment of mitochondrial bioenergetics

doi: https://doi.org/10.13052/jsame2245-4551.2018021
N. A. Brazhe1, E. I. Nikelshparg1, A. A. Semenova2, E. A. Goodilin2,3, A. A. Baizhumanov1, S. M. Novikov4, G. V. Maksimov1 and O. Sosnovtseva5

1Biophysics Department, Biological Faculty, Moscow State University, Moscow, Russia
2Department of Nanomaterials, Faculty of Material Sciences, Moscow State University, Moscow, Russia
3Department of Inorganic Chemistry, Faculty of Chemistry, Moscow State University, Moscow, Russia
4Laboratory of Nanooptics and Plasmonics, MIPT, Dolgoprudny, Russia
5Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark

Abstract: [+]    |    Download File [ 91KB ]    |   Read Article Online

Abstract: Selective and sensitive investigation of components of the electron transport chain in functional mitochondria is important for fundamental biophysical research and for development of new biomedical diagnostic tools. Up-to-day methods – fluorescent microscopy, absorption spectroscopy and registration of oxygen consumption – provide only indirect information about the redox state of electron transport chain complexes. We suggested a novel label-free approach based on the surface-enhanced Raman spectroscopy (SERS) to monitor conformational changes and redox state of cytochrome c in electron transport chain of functional mitochondria.

Probing local electronic property of two-dimensional materials by atomic force microscopy

doi: https://doi.org/10.13052/jsame2245-4551.2018020
Zegao Wang1,2 and Mingdong Dong1

1Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK -8000 Aarhus C, Denmark
2Department of Materials Science, Sichuan University, 601165 Chengdu, China

Abstract: [+]    |    Download File [ 81KB ]    |   Read Article Online

Abstract: Compared to zero-bandgap graphene, 2D layered transition metal dichalcogenides (TMDs) with the chemical formula MX2 (where M=group IVB-VIIB metal and X=chalcogen) have brought new possibility for the applications in ultralow-power electronics due to the reasonable bandgap. Currently, the carrier mobilities of TMDs at ambient conditions are a little bit low which limit their practical applications. Many strategies, for example synthesizing new member of 2D TMDs, revealing the transport mechanism and optimizing the device configuration are acknowledged as the promising methods. Except metallic and insulate property, many 2D layered materials exhibit semiconducting behavior including ntype, p-type or ambipolar, which could be used to fabricate various electronics. Compared to unipolar (n-type or p-type) transistors, ambipolar transistors, which can easily switch between n-type and p-type behavior by applying an electric field, are most promising candidates since they can effectively simplify circuit design and save the layout area in CMOS.

Study of Two Dimensional Electron Gas Formation at AlGaN/GaN Interfaces using Kelvin Probe Force Microscopy

doi: https://doi.org/10.13052/jsame2245-4551.2018019
P. Caban1, R. Thorpe2, L. Feldman2, K. Pedersen3 and V. N. Popok1

1Institute of Electronic Materials Technology, 01-919 Warsaw, Poland
2Department of Physics & Astronomy, Rutgers, The State University of New Jersey, 08854 Piscataway, USA
3Department of Materials and Production, Aalborg University, 9220 Aalborg, Denmark

Abstract: [+]    |    Download File [ 336KB ]    |   Read Article Online

Abstract: AlGaN/GaN heterostructures are of high research and industrial interest for the production of high electron mobility transistors utilizing the two-dimensional electron gas (2DEG) induced at the interface due to polarization effects. Critical AlGaN thickness is an important practical parameter which is under the study in this work.

Frictional behavior of two-dimensional materials

doi: https://doi.org/10.13052/jsame2245-4551.2018018
Suzhi Li1,2,3, Qunyang Li4, Robert W. Carpick5, Peter Gumbsch3,6 and Ju Li1,2

1Xi’an Jiaotong University, Xi’an 710049, China
2Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
3Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
4Tsinghua University, Beijing 100084, China
5University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
6Fraunhofer Institute for Mechanics of Materials IWM, 79108 Freiburg, Germany

Abstract: [+]    |    Download File [ 527KB ]    |   Read Article Online

Abstract: Friction occurs when surfaces of solid bodies touch and move against each other. Energy is thereby converted into heat that is lost. In order to reduce the friction in the metallic elements during sliding, for example in automobiles or industrial machines, materials with a lamellar structure are commonly used as the solid lubricants. One of the dry lubricants is graphite, which has a three-dimensional layered structure.

