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  • 1.
    Amorim, Rodrigo G.
    et al.
    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.
    Silicene as a new potential DNA sequencing device2015In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 26, no 15, article id 154002Article in journal (Refereed)
    Abstract [en]

    Silicene, a hexagonal buckled 2D allotrope of silicon, shows potential as a platform for numerous new applications, and may allow for easier integration with existing silicon-based microelectronics than graphene. Here, we show that silicene could function as an electrical DNA sequencing device. We investigated the stability of this novel nano-bio system, its electronic properties and the pronounced effects on the transverse electronic transport, i.e., changes in the transmission and the conductance caused by adsorption of each nucleobase, explored by us through the non-equilibrium Green's function method. Intriguingly, despite the relatively weak interaction between nucleobases and silicene, significant changes in the transmittance at zero bias are predicted by us, in particular for the two nucleobases cytosine and guanine. Our findings suggest that silicene could be utilized as an integrated-circuit biosensor as part of a lab-on-a-chip device for DNA sequencing.

  • 2.
    Araujo, Moyses
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Blomqvist, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Chen, Ping
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Superionicity in the hydrogen storage material Li2NH: Molecular dynamics simulations2009In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 79, no 17, p. 172101-Article in journal (Refereed)
    Abstract [en]

    We have employed ab initio molecular dynamics simulations in an attempt to study a temperature-induced order-disorder structural phase transformation that occurs in Li2NH at about 385 K. A structural phase transition was observed by us in the temperature range 300-400 K, in good agreement with experiment. This transition is associated with a melting of the cation sublattice (Li+), giving rise to a superionic phase, which in turn is accompanied by an order-disorder transition of the N-H bond orientation. The results obtained here can contribute to a better understanding of the hydrogen storage reactions involving Li2NH and furthermore broaden its possible technological applications toward batteries and fuel cells.

  • 3.
    Araujo, Rafael B.
    et al.
    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.
    de Almeida, J. S.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ferreira da Silva, A.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Lithium transport investigation in LixFeSiO4: A promising cathode material2013In: Solid State Communications, ISSN 0038-1098, E-ISSN 1879-2766, Vol. 173, p. 9-13Article in journal (Refereed)
    Abstract [en]

    In this paper we investigate lithium mobility in both Li2FeSiO4 and its   half-lithiated state LiFeSiO4 considering an orthorhombic crystal   structure. We find that the calculated activation energy of Li+ ions   hopping between adjacent equilibrium sites predicts two least hindered   diffusion pathways in both materials. One of them is along the [100]   direction characterizing an ionic diffusion in a straight line and the   other follows a zig-zag way between the Fe-Si-O layers. We also show   that diffusion of Li+ ions in the half-lithiated structure follows the   same behavior as in the lithiated structure. As a whole, the activation   energies for the investigated compounds present a greater value compared   with the activation energies in currently used materials such as   LiFePO4. The results were calculated in the framework of density   functional theory in conjunction with the climbing image nudged elastic   band method. The Hubbard term was added to the Kohn-Sham Hamiltonian to   overcome the delocalization problem of d electrons. Furthermore, the   diffusion coefficients were calculated for both structures considering   temperatures ranging from 300 to 700 K. (C) 2013 Elsevier Ltd. All   rights reserved.

  • 4. Araujo, Rafael Barros Neves de
    et al.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    de Almeida, J. S.
    Ferreira da Silva, A.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    First-principles investigation of Li ion diffusion in Li2FeSiO42013In: Solid State Ionics, ISSN 0167-2738, E-ISSN 1872-7689, Vol. 247, p. 8-14Article in journal (Refereed)
    Abstract [en]

    We have studied the Li-ion migration and the electrochemical performance of Li2FeSiO4 in the monoclinic crystal structure with P2(1) symmetry and the related delithiated system LiFeSiO4. For this purpose, the framework of the density functional theory within the generalized gradient approximation in conjunction with the climbing image nudged elastic band method was used. Addition of the Hubbard term was also considered in the Kohn-Sham Hamiltonian to better model the d electrons of the metal ions in this material. The calculated activation energies for Li ion migration are found to decrease by around 20% with the Hubbard term inclusion in the chosen diffusion pathways of Li2FeSiO4. Regarding the delithiated structure, the activation energies were found to be sensitive to the Hubbard term addition, however no general behavior such as in the lithiated structure was found. Furthermore, the diffusion coefficients were calculated considering temperatures of 300 K, 500 K, and 700 K.

  • 5.
    Araújo, C. Moysés
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Blomqvist, Andreas
    Scheicher, Ralph H.
    Ahuja, Rajeev
    Structural transition in lithium imide triggered by melting of cation sublatticeIn: Phys. Rev. Lett.Article in journal (Refereed)
  • 6.
    Araújo, C. Moysés
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Condensed Matter Theory.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Condensed Matter Theory.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Condensed Matter Theory.
    Thermodynamic analysis of hydrogen sorption reactions in Li-Mg-N-H systems2008In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 92, no 2, p. 021907-Article in journal (Refereed)
    Abstract [en]

    We report a comprehensive first-principles study of the thermodynamics of the hydrogen release reaction from xLiH-yMg(NH2)(2) mixtures involving the composition ratios (x=2, y=1), (x=8, y=3), and (x=12, y=3), with special emphasis on the effect of the different intermediate steps. For all three mixing ratios of LiH/Mg(NH2)(2) we find that the hydrogen release is initiated by the same reaction with an enthalpy of 46.1 kJ/mol of H-2 in excellent agreement with recent experimental results. Additionally, we also investigated the substitution of LiH by MgH2 as reaction partner of Mg(NH2)(2) in the fully hydrogenated state.

  • 7.
    Araújo, C. Moysés
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Jena, Puru
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    On the structural and energetic properties of the hydrogen absorber Li2Mg(NH)22007In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 91, no 9, p. 091924-Article in journal (Refereed)
    Abstract [en]

    The authors have performed density functional theory based calculations of several possible conformations for the crystal structure of Li2Mg(NH)2 and they confirm the α phase, resolved from both x-ray and neutron diffraction data, as the ground-state configuration. It is also found that although the N-H bond is stronger in Li2Mg(NH)2 than in Li2NH, hydrogen release from Li2Mg(NH)2/LiH mixture displays more favorable thermodynamics than that from the Li2NH/LiH mixture. The insights gained from this seemingly counterintuitive result should prove helpful in the search for promising hydrogen storage materials.

