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First principles simulations of electron transport at the molecule-solid interface
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis I concentrate on the description of electron transport properties of microscopic objects, including molecular junctions and nano junctions, in particular, inelastic electron tunneling in surface-adsorbate systems are examined with more contemplations. Boosted by the rapid advance in experimental techniques at the microscopic scale, various electric experiments and measurements sprung up in the last decade. Electric devices, such as transistors, switches, wires, etc. are expected to be integrated into circuit and performing like traditional semiconductor integrated circuit (IC). On the other hand, detailed information about transport properties also provides new physical observable quantities to characterize the systems. For molecular electronics, which is in the state of growing up, its further applications demands more thorough understanding of the underlying mechanism, for instance, the effects of molecular configuration and conformation, inter- or intra-molecular interactions, molecular-substrate interactions, and so on. Inelastic electron tunneling spectroscopy (IETS), which reflects vibration features of the system, is also a finger print property, and can thus be employed to afford the responsibility of single molecular identification with the help of other experimental techniques and theoretical simulations.There are two parts of work presented in this thesis, the first one is devoted to the calculation of electron transport properties of molecular or nano junctions: we have designed a negative differential resistance (NDR) device based on graphene nanoribbons (GNRs), where the latter is a star material in scientific committee since its birth;The transport properties of DNA base-pair junctions are also examined by theoretical calculation, relevant experimental results on DNA sequencing have been explained and detailed issues are suggested.The second part focused on the simulation of scanning tunneling microscope mediated IETS (STM-IETS). We have implemented a numerical scheme to calculate the inelastic tunneling intensity based on Tersoff-Hamann approximation and finite difference method, benchmark results agree well with experimental and previous theoretical ones; Two applications of single molecular chemical identification are also presented following benchmarking.

Place, publisher, year, edition, pages
Stockholm: KTH , 2010. , xii, 70 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2010:8
Keyword [en]
first principles, electron transport, solid surface, inelastic electron tunneling
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-12870ISBN: 978-91-7415-629-4 (print)OAI: oai:DiVA.org:kth-12870DiVA: diva2:319466
Public defence
2010-06-10, FB54, Roslagstullsbacken 21, Albanova University Center, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC20100630Available from: 2010-05-25 Created: 2010-05-18 Last updated: 2012-03-27Bibliographically approved
List of papers
1. Graphene nanoribbon as a negative differential resistance device
Open this publication in new window or tab >>Graphene nanoribbon as a negative differential resistance device
2009 (English)In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 94, no 17, 173110- p.Article in journal (Refereed) Published
Abstract [en]

We present a theoretical study on electronic structure and elastic transport properties of armchair graphene nanoribbon based junctions by using density functional theory calculations and nonequilibrium Green's function technique. The I-V characteristics of various junctions are examined, which all exhibit robust negative differential resistance (NDR) phenomena. It is found that such NDR behaviors originate from the interaction between the narrow density of states of the doped leads and the discrete states in the scattering region.

Keyword
density functional theory; electronic density of states; graphene; Green's function methods; impurity states; nanocontacts; nanoelectronics; negative resistance devices; nitrogen; semiconductor devices; semiconductor materials
Identifiers
urn:nbn:se:kth:diva-13055 (URN)10.1063/1.3126451 (DOI)000265738700069 ()2-s2.0-65449166838 (Scopus ID)
Note
QC20100525Available from: 2010-05-25 Created: 2010-05-25 Last updated: 2017-12-12Bibliographically approved
2. Important structural factors controlling the conductance of DNA pairs in molecular junctions
Open this publication in new window or tab >>Important structural factors controlling the conductance of DNA pairs in molecular junctions
Show others...
2010 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 33, 14240-14242 p.Article in journal (Refereed) Published
Abstract [en]

It has been demonstrated experimentally that DNA base pairs and sequences can be identified by measuring their current changes in metal junctions. We report here a first principles study on electron transport properties of DNA base pairs in gold metal junctions. It is found that the experimentally observed electrode-separation-width-dependent current changes of DNA base pairs are not due to the difference in number of hydrogen bonds involved in different base pairs as proposed in earlier experimental studies but caused by the difference in their stacking structures. It reveals that such an electronic read-out technique is not exact, but practically useful since the statistically favorable misaligned junctions do show distinct dependence on the character of the base pair. 

