uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Scheicher, Ralph H.
Alternative names
Publications (10 of 87) Show all publications
Feliciano, G. T., Sanz-Navarro, C., Coutinho-Neto, M. D., Ordejon, P., Scheicher, R. H. & Rocha, A. R. (2018). Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach. Journal of Physical Chemistry B, 122(2), 485-492
Open this publication in new window or tab >>Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach
Show others...
2018 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 2, p. 485-492Article in journal (Refereed) Published
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.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-343858 (URN)10.1021/acs.jpcb.7b03475 (DOI)000423140600010 ()28721724 (PubMedID)
Funder
Swedish Research CouncilEU, Horizon 2020, 676598
Available from: 2018-03-02 Created: 2018-03-02 Last updated: 2018-03-02Bibliographically approved
Vovusha, H., Amorim, R. G., Scheicher, R. H. & Sanyal, B. (2018). Controlling the orientation of nucleobases by dipole moment interaction with graphene/h-BN interfaces. RSC Advances, 8(12), 6527-6531
Open this publication in new window or tab >>Controlling the orientation of nucleobases by dipole moment interaction with graphene/h-BN interfaces
2018 (English)In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 8, no 12, p. 6527-6531Article in journal (Refereed) Published
Abstract [en]

The interfaces in 2D hybrids of graphene and h-BN provide interesting possibilities of adsorbing and manipulating atomic and molecular entities. In this paper, with the aid of density functional theory, we demonstrate the adsorption characteristics of DNA nucleobases at different interfaces of 2D hybrid nanoflakes of graphene and h-BN. The interfaces provide stronger binding to the nucleobases in comparison to pure graphene and h-BN nanoflakes. It is also revealed that the individual dipole moments of the nucleobases and nanoflakes dictate the orientation of the nucleobases at the interfaces of the hybrid structures. The results of our study point towards a possible route to selectively control the orientation of individual molecules in biosensors.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2018
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-347655 (URN)10.1039/c7ra11664k (DOI)000425034000041 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilCarl Tryggers foundation
Available from: 2018-04-06 Created: 2018-04-06 Last updated: 2018-04-06Bibliographically approved
Prasongkit, J., Martins, E. d., de Souza, F. A. L., Scopel, W. L., Amorim, R. G., Amornkitbamrung, V., . . . Scheicher, R. H. (2018). Topological Line Defects Around Graphene Nanopores for DNA Sequencing. The Journal of Physical Chemistry C, 122(13), 7094-7099
Open this publication in new window or tab >>Topological Line Defects Around Graphene Nanopores for DNA Sequencing
Show others...
2018 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 13, p. 7094-7099Article in journal (Refereed) Published
Abstract [en]

