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Quantum transport and geometric integration for molecular systems
KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Molecular electronics is envisioned as a possible next step in device miniaturization. It is usually taken to mean the design and manufacturing of electronic devices and applications where organic molecules work as the fundamental functioning unit. It involves the measurement and manipulation of electronic response and transport in molecules attached to conducting leads. Organic molecules have the advantages over conventional solid state electronics of inherent small sizes, endless chemical diversity and ambient temperature low cost manufacturing.

In this thesis we investigate the switching and conducting properties of photoswitching dithienylethene derivatives. Such molecules change their conformation in solution when acted upon by light. Photochromic molecules are attractive candidates for use in molecular electronics because of the switching between different states with different conducting properties. The possibility of optically controlling the conductance of the molecule attached to conducting leads may lead to new device implementations.

The switching reaction is investigated with potential energy calculations for different values of the reaction coordinate between the closed and the open isomer. The electronic and atomic structure calculations are performed with Density Functional Theory (DFT). The potential energy barrier separating the open and closed isomer is investigated, as well as the nature of the excited states involved in the switching.

The conducting properties of the molecule inserted between gold, silver and nickel leads is calculated within the Non Equilibrium Green Function theory (NEGF). The molecule is found to be a good conductor in both conformations, with the low-bias current for the closed one being about 20 times larger than that of the open in the case of gold contacts, and over 30 times larger in the case of silver contacts. For the Ni leads the current for the closed isomer is almost 40 times larger than that of the open. Importantly, the current-voltage characteristics away from the linear response is largely determined by molecular orbital re-hybridization in an electric field, in close analogy to what happens for Mn12 molecules. However in the case of dithienylethene attached to Au and Ag such a mechanism is effective also in conditions of strong electronic coupling to the electrodes.

In reality these molecules are in constant motion, and the dynamical properties has to be considered. In this thesis such a line of work is initiated. In order to facilitate efficient and stable dynamical simulations of molecular systems the extended Lagrangian formulation of Born-Oppenheimer molecular dynamics have been implemented in two different codes. The extended Lagrangian framework enables the geometric integration of both the nuclear and electronic degrees of freedom. This provides highly efficient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence.

In the density functional theory code FreeON, different symplectic integrators up to the 6th order have been adapted and optimized. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements. Geometric integration schemes, including a weak dissipation to remove numerical noise, are developed and implemented in the self-consistent tight-binding code LATTE. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. The modification of the integration breakes symplecticity and introduces a global energy drift. The systematic driftin energy and the broken symplecticity can be kept arbitrarily small without significant perturbations of the molecular trajectories.

Place, publisher, year, edition, pages
Stockholm: KTH , 2010. , x, 89 p.
Keyword [en]
density functional theory, ab initio, first principles, electron transport, photoswitching, molecular dynamics, geometric integration
National Category
Condensed Matter Physics Other Physics Topics
Identifiers
URN: urn:nbn:se:kth:diva-26780ISBN: 978-91-7415-810-6 (print)OAI: oai:DiVA.org:kth-26780DiVA: diva2:373934
Public defence
2010-12-20, F3, Lindstedtsvägen 26, KTH, Stockholm, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council, H 6397
Note
QC 20101202Available from: 2010-12-02 Created: 2010-11-26 Last updated: 2012-01-11Bibliographically approved
List of papers
1. Extended Lagrangian Born-Oppenheimer molecular dynamics with dissipation
Open this publication in new window or tab >>Extended Lagrangian Born-Oppenheimer molecular dynamics with dissipation
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2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 21, 214109- p.Article in journal (Refereed) Published
Abstract [en]

Stability and dissipation in the propagation of the electronic degrees of freedom in time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [Niklasson , Phys. Rev. Lett. 97, 123001 (2006); Phys. Rev. Lett. 100, 123004 (2008)] are analyzed. Because of the time-reversible propagation the dynamics of the extended electronic degrees of freedom is lossless with no dissipation of numerical errors. For long simulation times under "noisy" conditions, numerical errors may therefore accumulate to large fluctuations. We solve this problem by including a dissipative external electronic force that removes noise while keeping the energy stable. The approach corresponds to a Langevin-like dynamics for the electronic degrees of freedom with internal numerical error fluctuations and external, approximately energy conserving, dissipative forces. By tuning the dissipation to balance the numerical fluctuations the external perturbation can be kept to a minimum.

Keyword
ab initio calculations, fluctuations, molecular dynamics method
National Category
Materials Engineering
Identifiers
urn:nbn:se:kth:diva-26991 (URN)10.1063/1.3148075 (DOI)000266674400010 ()2-s2.0-67249126946 (Scopus ID)
Note
QC 20101201Available from: 2010-12-01 Created: 2010-12-01 Last updated: 2017-12-12Bibliographically approved
2. Higher-order symplectic integration in Born-Oppenheimer molecular dynamics
Open this publication in new window or tab >>Higher-order symplectic integration in Born-Oppenheimer molecular dynamics
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2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, no 24Article in journal (Refereed) Published
Abstract [en]

The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, C. J. Tymczak, and M. Challacombe, Phys. Rev. Lett. 100, 123004 (2008); Phys. Rev. Lett. 97, 123001 (2006)] enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the sixth order have been adapted and optimized in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular, for the case of very high accuracy requirements.