Keyword
Base pairs, Current change, DNA base pairs, Experimental studies, First-principles study, Metal junctions, Molecular junction, Stacking structures, Structural factor
Identifiers
urn:nbn:se:kth:diva-13854 (URN)10.1021/jp100798g (DOI)000280961800039 ()2-s2.0-77955889117 (Scopus ID)
Note
QC 20120328. Updated from submitted to published.Available from: 2010-06-30 Created: 2010-06-30 Last updated: 2017-12-12Bibliographically approved
3. Identifying configuration and orientation of adsorbed molecules by inelastic electron tunneling spectra
Open this publication in new window or tab >>Identifying configuration and orientation of adsorbed molecules by inelastic electron tunneling spectra
2010 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 6, 064702- p.Article in journal (Refereed) Published
Abstract [en]

Scanning tunneling microscopy (STM) topographical images and inelastic electron tunneling spectra (IETS) of a cis-2-butene molecule adsorbed on a Pd(110) surface have been simulated by first-principles calculations. Calculations have eliminated the ambiguity between the STM image and the adsorption orientation caused by the symmetry of the system and local chemical environment. A combination of STM images and IETS spectra has been shown to be particularly useful in determining the configuration of the molecule on the surface. (C) 2010 American Institute of Physics. [doi:10.1063/1.3474807]

Keyword
ab initio calculations, adsorption, organic compounds, scanning tunnelling microscopy, tunnelling spectra
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-26849 (URN)10.1063/1.3474807 (DOI)000280941800030 ()2-s2.0-77955754881 (Scopus ID)
Note
QC 20101206Available from: 2010-12-06 Created: 2010-11-29 Last updated: 2017-12-12Bibliographically approved
4. Simulation of inelastic electronic tunneling spectra of adsorbates from first principles
Open this publication in new window or tab >>Simulation of inelastic electronic tunneling spectra of adsorbates from first principles
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 134707Article in journal (Refereed) Published
Abstract [en]

We present first-principles simulations for inelastic electron tunneling spectra of molecules adsorbed on metal surface as measured in scanning tunneling microscopy experiments. Both elastic and inelastic tunneling processes are modeled in terms of Tersoff-Hamann approximation with a full vibration analysis at density functional theory levels. The calculated spectra of carbon oxide and acetylene molecules adsorbed on Cu(100) surface have well reproduced their experimental counterparts. The inelastic electron tunneling images of the observable vibration modes have been provided. The performance of gradient-corrected density functional is compared with that of local density functional.

Keyword
MOLECULE VIBRATIONAL SPECTROSCOPY; TOTAL-ENERGY CALCULATIONS; WAVE BASIS-SET; MICROSCOPE; CU(100); CO; EXCITATION
Identifiers
urn:nbn:se:kth:diva-13059 (URN)10.1063/1.3106235 (DOI)000265053200055 ()2-s2.0-64549133389 (Scopus ID)
Note
QC20100525Available from: 2010-05-25 Created: 2010-05-25 Last updated: 2017-12-12Bibliographically approved
5. Determining tautomer structures of a melamine molecule adsorbed onCu(001) by inelastic electron tunneling spectroscopy
Open this publication in new window or tab >>Determining tautomer structures of a melamine molecule adsorbed onCu(001) by inelastic electron tunneling spectroscopy
Show others...
(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:kth:diva-13860 (URN)
Note
QC20100630Available from: 2010-06-30 Created: 2010-06-30 Last updated: 2010-06-30Bibliographically approved

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