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  • 1.
    Pathak, Biswarup
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Löfås, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Prasongkit, Jariyanee
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Double-functionalized nanopore-embedded gold electrodes for rapid DNA sequencing2012In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 100, no 2, p. 023701-Article in journal (Refereed)
    Abstract [en]

    We have studied the effect of double-functionalization on gold electrodes for improving nanopore-based DNA sequencing. The functionalizing molecular probes are, respectively, capable of temporarily forming hydrogen bonds with both the nucleobase part and the phosphate group of the target DNA, thus potentially minimizing the structural fluctuations of a single-stranded DNA molecule passing between the gold electrodes. The results of our first-principles study indicate that the proposed setup yields current signals that differ by at least 1 order of magnitude for the four different nucleic acid bases, thus offering the possibility to electrically distinguish them.

  • 2.
    Prasongkit, Jariyanee
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Molecular Electronics: Insight from Ab-Initio Transport Simulations2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents the theoretical studies of electronic transport in molecular electronic devices. Such devices have been proposed and investigated as a promising new approach that complements conventional silicon-based electronics. To design and fabricate future nanoelectronic devices, it is essential to understand the conduction mechanism at a molecular or atomic level. Our approach is based on the non-equilibrium Green's function method (NEGF) combined with density functional theory (DFT). We apply the method to study the electronic transport properties of two-probe systems consisting of molecules or atomic wires sandwiched between leads. A few molecular electronic devices are characterized; namely, conducting molecular wires, molecular switches and molecular recognition sensors. The considered applications are interconnection of different nanoelectronic units with cumulene molecular wires; adding switching functionality to the molecular connectors by applying stress to the CNT-cumulene-CNT junction or by introducing phthalocyanine unit; sensing of individual nucleotides, e.g., for DNA sequencing applications. The obtained results provide useful insights into the electron transport properties of molecules. Several interesting and significant features are analyzed and explained in particular such as, level pinning, negative differential resistance, interfering of conducting channels etc.

    List of papers
    1. Cumulene molecular wire conductance from first principles
    Open this publication in new window or tab >>Cumulene molecular wire conductance from first principles
    2010 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 81, no 11, p. 115404-Article in journal (Refereed) Published
    Abstract [en]

    We present first principles calculations of current-voltage characteristics (IVC) and conductance of Au(111):S-2-cumulene-S-2:Au(111) molecular wire junctions with realistic contacts. The transport properties are calculated using full self-consistent ab initio nonequilibrium Green's function density-functional theory methods under external bias. The conductance of the cumulene wires shows oscillatory behavior depending on the number of carbon atoms (double bonds). Among all conjugated oligomers, we find that cumulene wires with odd number of carbon atoms yield the highest conductance with metalliclike ballistic transport behavior. The reason is the high density of states in broad lowest unoccupied molecular orbital levels spanning the Fermi level of the electrodes. The transmission spectrum and the conductance depend only weakly on applied bias, and the IVC is nearly linear over a bias region of +/- 1 V. Cumulene wires are therefore potential candidates for metallic connections in nanoelectronic applications.

    National Category
    Physical Sciences Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-137108 (URN)10.1103/PhysRevB.81.115404 (DOI)000276248800117 ()
    Available from: 2010-12-15 Created: 2010-12-15 Last updated: 2017-12-11Bibliographically approved
    2. Conductance of linear carbon wires bridging carbon nanotubes
    Open this publication in new window or tab >>Conductance of linear carbon wires bridging carbon nanotubes
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The cumulenes bridging two-dimensional electrodes provide a model for interconnecting molecular electronics circuit with one of the most conductive molecular wires known. In recent experiments cumulene molecules bridging graphene sheets were observed [PRL 102, 205501 (2009)], thus demonstrating the mechanical way of producing cumulenes. Appearance of carbon wires: cumulenes and polynes, is also feasible between graphene sheets or carbon nanotubes (CNTs). In this work, we study structure and conductance of these wires  suspended between CNTs of different chirality (zigzag and armchair), and graphene sheets (infinite radii CNTs) and corresponding conductance variation upon stretching. We find the geometrical structures of the carbon wire bridging CNT similar to the experimentally observed in the carbon wires obtained between graphene electrodes. We show a capability to modulate the conductance by changing bridging sites between the carbon wire and CNT without breaking the wire. Observed current modulation via cumulene wire stretching/elongation together with CNT stability makes it a promising candidate for mechano-switching device in molecular nanoelectronics.