  • 8.
    Arjmandi-Tash, Hadi
    et al.
    Leiden Univ, Leiden Inst Chem, Fac Sci, NL-2333 CC Leiden, Netherlands..
    Bellunato, Amedeo
    Leiden Univ, Leiden Inst Chem, Fac Sci, NL-2333 CC Leiden, Netherlands..
    Wen, Chenyu
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Olsthoorn, Rene C.
    Leiden Univ, Leiden Inst Chem, Fac Sci, NL-2333 CC Leiden, Netherlands..
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Zhang, Shi-Li
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Schneider, Gregory F.
    Leiden Univ, Leiden Inst Chem, Fac Sci, NL-2333 CC Leiden, Netherlands..
    Zero-Depth Interfacial Nanopore Capillaries2018In: Advanced Materials, ISSN 0935-9648, E-ISSN 1521-4095, Vol. 30, no 9, article id 1703602Article in journal (Refereed)
    Abstract [en]

    High-fidelity analysis of translocating biomolecules through nanopores demands shortening the nanocapillary length to a minimal value. Existing nanopores and capillaries, however, inherit a finite length from the parent membranes. Here, nanocapillaries of zero depth are formed by dissolving two superimposed and crossing metallic nanorods, molded in polymeric slabs. In an electrolyte, the interface shared by the crossing fluidic channels is mathematically of zero thickness and defines the narrowest constriction in the stream of ions through the nanopore device. This novel architecture provides the possibility to design nanopore fluidic channels, particularly with a robust 3D architecture maintaining the ultimate zero thickness geometry independently of the thickness of the fluidic channels. With orders of magnitude reduced biomolecule translocation speed, and lowered electronic and ionic noise compared to nanopores in 2D materials, the findings establish interfacial nanopores as a scalable platform for realizing nanofluidic systems, capable of single-molecule detection.

  • 9. Aryal, M. M.
    et al.
    Mishra, D. R.
    Paudyal, D. D.
    Byahut, S.
    Maharjan, N. B.
    Adhikari, N. P.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Jeong, Junho
    Badu, S. R.
    Pink, R. H.
    Chow, Lee
    Das, T. P.
    Understanding of nuclear quadrupole interactions of Cl-35, Br-79 and I-129 and binding energies of solid halogens at first-principles level2007In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 176, no 1-3, p. 51-57Article in journal (Refereed)
    Abstract [en]

    This paper deals with the understanding at a first-principles level of the nuclear quadrupole interaction (NQI) parameters of solid chlorine, bromine and iodine as well as the intermolecular binding of these molecules in the solid. The electronic structure investigations that we have carried out to study these properties of the solid halogens are based on the Hartree-Fock Cluster approach using the Roothaan variational procedure with electron correlation effects included using many-body perturbation theory with the empty orbitals used in the perturbation theory investigations for the excited states. The results of our investigations provide good agreement with the measured NQI parameters primarily from the Hartree-Fock one electron wave-functions with many-body effects making minor contributions. The binding (dissociation) energies for the molecules with the solid state environment on the other hand arises from intermolecular many body effects identified as the Van der Waals attraction with one-electron Hartree-Fock contribution being repulsive in nature.

  • 10. Berseth, Polly A
    et al.
    Harter, Andrew G
    Zidan, Ragaiy
    Blomqvist, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Araújo, C Moysés
    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.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Jena, Puru
    Carbon nanomaterials as catalysts for hydrogen uptake and release in NaAlH42009In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 9, no 4, p. 1501-1505Article in journal (Refereed)
    Abstract [en]

    A synergistic approach involving experiment and first-principles theory not only shows that carbon nanostructures can be used as catalysts for hydrogen uptake and release in complex metal hydrides such as sodium alanate, NaAlH(4), but also provides an unambiguous understanding of how the catalysts work. Here we show that the stability of NaAlH(4) originates with the charge transfer from Na to the AlH(4) moiety, resulting in an ionic bond between Na(+) and AlH(4)(-) and a covalent bond between Al and H. Interaction of NaAlH(4) with an electronegative substrate such as carbon fullerene or nanotube affects the ability of Na to donate its charge to AlH(4), consequently weakening the Al-H bond and causing hydrogen to desorb at lower temperatures as well as facilitating the absorption of H(2) to reverse the dehydrogenation reaction. In addition, based on our experimental observations and theoretical calculations it appears the curvature of the carbon nanostructure plays a role in the catalytic process. Ab initio molecular dynamics simulation further reveals the time evolution of the charge transfer process.

  • 11.
    Blomqvist, Andreas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Araujo, Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Scheicher, Ralph Hendrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Srepusharawoot, Pornjuk
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Li, Wen
    Chen, Ping
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Hydrogen as promoter and inhibitor of superionicity: A case study on Li-N-H systems2010In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 82, no 2, p. 024304-Article in journal (Refereed)
    Abstract [en]

    Materials which possess a high lithium ion conductivity are very attractive for battery and fuel cell applications. Hydrogenation of the fast-ion conductor lithium nitride (Li3N) leads to the formation of lithium imide (Li2NH) and subsequently of lithium amide (LiNH2). Using ab initio molecular dynamics simulations, we carried out a comparative study of the Li diffusion in these three systems. The results demonstrate that hydrogen can work as both promoter and inhibitor of Li mobility, with the lowest transition temperature to the superionic state occurring in Li2NH. Furthermore, we show that the creation of Li vacancies strongly affects Li diffusion in Li3N, but not so in Li2NH. Finally, we explain our findings with the help of a simple model.

  • 12.
    de Souza, Fabio A. L.
    et al.
    Fed Inst Educ Sci & Technol Espirito Santo, Ibatiba, ES, Brazil.;Univ Fed Espirito Santo, Dept Fis, Vitoria, ES, Brazil..
    Amorim, Rodrigo G.
    Univ Fed Fluminense, ICEx, Dept Fis, Volta Redonda, RJ, Brazil..
    Prasongkit, Jariyanee
    Nakhon Phanom Univ, Div Phys, Fac Sci, Nakhon Phanom 48000, Thailand.;Nanotec KKU Ctr Excellence Adv Nanomat Energy Pro, Khon Kaen 40002, Thailand..
    Scopel, Wanderlä L.
    Univ Fed Espirito Santo, Dept Fis, Vitoria, ES, Brazil..
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Rocha, Alexandre R.
    Univ Estadual Paulista, Inst Fis Teor, Sao Paulo, Brazil.;MIT, Dept Chem Engn, Cambridge, MA 02139 USA..
    Topological line defects in graphene for applications in gas sensing2018In: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 129, p. 803-808Article in journal (Refereed)
    Abstract [en]

    Topological line defects in graphene synthesized in a highly controlled manner open up new research directions for nanodevice applications. Here, we investigate two types of extended line defects in graphene, namely octagonal/pentagonal and heptagonal/pentagonal reconstructions. A combination of density functional theory and non-equilibrium Green's function methods was utilized in order to explore the application potential of this system as an electronic gas sensor. Our findings show that the electric current is confined to the line defect through gate voltage control, which combined with the enhanced chemical reactivity at the grain boundary, makes this system a highly promising candidate for gas sensor applications. As a proof of principle, we evaluated the sensitivity of a prototypical device toward NO2 molecule, demonstrating that it is indeed possible to reliably detect the target molecule.