The Last Nanometer – Hydration Structure of DNA and Solid Surfaces Probed by Ultra High Resolution AFM

doi: https://doi.org/10.13052/jsame2245-4551.2018017
Uri Sivan

Technion – Israel Institute of Technology, Haifa, Israel

Abstract: [+]    |    Download File [ 177KB ]    |   Read Article Online

Abstract: Recent advancements in atomic force microscopy facilitate atomic-resolution threedimensional mapping of hydration layers next to macromolecules and solid surfaces. These maps provide unprecedented information on the way water molecules organize and bind these objects. Since the hydration structure governs the energetics of solvation and interactions between objects immersed in solution, the new data are invaluable when trying to resolve fundamental questions such as identification of molecular binding sites and interaction mechanisms.

Self-recovery, Fatigue and Anti-fatigue of Supramolecular Elastomers

doi: https://doi.org/10.13052/jsame2245-4551.2018016
A.D. Drozdov and J. deClaville Christiansen

Aalborg University, Aalborg, Denmark

Abstract: [+]    |    Download File [ 151KB ]    |   Read Article Online

Abstract: Supramolecular elastomers (SMEs) are three-dimensional networks of polymer chains bridged by covalent cross-links and non-covalent bonds with finite lifetimes. The reversible noncovalent bonding is based on (i) metal-ligand coordination, (ii) electrostatic interaction, (iii) hydrophobic association, (iv) hydrogen bonding, and (v) host-guest recognition. An advantage of these materials compared with conventional vulcanized rubbers and thermoplastic elastomers is their ability of rapid self-healing after damage at ambient temperature. The mechanical response of SMEs is characterized by (i) rapid relaxation of stresses (with the characteristic time of a few minutes), (ii) self-recovery (a monotonic reduction in plastic strain with time after cyclic loading), and (iii) anti-fatigue (an increase in maximum stress with number of cycles under deformation programs with intervals of recovery between cycles).

Molecularly Guided Assembly of Colloidal Nanoparticles in Solution and on Substrates

doi: https://doi.org/10.13052/jsame2245-4551.2018015
Sarah Lerch1, Björn M. Reinhard2 and Kasper Moth-Poulsen1,∗

1Chalmers University of Technology, Gothenburg, Sweden
2Boston University, Boston, Massachusetts, USA

Abstract: [+]    |    Download File [ 329KB ]    |   Read Article Online

Abstract: Plasmonic nanoparticles are increasingly important tools in sensing, drug delivery and catalysis, but an increasing number of synthetic and assembly techniques are required to design the desired nanostructures. Synthesis of nanoparticles and the assembly of these particles into larger combinations typically fall into two categories: top-down methods, typically using lithographic or nanoimprinting techniques, and bottom-up synthesis, typically using molecularly guided self-assembly of colloidal particles. There are advantages for each method, primarily associated with the control of assembly in the top-down methods versus the versatility and variety of colloidal particles available for the bottom-up synthesis.

Self-assembly of block-copolymer structures for in-situ nano-lithography

doi: https://doi.org/10.13052/jsame2245-4551.2018014
Emil Ludvigsen1, Agnieszka Telecka1, Tao Li1,2, Sokol Ndoni 1 and Rafael Taboryski1,∗

1Technical University of Denmark, Kgs. Lyngby, Denmark
2University College London, London, UK

Abstract: [+]    |    Download File [ 307KB ]    |   Read Article Online

Abstract: In this paper we report how block-copolymer (BCP) self-assembly of polystyrene–b– polydimethylsiloxane (PS–PDMS) is used for in-situ nano-lithography to fabricate hexagonally ordered nanostructures on the surface of Si.[1] This is done by forming an in-situ etch mask on the Si surface by spin coating of the BCP in solution and subsequent solvent annealing, and reactive ion-etching (RIE) steps. The wetting properties of the fabricated structures are studied to reveal a multitude of possible wetting and anti-wetting configurations, depending on the subsequent fabrication and surface coating steps.