    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-160469 (URN)
    Projects
    KoF U3MEC
    Available from: 2011-10-24 Created: 2011-10-24 Last updated: 2012-04-25
    3. Interference effects in phtalocyanine controlled by H-H tautomerization: Potential two-terminal unimolecular electronic switch
    Open this publication in new window or tab >>Interference effects in phtalocyanine controlled by H-H tautomerization: Potential two-terminal unimolecular electronic switch
    2011 (English)In: Physical Review B Condensed Matter, ISSN 0163-1829, E-ISSN 1095-3795, Vol. 84, no 16, p. 165437-Article in journal (Refereed) Published
    Abstract [en]

    We investigate the electrical transport properties of two hydrogen tautomer configurations of phthalocyanine (H2Pc) connected to cumulene and gold leads. Hydrogen tautomerization affects the electronic state of H2Pc by switching the character of molecular orbitals with the same symmetry close to the Fermi level. The near degeneracy between the HOMO and HOMO-1 leads to pronounced interference effects, causing a large change in current for the two tautomer configurations, especially in the low-bias regime. Two types of planar junctions are considered: cumulene-H2Pc-cumulene and gold-H2Pc-gold. Both demonstrate a prominent difference in molecular conductance between ON and OFF states. In addition, junctions with gold leads show pronounced negative differential resistance (NDR) at high bias voltage, as well as weak NDR at intermediate bias.

    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-160466 (URN)10.1103/PhysRevB.84.165437 (DOI)000296371200009 ()
    Projects
    KoF U3MEC
    Available from: 2011-10-24 Created: 2011-10-24 Last updated: 2017-12-08Bibliographically approved
    4. Transverse Conductance of DNA Nucleotides in a Graphene Nanogap from First Principles
    Open this publication in new window or tab >>Transverse Conductance of DNA Nucleotides in a Graphene Nanogap from First Principles
    Show others...
    2011 (English)In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 11, no 5, p. 1941-1945Article in journal (Refereed) Published
    Abstract [en]

    The fabrication of nanopores in atomically thin graphene has recently been achieved, and translocation of DNA has been demonstrated. Taken together with an earlier proposal to use graphene nanogaps for the purpose of DNA sequencing, this approach can resolve the technical problem of achieving single-base resolution in electronic nucleobase detection. We have theoretically evaluated the performance of a graphene nanogap setup for the purpose of whole-genome sequencing, by employing density functional theory and the nonequilibrium Green's function method to investigate the transverse conductance properties of nucleotides inside the gap. In particular, we determined the electrical tunneling current variation at finite bias due to changes in the nucleotides orientation and lateral position. Although the resulting tunneling current is found to fluctuate over several orders of magnitude, a distinction between the four DNA bases appears possible, thus ranking the approach promising for rapid whole-genome sequencing applications.

    Keywords
    DNA sequencing, graphene, nanogap, ab initio, electronic transport, molecular electronics
    National Category
    Atom and Molecular Physics and Optics
    Research subject
    Physics with spec. in Atomic, Molecular and Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-153682 (URN)10.1021/nl200147x (DOI)000290373000015 ()21495701 (PubMedID)
    Projects
    KoFF U3MEC
    Funder
    Swedish Research Council, 113501971
    Available from: 2011-05-18 Created: 2011-05-17 Last updated: 2017-12-11Bibliographically approved
    5. Theoretical Study of Electronic Transport through DNA Nucleotides in a Double-Functionalized Graphene Nanogap
    Open this publication in new window or tab >>Theoretical Study of Electronic Transport through DNA Nucleotides in a Double-Functionalized Graphene Nanogap
    Show others...
    2013 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, no 29, p. 15421-15428Article in journal (Refereed) Published
    Abstract [en]

    Graphene nanogaps and nanopores show potential for the purpose of electrical DNA sequencing, in particular because single-base resolution appears to be readily achievable. Here, we evaluated from first principles the advantages of a nanogap setup with functionalized graphene edges. To this end, we employed density functional theory and the non-equilibrium Green's function method to investigate the transverse conductance properties of the four nucleotides occurring in DNA when located between opposing functionalized graphene electrodes. In particular, we determined the electrical tunneling current variation as a function of the applied bias and analyzed the associated differential conductance at a voltage which appears suitable to distinguish between the four nucleotides. Intriguingly, we predict for one of the nucleotides (deoxyguanosine monophosphate) a negative differential resistance effect.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-208163 (URN)10.1021/jp4048743 (DOI)000322503600064 ()
    Available from: 2013-09-24 Created: 2013-09-24 Last updated: 2017-12-06Bibliographically approved
  • 3.
    Prasongkit, Jariyanee
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Mechano-switching devices from carbon wire-carbon nanotube junctions2013In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 87, no 15, p. 155434-155442Article in journal (Refereed)
    Abstract [en]