  • 13.
    de Souza, Fabio A. L.
    et al.
    Fed Inst Educ Sci & Technol Espirito Santo IFES, Ibatiba, ES, Brazil.;Univ Fed Espirito Santo, Dept Fis, Vitoria, ES, Brazil..
    Amorim, Rodrigo G.
    UFF, ICEx, Dept Fis, Volta Redonda, RJ, Brazil..
    Scopel, Wanderla L.
    Univ Fed Espirito Santo, Dept Fis, Vitoria, ES, Brazil..
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Electrical detection of nucleotides via nanopores in a hybrid graphene/h-BN sheet2017In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 9, no 6, p. 2207-2212Article in journal (Refereed)
    Abstract [en]

    Designing the next generation of solid-state biosensors requires developing detectors which can operate with high precision at the single-molecule level. Nano-scaled architectures created in two-dimensional hybrid materials offer unprecedented advantages in this regard. Here, we propose and explore a novel system comprising a nanopore formed within a hybrid sheet composed of a graphene nanoroad embedded in a sheet of hexagonal boron nitride (h-BN). The sensitive element of this setup is comprised of an electrically conducting carbon chain forming one edge of the nanopore. This design allows detection of DNA nucleotides translocating through the nanopore based on the current modulation signatures induced in the carbon chain. In order to assess whether this approach is feasible to distinguish the four different nucleotides electrically, we have employed density functional theory combined with the nonequilibrium Green's function method. Our findings show that the current localized in the carbon chain running between the nanopore and h-BN is characteristically modulated by the unique dipole moment of each molecule upon insertion into the pore. Through the analysis of a simple model based on the dipole properties of the hydrogen fluoride molecule we are able to explain the obtained findings.

  • 14. Deshpande, M D
    et al.
    Scheicher, Ralph H
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics IV.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics IV.
    Pandey, Ravindra
    Binding strength of sodium ions in cellulose for different water contents2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 30, p. 8985-8989Article in journal (Refereed)
    Abstract [en]

    The interaction strength of sodium ions (Na(+)) with cellulose is investigated from first principles for varying degrees of water content. We find that the interaction of water molecules and Na(+) can be studied independently at the various OH groups in cellulose which we categorize as two different types. In the absence of water, Na(+) forms strong ionic bonds with the OH groups of cellulose. When water molecules are anchored to the OH groups via hydrogen bonds, Na(+) can eventually no longer bind to the OH groups, but will instead interact with the oxygen atoms of the water molecules. Due to the rather weak attachment of the latter to the OH groups, Na(+) becomes effectively more mobile in the fully hydrated cellulose framework. The present study thus represents a significant step toward a first-principles understanding of the experimentally observed dependence of ionic conductivity on the level of hydration in cellulose network.

  • 15. Dubey, Archana
    et al.
    Saha, H. P.
    Pink, R. H.
    Badu, S. R.
    Mahato, Dip N.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Mahanti, Mahendra K.
    Chow, Lee
    Das, T. P.
    Nuclear quadrupole interactions and electronic structure of BF3 center dot H2O complex2007In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 176, no 1-3, p. 45-50Article in journal (Refereed)
    Abstract [en]

    This work deals with first-principles investigation of the electronic structure of the BF3 center dot H2O complex which is important in catalysis of organic reactions and polymerization. The dissociation energy of the BF3 center dot H2O complex and the nuclear quadrupole interaction parameters for the excited nuclear state F-19* (I = 5/2) of the fluorine nuclei have been studied. Our investigation shows that the complexation bond BO between the BF3 and H2O units is strongly influenced by the larger electronegativity of Oxygen as compared to Nitrogen in BF3 center dot NH3. The quadrupole coupling constants of F-19* and the asymmetry parameter are however quite close to those for BF3 center dot NH3. The likely reasons for these features of these two important catalytic systems are suggested.

  • 16.
    Feliciano, Gustavo T.
    et al.
    Univ Estadual Paulista UNESP, Inst Quim, Dept Fis Quim, Araraquara.
    Sanz-Navarro, Carlos
    CSIC, Catalan Inst Nanosci & Nanotechnol ICN2, Campus UAB, Barcelona; Barcelona Inst Sci & Technol, Campus UAB, Barcelona.
    Coutinho-Neto, Mauricio Domingues
    Univ Fed ABC, Ctr Ciencias Nat & Humanas, Santo Andre.
    Ordejon, Pablo
    CSIC, Catalan Inst Nanosci & Nanotechnol ICN2, Campus UAB, Barcelona; Barcelona Inst Sci & Technol, Campus UAB, Barcelona .
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Rocha, Alexandre Reily
    Univ Estadual Paulista UNESP, Inst Fis Teor, Sao Paulo; MIT, Dept Chem Engn, Cambridge.
    Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 2, p. 485-492Article in journal (Refereed)
    Abstract [en]

    The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green’s function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent.

  • 17. Feliciano, Gustavo T.
    et al.
    Sanz-Navarro, Carlos
    Coutinho-Neto, Mauricio Domingues
    Ordejon, Pablo
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Rocha, Alexandre Reily
    Capacitive DNA Detection Driven by Electronic Charge Fluctuations in a Graphene Nanopore2015In: Physical Review Applied, ISSN 2331-7019, Vol. 3, no 3, article id 034003Article in journal (Refereed)
    Abstract [en]

    The advent of parallelized automated methods for rapid whole-genome analysis has led to an exponential drop in costs, thus greatly accelerating biomedical research and discovery. Third-generation sequencing techniques, which would utilize the characteristic electrical conductance of the four different nucleotides, could facilitate longer base read lengths and an even lower price per genome. In this work, we propose and apply a quantum-classical hybrid methodology to quantitatively determine the influence of the solvent on the dynamics of DNA and the resulting electron transport properties of a prototypic sequencing device utilizing a graphene nanopore through which the nucleic-acid chain is threaded. Our results show that charge fluctuations in the nucleotides are responsible for characteristic conductance modulations in this system, which can be regarded as a field-effect transistor tuned by the dynamic aqueous environment.

  • 18. Gowtham, S.
    et al.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Pandey, Ravindra
    Karna, Shashi P.
    Physisorption of nucleobases on graphene: Density-functional calculations2007In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 76, no 3, p. 033401-Article in journal (Refereed)
    Abstract [en]

    We report the results of our first-principles investigation on the interaction of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) with graphene, carried out within the density-functional theory framework, with additional calculations utilizing Hartree-Fock plus second-order Møller-Plesset perturbation theory. The calculated binding energy of the nucleobases shows the following hierarchy: G>A~T~C>U, with the equilibrium configuration being rather similar for all five of them. Our results clearly demonstrate that the nucleobases exhibit significantly different interaction strengths when physisorbed on graphene. The stabilizing factor in the interaction between the base molecule and graphene sheet is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study represents a significant step toward a first-principles understanding of how the base sequence of DNA can affect its interaction with carbon nanotubes, as observed experimentally.