Keyword
ab initio calculations, molecular dynamics method, potential energy, surfaces, SCF calculations, matrix, trajectories, orbitals
Identifiers
urn:nbn:se:kth:diva-19090 (URN)10.1063/1.3268338 (DOI)000273217000011 ()2-s2.0-73649144532 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
3. Investigation of the Conducting Properties of a Photoswitching Dithienylethene Molecule
Open this publication in new window or tab >>Investigation of the Conducting Properties of a Photoswitching Dithienylethene Molecule
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2010 (English)In: ACS NANO, ISSN 1936-0851, Vol. 4, no 5, 2635-2642 p.Article in journal (Refereed) Published
Abstract [en]

Photoswitching molecules are attractive candidates as organic materials for optoelectronics applications because light impulses can switch them between states with different conducting characteristics. Here, we report a fully self-consistent density functional theory calculation of the electron transport properties of photoswitching dithienylethene attached to Au leads in both the open and closed conformations. The molecule is found to be a good conductor in both conformations, with the low-bias current for the closed one being about 20 times larger than that of the open. Importantly, the current voltage characteristics away from the linear response are largely determined by molecular orbital rehybridization in an electric field, in close analogy to what happens for Mn-12 molecules. However, in the case of dithienylethene attached to Au, such a mechanism is effective also in conditions of strong electronic coupling to the electrodes. This makes the dithienylethene family an intriguing materials platform for constructing highly conducting organic optoelectronics switches.

Keyword
density functional theory, nonequilibrium Green's function theory, self-consistent, molecular electronics, opto-electronics, electron transport, molecular conduction, photoswitching, polarization, rehybridization
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-26163 (URN)10.1021/nn100217r (DOI)000277976900019 ()2-s2.0-77952903614 (Scopus ID)
Note
QC 20101119Available from: 2010-11-19 Created: 2010-11-19 Last updated: 2011-01-12Bibliographically approved
4. Comparison between s- and d-electron mediated transport in a photoswitching dithienylethene molecule using ab initio transport methods
Open this publication in new window or tab >>Comparison between s- and d-electron mediated transport in a photoswitching dithienylethene molecule using ab initio transport methods
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2011 (English)In: Physical Review B Condensed Matter, ISSN 0163-1829, E-ISSN 1095-3795, Vol. 84, no 16, 165402- p.Article in journal (Refereed) Published
Abstract [en]

The influence of the electrode's Fermi surface on the transport properties of a photoswitching molecule is investigated with state-of-the-art ab initio transport methods. We report results for the conducting properties of the two forms of dithienylethene attached either to Ag or to nonmagnetic Ni leads. The I-V curves of the Ag/dithienylethene/Ag device are found to be very similar to those reported previously for Au. In contrast, when Ni is used as the electrode material the zero-bias transmission coefficient is profoundly different as a result of the role played by the Ni d bands in the bonding between the molecule and the electrodes. Intriguingly, despite these differences the overall conducting properties depend little on the electrode material. We thus conclude that electron transport in dithienylethene is, for the cases studied, mainly governed by the intrinsic electronic structure of the molecule.

Keyword
PHOTOCHROMIC REACTION; DEVICES; SWITCH
National Category
Other Physics Topics Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-26957 (URN)10.1103/PhysRevB.84.165402 (DOI)000295487200008 ()2-s2.0-80455167928 (Scopus ID)
Funder
Swedish Research Council, H 6397Swedish e‐Science Research Center
Note
QC 20101202. Updated from submitted to published. Previous title: Comparison between s- and d-electron mediated transport in a photoswitching dithienylethene moleculeAvailable from: 2010-12-02 Created: 2010-11-30 Last updated: 2017-12-12Bibliographically approved
5. Geometric integration in extended lagrangian self consistent tight-binding molecular dynamics
Open this publication in new window or tab >>Geometric integration in extended lagrangian self consistent tight-binding molecular dynamics
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(English)Article in journal (Other academic) Submitted
Abstract [en]

Geometric integration schemes for extended Lagrangian self-consistent tight-binding molecular dynamics, including a weak dissipation to remove numerical noise, are developed and analyzed. The extended Lagrangian framework enables the geometric integration of both the nuclear andelectronic degrees of freedom. This provides highly effcient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence. We investigate three different geometric integration schemes: i) regular time reversible Verlet, ii) secondorder optimal symplectic, and iii) third order optimal symplectic. We look at energy conservation, accuracy and stabilitty as a function of dissipation, integration time step, and SCF convergence. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. The modification of the integration breakes symplecticity and introduces a global energy drift. The systematic drift in energy and the broken symplecticity can be kept arbitrarily small without significant perturbations of the molecular trajectories. However, we have yet to find a formalism for the inclusion of the dissipation in higher-order symplectic integration methods with a more optimal balance between efficient damping and minimal global energy drift.

National Category
Other Physics Topics Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-26959 (URN)
Note
QC 20101202Available from: 2010-12-02 Created: 2010-11-30 Last updated: 2010-12-02Bibliographically approved
6. Spin-polarized conduction in a photoswitching dithienylethene molecule attached to Ni leads
Open this publication in new window or tab >>Spin-polarized conduction in a photoswitching dithienylethene molecule attached to Ni leads
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(English)Article in journal (Other academic) Submitted
Abstract [en]

The finite-bias conduction properties of the photoswitching dithienyle the molecule attached to spin-polarized nickel electrodes are investigated. We find that the ratio of conduction between the open and closed isomers is around 60 at low bias, decreasing to 50 at a bias of 1 V. The I ¡ Vcharacteristics for the spin up and spin down channels are very similar, despite the fact that the Ni electrode density of states is very different for the two cases - Ni is known to be a so-called strong ferromagnet meaning that it is almost completely spin polarized at the Fermi level.

National Category
Condensed Matter Physics Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-26960 (URN)
Funder
Swedish Research Council, H 6397
Note
QS 20120328Available from: 2010-12-02 Created: 2010-11-30 Last updated: 2012-03-28Bibliographically approved

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