Fabrication of DNA Concatemers Containing Multiple Modifications

doi: https://doi.org/10.13052/jsame2245-4551.2018013
Liat Katrivas and Alexander Kotlyar

Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel

Abstract: [+]    |    Download File [ 204KB ]    |   Read Article Online

Abstract: Here we describe the construction of double stranded (ds) concatemers composed of short (6- 10 bases) repeating tandem oligonucleotides units containing modified nucleotides. The synthesis of incudes: self-association of the 5’-end phosphorylated half-complementary oligonucleotides into long (hundreds of base pairs) ds nucleic acid polymers and covalent linkage of the oligonucleotides in the strand by DNA ligase (Fig. 1B). The oligonucleotides containing various modified nucleotides can be assembled into long (hundreds of nanometers) ds concatamers. One of these nucleotides is amino-modified thymine in which the amino group is linked to 5-position of the pyrimidine ring via two or six carbon atom spacer arms.

Probing the dielectric constant at the nanoscale: from thin films to DNA and confined water

doi: https://doi.org/10.13052/jsame2245-4551.2018012
Laura Fumagalli

School of Physics and Astronomy - Condensed Matter Physics, University of Manchester, Manchester, UK
National Graphene Institute, Manchester, UK

Abstract: [+]    |    Download File [ 99KB ]    |   Read Article Online

Abstract: The dielectric constant (or electric polarizability), e r, is a fundamental physical property of matter which depends on chemical composition, structure and phase. It plays a crucial role in a wide range of phenomena and disciplines, from physics and materials science to chemistry and molecular biology. For example, in physics, it is inherently linked to charge storage and electric transport. In biology, it modulates long-range electrostatic and van der Waals interactions that are crucial for macromolecular assembly and interactions. Yet, probing local dielectric properties has remained a long-standing technical challenge because the signals that have to be detected are extremely weak and buried into non-local and geometric artefacts.

Single molecule fluorescence investigations of DNA-based self-assembled structures

doi: https://doi.org/10.13052/jsame2245-4551.2018011
Victoria Birkedal

Department of Chemistry, Aarhus University, Aarhus, Denmark
Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark

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Abstract: DNA can fold into a number of secondary structures that play a role in the regulation of gene expression [1]. It can also be harnessed as a building block in the field of DNA nanotechnology to create both static and dynamic DNA structures of all shapes with sizes ranging from a few to several hundreds of nanometers [2]. Owing to their phenomenal addressability, these DNA nanostructures are attractive platforms for organizing matter at the molecular level and provide high flexibility for positioning fluorescent molecules.

Printing of self-assembled DNA hybrid materials

doi: https://doi.org/10.13052/jsame2245-4551.2018009
Tom Bamford1, Raushan Nurdillayeva2, Benjamin Horrocks1 and Andrew Pike1

1Chemical Nanosciecne Laboratory, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
2Khoja Akhmet Yassawi International Kazakh-Turkish University, Turkistan, 161200, Kazakhstan

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Abstract: The conductivity of DNA-templated nanowires is less than that of bulk material or other types of nanowire, and as their structure is granular they are not usually useful as interconnects. Single nanowire devices are rather fragile and a single break can destroy the device completely meaning networks or bundles of nanowires are used instead. The simple drop-casting of DNA-templated nanowires leads to the formation of networks due to the intermolecular interactions as the liquid evaporates. However, this deposition process lacks control and the final pattern is of low resolution. On the other hand, inkjet printing is the controlled deposition of material at high resolution and has been routinely used to print conductive materials. Most conductive inks contain metal nanoparticles and are formulated at concentrations much higher than DNA-templated nanowires. Here we report the use of inkjet printing to prepare patterns of DNA-hybrid materials for electrical characterisation.

Toward electronically-functional, self-assembling DNA nanostructures

doi: https://doi.org/10.13052/jsame2245-4551.2018008
S. Vecchioni1, M. C. Capece2, E. Toomey3, L. J. Rothschild4 and S. J. Wind5,∗

1Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
2Department of Chemistry, Stanford University, Stanford, CA 94305, USA
3Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4NASA Ames Research Center, Biospheric Science Branch, Moffett Field, CA 94035, USA
5Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA

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Abstract: Recent work has demonstrated that DNA, ordinarily considered a weak conductor, can be functionalized to carry electronic charge by site-specific incorporation of single silver ions inside the double helix via the non-canonical pairing of mismatched cytosines through Ag+ coordination: (dC:Ag+:dC) [1,2]. Through the alteration of sequence composition and cation availability, a variety of nanowires can be synthesized with tuneable length, ion distribution, and uniformity. These wires are more thermostable than Watson-Crick DNA, can shield intercalated Ag+ from aqueous solvents, and are able to form in the absence of cluster contamination. We use computational sequence design algorithms to introduce nonlinear geometry to these nanowires, with the goal of creating self-assembling DNA nanostructures that may have potential for neural architectures from electrically-functional oligonucleotide components.