  • 19. Gowtham, S.
    et al.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Condensed Matter Theory.
    Pandey, Ravindra
    Karna, Shashi P.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Condensed Matter Theory.
    First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes2008In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 19, no 12, p. 125701-Article in journal (Refereed)
    Abstract [en]

    We report the results of our first-principles study based on density functional theory on the interaction of the nucleic acid base molecules adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U), with a single-walled carbon nanotube (CNT). Specifically, the focus is on the physisorption of base molecules on the outer wall of a (5, 0) metallic CNT possessing one of the smallest diameters possible. Compared to the case for CNTs with large diameters, the physisorption energy is found to be reduced in the high-curvature case. The base molecules exhibit significantly different interaction strengths and the calculated binding energies follow the hierarchy G>A>T>C>U, which appears to be independent of the tube curvature. The stabilizing factor in the interaction between the base molecule and CNT is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study provides an improved understanding of the role of the base sequence in deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) in their interactions with carbon nanotubes of varying diameters.

  • 20.
    Haldar, Soumyajyoti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Amorim, Rodrigo Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Sanyal, Biplab
    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.
    Rocha, Alexandre R.
    Energetic stability, STM fingerprints and electronic transport properties of defects in graphene and silicene2016In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 6, no 8, p. 6702-6708Article in journal (Refereed)
    Abstract [en]

    Novel two-dimensional materials such as graphene and silicene have been heralded as possibly revolutionary in future nanoelectronics. High mobilities, and in the case of silicene, its seemingly natural integration with current electronics could make them the materials of next-generation devices. Defects in these systems, however, are unavoidable particularly in large-scale fabrication. Here we combine density functional theory and the non-equilibrium Green’s function method to simulate the structural, electronic and transport properties of different defects in graphene and silicene. We show that defects are much more easily formed in silicene, compared to graphene. We also show that, although qualitatively similar, the effects of different defects occur closer to the Dirac point in silicene, and identifying them using scanning tunneling microscopy is more difficult particularly due to buckling. This could be overcome by performing direct source/drain measurements. Finally we show that the presence of defects leads to an increase in local current from which it follows that they not only contribute to scattering, but are also a source of heating.

  • 21. He, Haiying
    et al.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics IV.
    Pandey, Ravindra
    Rocha, Alexandre Reily
    Sanvito, Stefano
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics IV.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics IV.
    Karna, Shashi P.
    Functionalized Nanopore-Embedded Electrodes for Rapid DNA Sequencing2008In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 112, no 10, p. 3456-3459Article in journal (Refereed)
    Abstract [en]

    With the aim of improving nanopore-based DNA sequencing, we explored the effects of functionalizing the embedded gold electrodes with purine and pyrimidine molecules. Hydrogen bonds formed between the molecular probe and target bases stabilize the scanned DNA unit against thermal fluctuations and thus greatly reduce noise in the current signal. The results of our first-principles study indicate that this proposed scheme could allow DNA sequencing with a robust and reliable yield, producing current signals that differ by at least 1 order of magnitude for the different bases.

  • 22. He, Yuhui
    et al.
    Scheicher, Ralph
    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.
    Long, Shibing
    Huo, Zongliang
    Liu, Ming
    DNA sequencing with nanopore-embedded bilayer-graphene nanoelectrodes2010In: ICSICT-2010 - 2010 10th IEEE International Conference on Solid-State and Integrated Circuit Technology, Proceedings, p. 1483-1485Article in journal (Refereed)
  • 23. He, Yuhui
    et al.
    Scheicher, Ralph
    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.
    Long, Shibing
    Ji, Zhuoyu
    Yu, Zhaoan
    Liu, Ming
    Fast DNA sequencing via transverse differential conductance2010Conference paper (Refereed)
    Abstract [en]

    We propose using characteristic transverse differential conductance for solid-state nanopore-based DNA sequencing and have explored this idea by performing molecular dynamics simulations on the translocation progress of single-stranded DNA molecule through the nanopore, and calculating the associated transverse differential conductance. Our results show that measurement of the transverse differential conductance is suitable to successfully discriminate between the four nucleotide types, and we show that this identification could even withstand electrical noise caused by fluctuations due to changes in the DNA orientation. Our findings demonstrate several compelling advantages of the differential conductance approach, which may lead to important applications in rapid genome sequencing.

  • 24.
    He, Yuhui
    et al.
    Laboratory of Nano-Fabrication and Novel Devices Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, China.
    Scheicher, Ralph H.
    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.
    Long, Shibing
    Laboratory of Nano-Fabrication and Novel Devices Integrated, Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, China.
    Huo, ZongLiang
    Laboratory of Nano-Fabrication and Novel Devices Integrated, Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, China.
    Liu, Ming
    Laboratory of Nano-Fabrication and Novel Devices Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, China.
    Enhanced DNA Sequencing Performance Through Edge-Hydrogenation of Graphene Electrodes2011In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 21, no 14, p. 2674-2679Article in journal (Refereed)
    Abstract [en]

    The use of graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing is proposed, and molecular dynamics simulations in conjunction with electronic transport calculations are performed to explore the potential merits of this idea. The results of the investigation show that, compared to the unhydrogenated system, edge-hydrogenated graphene electrodes facilitate the temporary formation of H-bonds with suitable atomic sites in the translocating DNA molecule. As a consequence, the average conductivity is drastically raised by about 3 orders of magnitude while exhibiting significantly reduced statistical variance. Furthermore, the effect of the distance between opposing electrodes is investigated and two regimes identified: for narrow electrode separation, the mere hindrance due to the presence of protruding hydrogen atoms in the nanopore is deemed more important, while for wider electrode separation, the formation of H-bonds becomes the dominant effect. Based on these findings, it is concluded that hydrogenation of graphene electrode edges represents a promising approach to reduce the translocation speed of DNA through the nanopore and substantially improve the accuracy of the measurement process for whole-genome sequencing.

  • 25. He, Yuhui
    et al.
    Shao, Lubing
    Scheicher, Ralph
    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.
    Long, Shibing
    Ji, Zhuoyu
    Yu, Zhaoan
    Liu, Ming
    Differential conductance as a promising approach for rapid DNA sequencing with nanopore-embedded electrodes2010In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 97, no 4, p. 043701-Article in journal (Refereed)
    Abstract [en]

    We propose an approach for nanopore-based DNA sequencing using characteristic transverse differential conductance. Molecular dynamics and electron transport simulations show that thetransverse differential conductance during the translocation of DNA through the nanopore isdistinguishable enough for the detection of the base sequence and can withstand electrical noisecaused by DNA structure fluctuation. Our findings demonstrate several advantages of the transverseconductance approach, which may lead to important applications in rapid genome sequencing.