    Well-known conductive molecular wires, such as cumulene or polyyne, provide a model for interconnectingmolecular electronics circuits. In recent experiments, the appearance of carbon wire bridging between twodimensional electrodes, i.e., graphene sheets, was observed [C. Jinet al.,Phys. Rev. Lett.102, 205501 (2009)], thusdemonstrating a mechanical way of producing cumulene. In this work, we studied the structure and conductanceof carbon wire suspended between carbon nanotubes (CNTs) of different chiralities (zigzag and armchair), andcorresponding conductance variation upon stretching. We found that the geometric structure of the carbon wirebridging CNTs was similar to the experimentally observed structures in carbon wire obtained between grapheneelectrodes. We show a way to modulate conductance by changing bridging sites between carbon wire and CNTswithout breaking the wire. Observed current modulation via cumulene wire stretching or elongation together withCNT junction stability makes this a promising candidate for use in mechano-switching devices for molecularnanoelectronics.

  • 4.
    Prasongkit, Jariyanee
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Pathak, Biswarup
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Theoretical Study of Electronic Transport through DNA Nucleotides in a Double-Functionalized Graphene Nanogap2013In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, no 29, p. 15421-15428Article in journal (Refereed)
    Abstract [en]

    Graphene nanogaps and nanopores show potential for the purpose of electrical DNA sequencing, in particular because single-base resolution appears to be readily achievable. Here, we evaluated from first principles the advantages of a nanogap setup with functionalized graphene edges. To this end, we employed density functional theory and the non-equilibrium Green's function method to investigate the transverse conductance properties of the four nucleotides occurring in DNA when located between opposing functionalized graphene electrodes. In particular, we determined the electrical tunneling current variation as a function of the applied bias and analyzed the associated differential conductance at a voltage which appears suitable to distinguish between the four nucleotides. Intriguingly, we predict for one of the nucleotides (deoxyguanosine monophosphate) a negative differential resistance effect.

  • 5.
    Prasongkit, Jariyanee
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Scheicher, Ralph
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Transport properties of nucleotides in a graphene nanogap for DNA sequencing2010In: ElecMol’10 5th International Meeting on Molecular Electronics December 6-10, 2010, 2010, p. 86-86Conference paper (Other academic)
  • 6.
    Prasongkit, Jariyanee
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Wendin, Goran
    Department of Microtechnology and Nanoscience-MC2, Chalmers University of Technology.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Interference effects in phtalocyanine controlled by H-H tautomerization: Potential two-terminal unimolecular electronic switch2011In: Physical Review B Condensed Matter, ISSN 0163-1829, E-ISSN 1095-3795, Vol. 84, no 16, p. 165437-Article in journal (Refereed)
    Abstract [en]

    We investigate the electrical transport properties of two hydrogen tautomer configurations of phthalocyanine (H2Pc) connected to cumulene and gold leads. Hydrogen tautomerization affects the electronic state of H2Pc by switching the character of molecular orbitals with the same symmetry close to the Fermi level. The near degeneracy between the HOMO and HOMO-1 leads to pronounced interference effects, causing a large change in current for the two tautomer configurations, especially in the low-bias regime. Two types of planar junctions are considered: cumulene-H2Pc-cumulene and gold-H2Pc-gold. Both demonstrate a prominent difference in molecular conductance between ON and OFF states. In addition, junctions with gold leads show pronounced negative differential resistance (NDR) at high bias voltage, as well as weak NDR at intermediate bias.

  • 7.
    Prasongkit, Jariyanee
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Shukla, Vivekanand
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Amornkitbamrung, Vittaya
    Division of Physics, Faculty of Science, Nakhon Phanom University.
    Ultrahigh-sensitive gas sensors based on doped phosphorene: A First-principles investigation2019In: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 497, article id UNSP 143660Article in journal (Other academic)
    Abstract [en]

    Recent significant advancements have been made in demonstrating the usage of phosphorene to detect the presence of gases leading to a new breed of gas sensor device. Based on pristine phosphorene, the devices can detect a small concentration of adsorbed molecules with high sensitivity at room temperature. In this work, we propose doping silicon and sulfur impurity atoms into phosphorene to drastically improve its gas sensing performance. We use a combination of density functional theory and non-equilibrium Green's function method to evaluate the sensitivity and selectivity of doped phosphorene nanosensors for four gases (NO, NO2, NH3, and CO). Both devices demonstrate a prominent distinction in conductance when the gas molecules are exposed to the sensor surface. We suggest the doped phosphorene may present advantages over the device based purely on phosphorene due to the ability to discriminate different gases controlled by types of dopants.

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