Novel DNA-Based Molecules and Their Charge Transport Properties

doi: https://doi.org/10.13052/jsame2245-4551.2018007
Danny Porath

Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Israel

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Abstract: Charge transport through molecular structures is interesting both scientifically and technologically. To date, DNA is the only type of polymer that transports significant currents over distances of more than a few nanometers in individual molecules. Nevertheless and in spite of large efforts to elucidate the charge transport mechanism through DNA a satisfying characterization and mechanistic description has not been provided yet. For molecular electronics, DNA derivatives are by far more promising than native DNA due to their improved charge-transport properties.

Small-angle Scattering of X-rays and Neutrons as Structural Tools in Nanoscience: Block Copolymer Micelles, Protein-detergent Complexes, Microgels and other Nanoparticles

doi: https://doi.org/10.13052/jsame2245-4551.2018006
Jan Skov Pedersen

Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark

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Abstract: Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are excellent experimental tools for obtaining structural information on macromolecules, selfassembled structures, and nanoparticles in solution. The techniques give information on shape, size and organization of particles and molecules of sizes up to hundreds of nanometers with sub-nm resolution. It also provides key parameters such as mass, maximum diameter and radius of gyration. In contrast to many other techniques, SAXS and SANS does not require any special sample preparation or deuteration, and can be performed for almost any solvent/buffer condition, however, D2O is usually used in the buffers for SANS as it enhances contrast and reduce background. Furthermore, the studied assemblies or particles may be amorphous or crystalline, may have disordered region or randomness, and may have (smaller) variation in size and shape without spoiling the possibility of structure determination. However, deriving detailed structural information from SAXS data requires sophisticated analysis approaches [1,2]. There has been a large progress in analysis within the last decades and this has led to broad field of applications of the SAXS and SANS methods. In this lecture, the basic principles and theory will be described and some recent applications to block copolymer micelles [3], protein-detergent complexes [4] and microgels [5] will be presented.

New Nanoscale Polymer Systems And Their Interaction With Living Objects

doi: https://doi.org/10.13052/jsame2245-4551.2018005
M. I. Shtilman1,∗, A. N. Kuskov1, P. P. Kulikov1, A. L. Luss1, A. V. Goryachaya1, V. T. Dzhedzheya1, S. A. Gusev2, P. Henrich-Noack3, L. Gurevich4, V. P. Torchilin5, A. M. Tsatsakis6

1D.I.Mendeleyev University of Chemical Technology of Russian, Department of Biomaterials. Moscow, Russia
2Clinical Center for Physical-Chemical Medicine, Moscow, Russia
3Institute of Medical Psychology, Otto-von-Guericke University, Magdeburg, Germany
4Aalborg University, Aalborg, Denmark
5Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA
6University of Crete, Medical School, Division Morphology, Greece

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Abstract: The synthesis methods and properties of amphiphilic polymers of N-vinylpyrrolidone, acrylamide, acrylic acid were studied and it was shown that these systems can be used for modification of liposomal membranes and as micelles-like aggregates [1,2]. To the date, methods have been developed for the preparation of nanoparticles based on such polymers with immobilized poorly-soluble or insoluble in water low molecular weight, biologically active compounds, such as indomethacin, diclofenac, amphotericin B, nystatin, 5- fluorouracil, rifabutin, felodipine, ionol, curcumin.

Drug delivery to the brain: How to overcome the blood-brain barrier?

doi: https://doi.org/10.13052/jsame2245-4551.2018004
Louiza Bohn Thomsen1

Laboratory of Neurobiology, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark

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Abstract: Neurological diseases such as Alzheimer’s disease and Parkinson Disease are becoming more prevalent worldwide. Unfortunately, treatment of neurological diseases is hindered by the inability of up to 98% of drugs with therapeutic relevance to cross the blood-brain barrier (BBB).