  • 26. He, Yuhui
    et al.
    Tsutsui, Makusu
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Bai, Fan
    Taniguchi, Masateru
    Kawai, Tomoji
    Thermophoretic Manipulation of DNA Translocation through Nanopores2013In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 7, no 1, p. 538-546Article in journal (Refereed)
    Abstract [en]

    Manipulating DNA translocation through nanopore is one crucial requirement for new ultrafast sequencing methods in the sense that the polymers have to be denatured, unraveled, and then propelled through the pore with very low speed. Here we propose and theoretically explore a novel design to fulfill the demands by utilizing cross-pore thermal gradient. The high temperature in the cis reservoir is expected to transform double-stranded DNA into single strands and that temperature would also prevent those single strands from intrastrand base-pairing, thus, achieving favorable polymer conformation for the subsequent translocation and sequencing. Then, the substantial temperature drop across the pore caused by the thermal-insulating membrane separating cis and trans chambers would stimulate thermophoresis of the molecules through nanopores. Our theoretical evaluation shows that the DNA translocation speeds will be orders smaller than the electrophoretic counterpart, while high capture rate of DNA Into nanopore Is maintained, both of which would greatly benefit the sequencing.

  • 27. He, Yuhui
    et al.
    Tsutsui, Makusu
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Fan, Chun
    Taniguchi, Masateru
    Kawai, Tomoji
    Mechanism of How Salt-Gradient-Induced Charges Affect the Translocation of DNA Molecules through a Nanopore2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 105, no 3, p. 776-782Article in journal (Refereed)
    Abstract [en]

    Experiments using nanopores demonstrated that a salt gradient enhances the capture rate of DNA and reduces its transfocation speed. These two effects can help to enable electrical DNA sequencing with nanopores. Here, we provide a quantitative theoretical evaluation that shows the positive net charges, which accumulate around the pore entrance due to the salt gradient, are responsible for the two observed effects: they reinforce the electric capture field, resulting in promoted molecule capture rate; and they induce cationic electroosmotic flow through the nanopore, thus significantly retarding the motion of the anionic DNA through the nanopore. Our multiphysical simulation results show that, during the polymer trapping stage, the former effect plays the major role, thus resulting in promoted DNA capture rate, while during the nanopore-penetrating stage the latter effect dominates and consequently reduces the DNA translocation speed significantly. Quantitative agreement with experimental results has been reached by further taking nanopore wall surface charges into account.

  • 28.
    Hinnemo, Malkolm
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Zhao, Jie
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Ahlberg, Patrik
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Hägglund, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Djurberg, Viktor
    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.
    Zhang, Shi-Li
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Zhang, Zhi-Bin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    On Monolayer Formation of Pyrenebutyric Acid on Graphene2017In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 33, no 15, p. 3588-3593Article in journal (Refereed)
    Abstract [en]

    As a two-dimensional material with high charge carrier mobility, graphene may offer ultrahigh sensitivity in biosensing. To realize this, the first step is to functionalize the graphene. This is commonly done by using 1-pyrenebutyric acid (PBA) as a linker for biornolecules. However, the adsorption of PBA on graphene remains poorly understood despite reports of successful biosensors functionalized via this route. Here, the PBA adsorption on graphene is characterized through a combination of Raman spectroscopy, ab initio calculations, and spectroscopic ellipsometry. The PBA molecules are found to form a self-assembled monolayer on graphene, the formation of which is self-limiting and Langmuirian. Intriguingly, in concentrated solutions, the PBA molecules are found to stand up and stack horizontally with their edges contacting the graphene surface. This morphology could facilitate a surface densely populated with carboxylic functional groups. Spectroscopic analyses show that the monolayer saturates at 5.3 PBA molecules per nm(2) and measures similar to 0.7 nm in thickness. The morphology study of this PBA monolayer sheds light on the pi-pi stacking of small-molecule systems on graphene and provides an excellent base for optimizing functionalization procedures.

  • 29.
    Hu, Shuanglin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Li, Shuyi
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Granqvist, Claes-Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Niklasson, Gunnar A.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Optical properties of Mg-doped VO2: Absorption measurements and hybrid functional calculations2012In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 101, no 20, p. 201902-Article in journal (Refereed)
    Abstract [en]

    Mg-doped VO2 thin films with thermochromic properties were made by reactive DC magnetron co-sputtering onto heated substrates, and spectral absorption was recorded at room temperature in the 0.5 < <(h)over bar>omega < 3.5 eV energy range. Clear evidence was found for a widening of the main band gap from 1.67 to 2.32 eV as the Mg/(V + Mg) atomic ratio went from zero to 0.19, thereby significantly lowering the luminous absorption. This technologically important effect could be reconciled with spin-polarized density functional theory calculations using the Heyd-Scuseria-Ernzerhof [Heyd et al., J. Chem. Phys. 118, 8207 (2003); ibid. 124, 219906 (2006)] hybrid functional. Specifically, the calculated luminous absorptance decreased when the Mg/(V + Mg) ratio was increased from 0.125 to 0.250.

  • 30.
    Hussain, Tanveer
    et al.
    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.
    Maark, Tuhina Adit
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Araujo, Carlos Moyses
    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.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ab initio study of lithium-doped graphane for hydrogen storage2011In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 96, no 2, p. 27013-Article in journal (Refereed)
    Abstract [en]

    Based on the first-principle density functional calculations we predict that Li-doped graphane (prehydrogenated graphene) can be a potential candidate for hydrogen storage. The calculated Li-binding energy on graphane is significantly higher than the Li bulk's cohesive energy ruling out any possibility of cluster formations in the Li-doped graphane. Our study shows that even with very low concentration (5.56%) of Li doping, the Li-graphane sheet can achieve a reasonable hydrogen storage capacity of 3.23 wt.%. The van der Waals corrected H(2) binding energies fall within the range of 0.12-0.29 eV, suitable for practical H(2) storage applications. 

  • 31. Jeong, Junho
    et al.
    Byahut, Sitaram
    Pink, R. H.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Huang, M. B.
    Chow, Lee
    Mishra, D. R.
    Aryal, M. M.
    Maharjan, N. B.
    Paudyal, D. D.
    Das, T. P.
    First-principles study of location of Er3+ ion-relationship to understanding of hyperfine interactions in the optoelectronic erbium-silicon system2007In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 178, no 1-3, p. 51-56Article in journal (Refereed)
    Abstract [en]

    The importance of hyperfine interactions in the Erbium-Silicon system is underscored by our first-principles Hartree-Fock Cluster investigations on the location of Erbium in Silicon. Our theoretical studies show that both substitutional and tetrahedral interstitial sites are stable for Er3+ ion with the latter having a larger binding energy. This conclusion is not completely supported by channeling experiments. It is suggested that Mossbauer measurements on Er-166 isotope would be valuable to compare experimental results with theoretical predictions of the hyperfine interactions of both magnetic and quadrupolar types to provide additional information about the location of Er3+.