Topological line defects in graphene represent an ideal way to produce highly controlled structures with reduced dimensionality that can be used in electronic devices. In this work, we propose using extended line defects in graphene to improve nucleobase selectivity in nanopore-based DNA sequencing devices. We use a combination of quantum mechanics/molecular mechanics and nonequilibrium Green's function methods to investigate the conductance modulation, fully accounting for solvent effects. By sampling over a large number of different orientations generated from molecular dynamics simulations, we theoretically demonstrate that distinguishing between the four nucleobases using line defects in a graphene-based electronic device appears possible. The changes in conductance are associated with transport across specific molecular states near the Fermi level and their coupling to the pore. Through the application of a specifically tuned gate voltage, such a device would be able to discriminate the four types of nucleobases more reliably than that of graphene sensors without topological line defects.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:uu:diva-352690 (URN)10.1021/acs.jpcc.8b00241 (DOI)000429625600009 ()
Funder
Swedish Research Council
Available from: 2018-06-08 Created: 2018-06-08 Last updated: 2018-06-08Bibliographically approved
de Souza, F. A. L., Amorim, R. G., Prasongkit, J., Scopel, W. L., Scheicher, R. H. & Rocha, A. R. (2018). Topological line defects in graphene for applications in gas sensing. Carbon, 129, 803-808
Open this publication in new window or tab >>Topological line defects in graphene for applications in gas sensing
Show others...
2018 (English)In: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 129, p. 803-808Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
PERGAMON-ELSEVIER SCIENCE LTD, 2018
Keywords
Nanosensor, Graphene, Electronic transport
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-347530 (URN)10.1016/j.carbon.2017.11.029 (DOI)000424885800094 ()
Funder
Carl Tryggers foundation Swedish Research Council
Available from: 2018-04-04 Created: 2018-04-04 Last updated: 2018-04-04Bibliographically approved
Arjmandi-Tash, H., Bellunato, A., Wen, C., Olsthoorn, R. C., Scheicher, R. H., Zhang, S.-L. & Schneider, G. F. (2018). Zero-Depth Interfacial Nanopore Capillaries. Advanced Materials, 30(9), Article ID 1703602.
Open this publication in new window or tab >>Zero-Depth Interfacial Nanopore Capillaries
Show others...
2018 (English)In: Advanced Materials, ISSN 0935-9648, E-ISSN 1521-4095, Vol. 30, no 9, article id 1703602Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2018
Keywords
2D nanopores, biomolecules, 1, f noise, mechanical stability, translocation speed
National Category
Condensed Matter Physics Atom and Molecular Physics and Optics Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-350489 (URN)10.1002/adma.201703602 (DOI)000426491600035 ()
Funder
Swedish Research Council, 621-2014-6300]EU, European Research Council, 335879
Available from: 2018-05-09 Created: 2018-05-09 Last updated: 2018-05-15Bibliographically approved
de Souza, F. A. L., Amorim, R. G., Scopel, W. L. & Scheicher, R. H. (2017). Electrical detection of nucleotides via nanopores in a hybrid graphene/h-BN sheet. Nanoscale, 9(6), 2207-2212
Open this publication in new window or tab >>Electrical detection of nucleotides via nanopores in a hybrid graphene/h-BN sheet
2017 (English)In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 9, no 6, p. 2207-2212Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2017
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-319864 (URN)10.1039/c6nr07154f (DOI)000395626600014 ()28120993 (PubMedID)
Funder
Carl Tryggers foundation Swedish Research Council
Available from: 2017-04-13 Created: 2017-04-13 Last updated: 2017-11-29Bibliographically approved
Sivaraman, G., Amorim, R. G., Scheicher, R. H. & Fyta, M. (2017). Insights into the detection of mutations and epigenetic markers using diamondoid-functionalized sensors. RSC Advances, 7(68), 43064-43072
Open this publication in new window or tab >>Insights into the detection of mutations and epigenetic markers using diamondoid-functionalized sensors
2017 (English)In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 68, p. 43064-43072Article in journal (Refereed) Published
Abstract [en]

Nanogaps functionalized with small diamond-like particles, diamondoids, have been shown to effectively distinguish between different DNA nucleotides. Here, we focus on the detection of mutations and epigenetic markers using such devices. Based on quantum mechanical simulations within the density functional theory approach coupled with the non-equilibrium Green's function scheme, we provide deeper insight into the inherent differences in detecting modified nucleotides. Our results strongly underline the influence of the type of functionalization molecule of the nanogap, as well its conformational details within the nanogap, on the sensing efficiency of the device. The electronic features for the mutations and epigenetic markers are compared to those for the respective canonical nucleotides that are detected by different devices. The calculations directly correlate the structural and electronic properties of the different nucleotides with the electronic transmission across the diamondoid-based device. The latter was found to be controlled by the functionalizing molecule and its binding to the nucleotides. We report on the direct connection of these characteristics to the sensitivity of the diamondoid-functionalized nanogaps, which could eventually be embedded in a nanopore device, and discuss the implications for DNA sensing.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-335533 (URN)10.1039/c7ra06889a (DOI)000409548200047 ()
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2017-12-07Bibliographically approved
Hinnemo, M., Zhao, J., Ahlberg, P., Hägglund, C., Djurberg, V., Scheicher, R. H., . . . Zhang, Z.-B. (2017). On Monolayer Formation of Pyrenebutyric Acid on Graphene. Langmuir, 33(15), 3588-3593
Open this publication in new window or tab >>On Monolayer Formation of Pyrenebutyric Acid on Graphene
Show others...
2017 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 33, no 15, p. 3588-3593Article in journal (Refereed) Published
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.