The blood-brain barrier (BBB) forms a chemical, physical and immunological barrier between the blood and the brain tissue. The BBB is formed by brain capillary endothelial cells (BCECs), which are interconnected by tight junctions, creating a tight seal between BCECs. Furthermore astrocytes and pericytes are situated in the near vicinity of the BCECs and helps strengthen the barrier properties of the BCECs.

Functional Electrospun Phospholipid Nano-microfibers

doi: https://doi.org/10.13052/jsame2245-4551.2018003
Ana C. Mendes, and Ioannis S. Chronakis*

Technical University of Denmark, DTU Food, Nano-BioScience Research Group, Kemitorvet, B202, DK-2800 Kgs. Lyngby, Denmark

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Abstract: Functional asolectin phospholipid nano-microfibers were developed using electrospinning processing with a range of fiber diameters and morphologies, depending on the phospholipid concentration and the solvent used [1,2]. Chloroform and dimethylformamide, isooctane, cyclohexane and limonene were used as solvents. A critical concentration of phospholipids is essential to favor the intermolecular association between the micelles, required for the formation of asolectin electrospun fibers. The dielectric constant of the solvents had a strong influence on the electrospinning jet split properties and affected the morphology of the electrospun asolectin nano-microfibers, while co-axial electrospinning could be used to tune their average diameter. The mechanical properties and the stability at ambient conditions of phospholipid fibers were assessed by nanoindentation using Atomic Force Microscopy [2]. Their elastic modulus was found to be approximately 17.2 ±1 MPa, and at a cycle of piezo expansion-retraction (loading-unloading) of a silicon tip on a fiber, a relatively high adhesion was observed during unloading. Moreover, the efficacy of electrospun phospholipid microfibers as antioxidants, encapsulation, and delivery matrices for bioactive compounds and transdermal drugs, were also confirmed [3,4].

Design of (Thermo)Responsive Polymer-Grafted Nanoparticles for Biological Applications

doi: https://doi.org/10.13052/jsame2245-4551.2018002
Erik Reimhult

University of Natural Resources and Life Sciences, Vienna, Austria

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Abstract: Nanoparticles grafted with polymers are used and developed for a multitude of biomedical and biotechnological applications (Figure 1), such as imaging contrast agents, hyperthermia treatment drug delivery, separation and purification [1,2]. Unique functions can be achieved for these applications by using nanoscale inorganic cores, such as nanoplasmonic metal cores or superparamagnetic oxide cores. However, the grafted polymer shell must prevent undesired colloidal interactions with biomolecules and cells that lead to aggregation and clearance to enable these functions in a biological environment; it also must promote desired specific biological interactions such as molecular and cellular targeting [1]. It is widely recognized that one of the best ways to achieve this is through grafting of the core particle with a dense brush of hydrophilic polymer, e.g. poly(ethylene glycol), which prevents protein and other biomolecules from binding to the particle and provides a scaffold for controlled functionalization with biofunctional ligands.

Immobilization of recombinant β-glucosidase on magnetic nanoparticles and its potential in production of ginsenoside F2 and Compound K

doi: https://doi.org/10.13052/jsame2245-4551.2018001
Bianling Zhang1, Zhengjun Fang1,2, Wanmin Liu1,2, Qiang Tao1,2 and Ru Zhang1,2

1College of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
2Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark

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Abstract: In the present study, BbBgl gene was cloned and expressed in E. coli BL21. The β- glucosidase was purified by Ni-NTA magnetic beads to obtain an enzyme with specific activity of 37 U/mg protein using pNP-Glc as substrate. The enzyme activity was optimized at pH 5.0, 35°C, 2 or 6 U/ml. The recombinant β-glucosidase was immobilized to magnetic Fe3O4 nanoparticles. Furthermore, the optimal conditions for the immobilization and some characteristics of immobilized enzyme were studied. The optimal immobilization conditions observed were enzyme 0.15 mg (1 mg/mL, 0.15 mL), magnetic Fe3O4 nanoparticles 3 mg, pH 5.0, immobilization time 4 h. The results showed that the optimal reaction temperature of immobilized enzyme kept in a high activity from 35°C to 40°C. Thermal stability of the immobilized enzyme also had an improvement, the residual activity retained 62% and 57% after 180 h at 35°C and 40°C, respectively, while free enzymes only showed 55% and 51% remnant activity at the same condition.

River Publishers: Journal of Self-Assembly and Molecular Electronics