  • 32.
    Johansson, Robert
    et al.
    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.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Effect of uniaxial strain on the site occupancy of hydrogen in vanadium from density-functional calculations2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 10301Article in journal (Refereed)
    Abstract [en]

    We investigate the influence of uniaxial strain on the site occupancy of hydrogen in vanadium, using density functional theory. The site occupancy is found to be strongly influenced by the strain state of the lattice. The results provide the conceptual framework for the atomistic description of the observed hysteresis in the alpha to beta phase transition in bulk, as well as the preferred octahedral occupancy of hydrogen in strained V layers.

  • 33.
    Johansson, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Muscas, Giuseppe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    George, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ahlberg, Martina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Kádaz, Krisztina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Arvanitis, Dmitri
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Eriksson, Olle
    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.
    Jönsson, Petra
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Structural characterization of amorphous Fe(1-x)ZrxManuscript (preprint) (Other academic)
  • 34.
    Johansson, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Pálsson, Gunnar K.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Effect of tetragonal distortion on the diffusion of hydrogen in vanadium studied with ab initio molecular dynamicsManuscript (preprint) (Other academic)
  • 35.
    Kim, Duck Young
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Dynamical stability of the cubic metallic phase of AlH3 at ambient pressure: Density functional calculations2008In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 78, no 10, p. 100102-Article in journal (Refereed)
    Abstract [en]

    We have characterized the high-pressure cubic phase of AlH3 from ab initio using density functional theory to determine mechanical as well as electronic properties and lattice dynamics (phonon-dispersion relations) from the response function method. Our zero-temperature phonon calculations show the softening of a particular mode with decreasing pressure, indicating the onset of a dynamic instability that continues to persist at ambient conditions. This instability can, however, be removed when finite electronic temperature effects are considered in the calculations. We furthermore identify a particular momentum transfer in the phonon-dispersion relation, matching a corresponding momentum transfer in the electronic band structure.

  • 36.
    Kim, Duck Young
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Scheicher, Ralph H.
    Ahuja, Rajeev
    High-Temperature Superconductivity in the Hydrogen-Dense Transition Metal Hydride YH3Article in journal (Refereed)
  • 37.
    Kim, Duck Young
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Predicted High-Temperature Superconducting State in the Hydrogen-Dense Transition-Metal Hydride YH3 at 40 K and 17.7 GPa2009In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 103, no 7, p. 077002-Article in journal (Refereed)
    Abstract [en]

    Metallization in pure hydrogen has been proposed to give rise to high-temperature superconductivity at pressures which still lie beyond the reach of contemporary experimental techniques. Hydrogen-dense materials offer an opportunity to study related phenomena at experimentally achievable pressures. Here we report the prediction of high-temperature superconductivity in yttrium hydride (YH3), with a T-c of 40 K at 17.7 GPa, the lowest reported pressure for hydrogen-dense materials to date. Specifically, we find that the face-centered cubic structure of YH3 exhibits superconductivity of different origins in two pressure regions. The evolution of T-c with pressure follows the corresponding change of s-d hybridization between H and Y, due to an enhancement of the electron-phonon coupling by a matching of the energy level from Y-H vibrations with the peak of the s electrons from the octahedrally coordinated hydrogen atoms.

  • 38.
    Kim, Duck Young
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Lebègue, S.
    Prasongkit, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Arnaud, B.
    Alouani, M.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Crystal structure of the pressure-induced metallic phase of SiH4 from ab initio theory2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 43, p. 16454-16459Article in journal (Refereed)
    Abstract [en]

    Metallization of pure solid hydrogen is of great interest, not least because it could lead to high-temperature superconductivity, but it continues to be an elusive goal because of great experimental challenges. Hydrogen-rich materials, in particular, CH4, SiH4, and GeH4, provide an opportunity to study related phenomena at experimentally achievable pressures, and they too are expected to be high-temperature superconductors. Recently, the emergence of a metallic phase has been observed in silane for pressures just above 60 GPa. However, some uncertainty exists about the crystal structure of the discovered metallic phase. Here, we show by way of elimination, that a single structure that possesses all of the required characteristics of the experimentally observed metallic phase of silane from a pool of plausible candidates can be identified. Our density functional theory and GW calculations show that a structure with space group P4/nbm is metallic at pressures > 60 GPa. Based on phonon calculations, we furthermore demonstrate that the P4/nbm structure is dynamically stable at > 43 GPa and becomes the ground state at 97 GPa when zero-point energy contributions are considered. These findings could lead the way for further theoretical analysis of metallic phases of hydrogen-rich materials and stimulate experimental studies.

  • 39.
    Kim, Duck Young
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    Mao, Ho-Kwang
    Kang, Tae W.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science.
    General trend for pressurized superconducting hydrogen-dense materials2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 7, p. 2793-2796Article in journal (Refereed)
    Abstract [en]

    The long-standing prediction that hydrogen can assume a metallic state under high pressure, combined with arguments put forward more recently that this state might even be superconducting up to high temperatures, continues to spur tremendous research activities toward the experimental realization of metallic hydrogen. These efforts have however so far been impeded by the enormous challenges associated with the exceedingly large required pressure. Hydrogen-dense materials, of the MH4 form ( where M can be, e. g., Si, Ge, or Sn) or of the MH3 form ( with M being, e. g., Al, Sc, Y, or La), allow for the rather exciting opportunity to carry out a proxy study of metallic hydrogen and associated high-temperature superconductivity at pressures within the reach of current techniques. At least one experimental report indicates that a superconducting state might have been observed already in SiH4, and several theoretical studies have predicted superconductivity in pressurized hydrogen-rich materials; however, no systematic dependence on the applied pressure has yet been identified so far. In the present work, we have used first-principles methods in an attempt to predict the superconducting critical temperature (T-c) as a function of pressure ( P) for three metal-hydride systems of the MH3 form, namely ScH3, YH3, and LaH3. By comparing the obtained results, we are able to point out a general trend in the T-c-dependence on P. These gained insights presented here are likely to stimulate further theoretical studies of metallic phases of hydrogen-dense materials and should lead to new experimental investigations of their superconducting properties.