National Category
Physical Chemistry Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-322804 (URN)10.1021/acs.langmuir.6b04237 (DOI)000399860000003 ()28350965 (PubMedID)
Available from: 2017-06-08 Created: 2017-06-08 Last updated: 2017-06-09Bibliographically approved
Mooij, L., Huang, W., Droulias, S. A., Johansson, R., Hartmann, O., Xin, X., . . . Hjörvarsson, B. (2017). The influence of site occupancy on diffusion of hydrogen in vanadium. Physical Review B, 95(6), Article ID 064310.
Open this publication in new window or tab >>The influence of site occupancy on diffusion of hydrogen in vanadium
Show others...
2017 (English)In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 95, no 6, article id 064310Article, review/survey (Refereed) Published
Abstract [en]

We investigate the effect of site occupancy on the chemical diffusion of hydrogen in strained vanadium. The diffusion rate is found to decrease substantially, when hydrogen is occupying octahedral sites as compared to tetrahedral sites. Profound isotope effects are observed when comparing the diffusion rate of H and D. The changes in the diffusion rate are found to be strongly influenced by the changes in the potential energy landscape, as deduced from first-principles molecular dynamics calculations.

National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:uu:diva-275058 (URN)10.1103/PhysRevB.95.064310 (DOI)000395988800002 ()
Note

The manuscript version of this article is part of two PhD theses: http://uu.diva-portal.org/smash/record.jsf?pid=diva2:900624

http://uu.diva-portal.org/smash/record.jsf?pid=diva2:950756

Available from: 2016-01-28 Created: 2016-01-28 Last updated: 2018-05-14Bibliographically approved
Sivaraman, G., Amorim, R. G., Scheicher, R. H. & Fyta, M. (2016). Benchmark investigation of diamondoid-functionalized electrodes for nanopore DNA sequencing. Nanotechnology, 27(41), Article ID 414002.
Open this publication in new window or tab >>Benchmark investigation of diamondoid-functionalized electrodes for nanopore DNA sequencing
2016 (English)In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 27, no 41, article id 414002Article in journal (Refereed) Published
Abstract [en]

Small diamond-like particles, diamondoids, have been shown to effectively functionalize gold electrodes in order to sense DNA units passing between the nanopore-embedded electrodes. In this work, we present a comparative study of Au(111) electrodes functionalized with different derivatives of lower diamondoids. Focus is put on the electronic and transport properties of such electrodes for different DNA nucleotides placed within the electrode gap. The functionalization promotes a specific binding to DNA leading to different properties for the system, which provides a tool set to systematically improve the signal-to-noise ratio of the electronic measurements across the electrodes. Using quantum transport calculations, we compare the effectiveness of the different functionalized electrodes in distinguishing the four DNA nucleotides. Our results point to the most effective diamondoid functionalization of gold electrodes in view of biosensing applications.

Keywords
DNA sequencing, quantum transport, density functional theory, diamondoids, nanopore, nanogap
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:uu:diva-317710 (URN)10.1088/0957-4484/27/41/414002 (DOI)000394367200001 ()27607107 (PubMedID)
Funder
German Research Foundation (DFG), SFB 716Carl Tryggers foundation Swedish Research Council
Available from: 2017-03-17 Created: 2017-03-17 Last updated: 2017-11-29Bibliographically approved
Organisations

Search in DiVA

Show all publications