  • 40.
    Kim, Duck Young
    et al.
    Theory of Condensed Matter Group, Cavendish Laboratory, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Pickard, Chris J.
    Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom.
    Needs, R. J.
    Theory of Condensed Matter Group, Cavendish Laboratory, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Predicted Formation of Superconducting Platinum-Hydride Crystals under Pressure in the Presence of Molecular Hydrogen2011In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 107, no 11, p. 117002-Article in journal (Refereed)
    Abstract [en]

    Noble metals adopt close-packed structures at ambient pressure and rarely undergo structural transformation at high pressures. Platinum (Pt) is normally considered to be unreactive and is therefore not expected to form hydrides under pressure. We predict that platinum hydride (PtH) has a lower enthalpy than its constituents solid Pt and molecular hydrogen at pressures above 21.5 GPa. PtH transforms to a hexagonal close-packed or face-centered cubic (fcc) structure between 70 and 80 GPa. Linear response calculations indicate that PtH is a superconductor at these pressures with a critical temperature of about 10–25 K. These findings help to shed light on recent observations of pressure-induced metallization and superconductivity in hydrogen-rich materials. We show that the formation of fcc noble metal hydrides under pressure is common and examine the possibility of superconductivity in these materials.

  • 41. Kim, Sun-Woo
    et al.
    Kim, Hyun-Jung
    Choi, Jin-Ho
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Cho, Jun-Hyung
    Contrasting interedge superexchange interactions of graphene nanoribbons embedded in h-BN and graphane2015In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, no 3, article id 035443Article in journal (Refereed)
    Abstract [en]

    Based on first-principles density-functional theory calculations, we present a comparative study of the electronic structures of ultranarrow zigzag graphene nanoribbons (ZGNRs) embedded in a hexagonal boron nitride (BN) sheet and fully hydrogenated graphene (graphane) as a function of their width N (the number of zigzag C chains composing the ZGNRs). We find that ZGNRs/BN have the nonmagnetic ground state except at N = 5 and 6 that weakly stabilize as a half-semimetallic state, whereas ZGNRs/graphane with N >= 2 exhibit a strong antiferromagnetic coupling between ferromagnetically ordered edge states on each edge. It is revealed that the disparate magnetic properties of the two classes of ZGNRs are attributed to the contrasting interedge superexchange interactions arising from different interface structures: that is, the asymmetric interface structure of ZGNRs/BN gives a relatively short-range and weak superexchange interaction between the two inequivalent edge states, while the symmetric interface structure of ZGNRs/graphane gives a long-range, strong interedge superexchange interaction.

  • 42. Lata, K. Ramani
    et al.
    Sahoo, N.
    Dubey, Archana
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Condensed Matter Theory.
    Badu, S. R.
    Pink, R. H.
    Mahato, Dip N.
    Schulte, A. F.
    Saha, H. P.
    Maharjan, N. B.
    Chow, Lee
    Das, T. P.
    Investigation of the hyperfine properties of deoxy hemoglobin based on its electronic structure obtained by Hartree-Fock-Roothan procedure2008In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 181, no 1-3, p. 75-80Article in journal (Refereed)
    Abstract [en]

    The electronic structure of the heme unit of deoxyhemoglobin including the proximal imidazole has been studied using the first-principles Hartree-Fock procedure. Our results for the Fe-57m isomer shift and asymmetry parameter are in very good agreement with the values obtained from Mossbauer spectroscopy measurements. The Fe-57m nuclear quadrupole coupling constant is smaller than the experimental result and possible ways to improve the agreement in the future are discussed. Improved analysis of the Mossbauer data, removing some approximations made for deriving the magnetic hyperfine tensor for the Fe-57m nucleus, is suggested to allow quantitative comparison with our results in the future.

  • 43. Lee, Jun-Ho
    et al.
    Choi, Yun-Ki
    Kim, Hyun-Jung
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Cho, Jun-Hyung
    Physisorption of DNA Nucleobases on h-BN and Graphene: vdW-Corrected DFT Calculations2013In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, no 26, p. 13435-13441Article in journal (Refereed)
    Abstract [en]

    Using local, semilocal, and van der Waals energy-corrected density-functional theory (PBE + vdW) calculations, we present a comparative study of DNA nucleobases [guanine (G), adenine (A), thymine (T), and cytosine (C)] adsorbed on hexagonal boron nitride (h-BN) sheet and graphene. We find that, despite the very different electronic properties of BN sheet and graphene, the various nucleobase molecules have rather similar binding energies on the two types of sheets. The calculated binding energies of the four nucleobases using the local, semilocal, and PBE + vdW schemes are in the range of 0.54-0.75, 0.06-0.15, and 0.93-1.18 eV, respectively. In particular, the PBE + vdW scheme predicts not only a binding energy predominantly determined by vdW interactions between the base molecules and their substrates decreasing in the order of G > A > T >. C but also a very weak hybridization between the molecular levels of the nucleobases and the pi-states of the BN sheet or graphene. This physisorption of G, A, T, and C on the BN sheet (graphene) induces a small interfacial dipole, giving rise to an energy shift in the work function by 0.11 (0.22), 0.09 (0.15), -0.05 (0.01), and 0.06 (0.13) eV, respectively.

  • 44. Li, Nannan
    et al.
    Lee, Geunsik
    Yang, Jae Won
    Kim, Heeyoung
    Yeom, Min Sun
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Kim, Jai Sam
    Kim, Kwang S.
    Noncovalent Functionalization with Alkali Metal to Separate Semiconducting from Metallic Carbon Nanotubes: A Theoretical Study2013In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, no 8, p. 4309-4313Article in journal (Refereed)
    Abstract [en]

    Despite intense studies of carbon nanotubes for decades, the separation of semiconducting and metallic single-walled carbon nanotubes (SWNTs) remains to be one of the most important tasks to be resolved. Here we demonstrate that a K atom binds the semiconducting SWNTs more strongly than the metallic SWNTs, while this binding strength hierarchy is reversed for a K+ ion, consistent with experimental reports. This was shown by first-principles calculations, which properly describe the van der Waals interactions, and the origin of such results is explained. These results could be exploited as useful guidance toward separating semiconducting and metallic SWNTs via noncovalent functionalization.

  • 45. Li, Wen
    et al.
    Miao, Ling
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Xiong, Zhitao
    Wu, Guotao
    Araújo, C. Moysés
    Blomqvist, Andreas
    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.
    Feng, Yuanping
    Chen, Ping
    Li-Na ternary amidoborane for hydrogen storage: experimental and first-principles study2012In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 41, no 16, p. 4754-4764Article in journal (Refereed)
    Abstract [en]

    Li-Na ternary amidoborane, Na[Li(NH2BH3)(2)], was recently synthesized by reacting LiH and NaH with NH3BH3. This mixed-cation amidoborane shows improved dehydrogenation performance compared to that of single-cation amidoboranes, i.e., LiNH2BH3 and NaNH2BH3. In this paper, we synthesized the Li-Na ternary amidoborane by blending and re-crystallizing equivalent LiNH2BH3 and NaNH2BH3 in tetrahydrofuran (THF), and employed first-principles calculations and the special quasirandom structure (SQS) method to theoretically explore the likelihood for the existence of Li1-xNax(NH2BH3) for various Li/Na ratios. The thermodynamic, electronic and phononic properties were investigated to understand the possible dehydrogenation mechanisms of Na[Li(NH2BH3)(2)].

  • 46. Li, Wen
    et al.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Araujo, C. Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Wu, Guotao
    Blomqvist, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Wu, Chenzhang
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Feng, Yuan Ping
    Chen, Ping
    Understanding from First-Principles Why LiNH2BH3 · NH3BH3 Shows Improved Dehydrogenation over LiNH2BH3 and NH3BH32010In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 44, p. 19089-19095Article in journal (Refereed)
    Abstract [en]

    Lithium amidoborane-ammonia borane (LiNH2BH3 center dot NH3BH3, LiAB center dot AB for short) was synthesized recently. Compared with lithium amidoborane (LiNH2BH3, LiAB for short) and ammonia borane (NH3BH3, AB for short), this new ammonia borane derivative has better dehydrogenation kinetics and releases 14.8 wt % hydrogen with peak temperatures at ca. 80 and 140 degrees C, respectively. In this report, first-principles calculations were employed to reveal the differences in dehydrogenation properties of AB, LiAB, and LiAB center dot AB. Furthermore, we attempted to correlate the crystal structure and electronic properties with dehydrogenation performance. The results show that Li+ cations play similar roles in LiAB center dot AB as in LiAB in destabilizing the B-H and N-H bonds, and the mechanism of the first-step dehydrogenation of LiAB center dot AB is likely via the dissociation and combination of hydridic H delta-(B) from LiAB molecule and protonic H delta+(N) from the adjacent AB molecule, rather than from the [LiAB] or [AB] layer alone, resulting in the desorption of H-2 at lower temperatures.

  • 47. Li, Wen
    et al.
    Wu, Guotao
    Araujo, Moyses
    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.
    Blomqvist, Andreas
    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.
    Xiong, Zhitao
    Feng, Yuanping
    Chen, Ping
    Li+ ion conductivity and diffusion mechanism in α-Li3N and β-Li3N2010In: Energy & environmental science, ISSN 1754-5692, Vol. 3, no 10, p. 1524-1530Article in journal (Refereed)
    Abstract [en]

    beta-Li3N of hexagonal D-6h(4) (P6(3)/mmc) structure was synthesized by   high-energy ball milling commercial Li3N (composed of both alpha and   beta phases). Ionic conductivities of alpha-Li3N and beta-Li3N were   tested by direct current (D. C.) and alternating current (A. C.)   impedance methods. beta-Li3N exhibited the same order of magnitude of   Li+ ion conductivity (2.085 x 10(-4) S cm(-1)) as that of alpha-Li3N   (5.767 x 10(-4) S cm(-1)) at room temperature. First-principles   calculations were employed to simulate the diffusion mechanism of Li+   ion in alpha-Li3N and beta-Li3N. Our results indicate that the   diffusion of Li+ ion in beta-Li3N likely occurs between pure Li-beta(1)   planes, which is different from that in alpha-Li3N, where the diffusion   of Li+ ion occurs within Li2N plane. The Li+ ion migration energy  barriers (E-m) for alpha-Li3N and beta-Li3N are 0.007 eV and 0.038 eV, respectively.

  • 48. Mahato, Dip N.
    et al.
    Dubey, Archana
    Pink, R. H.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Condensed Matter Theory.
    Badu, S. R.
    Nagamine, K.
    Torikai, E.
    Saha, H. P.
    Chow, Lee
    Huang, M. B.
    Das, T. P.
    Theoretical investigation of nuclear quadrupole interactions in DNA at first-principles level2008In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 181, no 1-3, p. 81-86Article in journal (Refereed)
    Abstract [en]

    We have studied the nuclear quadrupole interactions (NQI) of the N-14, O-17 and H-2 nuclei in the nucleobases cytosine, adenine, guanine and thymine in the free state as well as when they are bonded to the sugar ring in DNA, simulated through a CH3 group attached to the nucleobases. The nucleobase uracil, which replaces thymine in RNA, has also been studied. Our results show that there are substantial indirect effects of the bonding with the sugar group in the nucleic acids on the NQI parameters e(2)qQ/h and eta. It is hoped that measurements of these NQI parameters in DNA will be available in the future to compare with our predictions. Our results provide the conclusion that for any property dependent on the electronic structures of the nucleic acids, the effects of the bonding between the nucleobases and the nucleic acid backbones have to be included.

  • 49. Mahato, Dip N.
    et al.
    Pink, R. H.
    Badu, S. R.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Dubey, Archana
    Saha, H. P.
    Chow, Lee
    Mahanti, Mahendra K.
    Huang, M. B.
    Das, T. P.
    First principles study of nuclear quadrupole interactions in the molecular solid BF3 and the nature of binding between the molecules2007In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 176, no 1-3, p. 15-20Article in journal (Refereed)
    Abstract [en]

    The electronic structures and nuclear quadrupole interactions (NQI) of the F-19* (I= 5/2) state of F-19 nucleus in solid BF3 are studied using the first-principles Hartree-Fock-Roothaan procedure including many-body electron correlation effects. The calculated NQI parameters, F-19* quadrupole coupling constant (e(2)qQ) and asymmetry parameter eta, were found to be in satisfactory agreement with experiment for the solid state system, which gives confidence in the reliability of the calculated electronic structures in the solid and hence the factors found to influence the binding of the molecules in the solid. It was found that the intermolecular binding energy primarily arises from Van der Waals (VDW) interactions between the molecules resulting from intermolecular many-body effects, which counteract the repulsive interactions between the molecules arising from one-electron Hartree-Fock (HF) theory.

  • 50.
    Martins, Ernane de Freitas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Sao Paulo State Univ UNESP, Inst Theoret Phys, Campus Sao Paulo, BR-01140070 Sao Paulo, Brazil;Univ Sao Paulo, Inst Phys, Sao Paulo, SP, Brazil.
    Feliciano, Gustavo Troiano
    Sao Paulo State Univ UNESP, Inst Chem, Campus Araraquara, BR-14800060 Araraquara, Brazil.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Rocha, Alexandre Reily
    Sao Paulo State Univ UNESP, Inst Theoret Phys, Campus Sao Paulo, BR-01140070 Sao Paulo, Brazil.
    Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates2019In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 24, no 5, article id 951Article in journal (Refereed)
    Abstract [en]

    In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green's functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.

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