---
_id: '14006'
abstract:
- lang: eng
text: We present a theoretical formalism for the calculation of attosecond delays
in molecular photoionization. It is shown how delays relevant to one-photon-ionization,
also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole
matrix elements provided by molecular quantum scattering theory. These results
are used to derive formulae for the delays measured by two-photon attosecond interferometry
based on an attosecond pulse train and a dressing femtosecond infrared pulse.
These effective delays are first expressed in the molecular frame where maximal
information about the molecular photoionization dynamics is available. The effects
of averaging over the emission direction of the electron and the molecular orientation
are introduced analytically. We illustrate this general formalism for the case
of two polyatomic molecules. N2O serves as an example of a polar linear molecule
characterized by complex photoionization dynamics resulting from the presence
of molecular shape resonances. H2O illustrates the case of a non-linear molecule
with comparably simple photoionization dynamics resulting from a flat continuum.
Our theory establishes the foundation for interpreting measurements of the photoionization
dynamics of all molecules by attosecond metrology.
article_number: '124306'
article_processing_charge: No
article_type: original
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Wörner HJ. Theory of attosecond delays in molecular photoionization.
The Journal of Chemical Physics. 2017;146(12). doi:10.1063/1.4977933
apa: Baykusheva, D. R., & Wörner, H. J. (2017). Theory of attosecond delays
in molecular photoionization. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4977933
chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond
Delays in Molecular Photoionization.” The Journal of Chemical Physics.
AIP Publishing, 2017. https://doi.org/10.1063/1.4977933.
ieee: D. R. Baykusheva and H. J. Wörner, “Theory of attosecond delays in molecular
photoionization,” The Journal of Chemical Physics, vol. 146, no. 12. AIP
Publishing, 2017.
ista: Baykusheva DR, Wörner HJ. 2017. Theory of attosecond delays in molecular photoionization.
The Journal of Chemical Physics. 146(12), 124306.
mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond
Delays in Molecular Photoionization.” The Journal of Chemical Physics,
vol. 146, no. 12, 124306, AIP Publishing, 2017, doi:10.1063/1.4977933.
short: D.R. Baykusheva, H.J. Wörner, The Journal of Chemical Physics 146 (2017).
date_created: 2023-08-10T06:36:19Z
date_published: 2017-03-28T00:00:00Z
date_updated: 2023-08-22T08:30:59Z
day: '28'
doi: 10.1063/1.4977933
extern: '1'
external_id:
pmid:
- '28388142'
intvolume: ' 146'
issue: '12'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '03'
oa_version: None
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theory of attosecond delays in molecular photoionization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 146
year: '2017'
...
---
_id: '14007'
abstract:
- lang: eng
text: 'In a recent article by Hockett et al (2016 J. Phys. B: At. Mol. Opt. Phys.
49 095602), time delays arising in the context of molecular single-photon ionization
are investigated from a theoretical point of view. We argue that one of the central
equations given in this article is incorrect and present a reformulation that
is consistent with the established treatment of angle-dependent scattering delays
(Eisenbud 1948 PhD Thesis Princeton University; Wigner 1955 Phys. Rev. 98 145–7;
Smith 1960 Phys. Rev. 118 349–6; Nussenzveig 1972 Phys. Rev. D 6 1534–42).'
article_number: '078002'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: 'Baykusheva DR, Wörner HJ. Comment on ‘Time delays in molecular photoionization.’
Journal of Physics B: Atomic, Molecular and Optical Physics. 2017;50(7).
doi:10.1088/1361-6455/aa62b5'
apa: 'Baykusheva, D. R., & Wörner, H. J. (2017). Comment on ‘Time delays in
molecular photoionization.’ Journal of Physics B: Atomic, Molecular and Optical
Physics. IOP Publishing. https://doi.org/10.1088/1361-6455/aa62b5'
chicago: 'Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time
Delays in Molecular Photoionization.’” Journal of Physics B: Atomic, Molecular
and Optical Physics. IOP Publishing, 2017. https://doi.org/10.1088/1361-6455/aa62b5.'
ieee: 'D. R. Baykusheva and H. J. Wörner, “Comment on ‘Time delays in molecular
photoionization,’” Journal of Physics B: Atomic, Molecular and Optical Physics,
vol. 50, no. 7. IOP Publishing, 2017.'
ista: 'Baykusheva DR, Wörner HJ. 2017. Comment on ‘Time delays in molecular photoionization’.
Journal of Physics B: Atomic, Molecular and Optical Physics. 50(7), 078002.'
mla: 'Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time Delays
in Molecular Photoionization.’” Journal of Physics B: Atomic, Molecular and
Optical Physics, vol. 50, no. 7, 078002, IOP Publishing, 2017, doi:10.1088/1361-6455/aa62b5.'
short: 'D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and
Optical Physics 50 (2017).'
date_created: 2023-08-10T06:36:29Z
date_published: 2017-03-15T00:00:00Z
date_updated: 2023-08-22T08:32:43Z
day: '15'
doi: 10.1088/1361-6455/aa62b5
extern: '1'
external_id:
arxiv:
- '1611.09352'
intvolume: ' 50'
issue: '7'
keyword:
- Condensed Matter Physics
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.09352
month: '03'
oa: 1
oa_version: Preprint
publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics'
publication_identifier:
eissn:
- 1361-6455
issn:
- 0953-4075
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Comment on ‘Time delays in molecular photoionization’
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2017'
...
---
_id: '14008'
abstract:
- lang: eng
text: Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically
been limited to large-scale facilities, to subpicosecond temporal resolution,
and to the condensed phase. We report the realization of TR-XAS with a temporal
resolution in the low femtosecond range by developing a tabletop high-harmonic
source reaching up to 350 electron volts, thus partially covering the spectral
region of 280 to 530 electron volts, where water is transmissive. We used this
source to follow previously unexamined light-induced chemical reactions in the
lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase.
By probing element-specific core-to-valence transitions at the carbon K-edge or
the sulfur L-edges, we characterized their reaction paths and observed the effect
of symmetry breaking through the splitting of absorption bands and Rydberg-valence
mixing induced by the geometry changes.
article_processing_charge: No
article_type: original
author:
- first_name: Yoann
full_name: Pertot, Yoann
last_name: Pertot
- first_name: Cédric
full_name: Schmidt, Cédric
last_name: Schmidt
- first_name: Mary
full_name: Matthews, Mary
last_name: Matthews
- first_name: Adrien
full_name: Chauvet, Adrien
last_name: Chauvet
- first_name: Martin
full_name: Huppert, Martin
last_name: Huppert
- first_name: Vit
full_name: Svoboda, Vit
last_name: Svoboda
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Andres
full_name: Tehlar, Andres
last_name: Tehlar
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Jean-Pierre
full_name: Wolf, Jean-Pierre
last_name: Wolf
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Pertot Y, Schmidt C, Matthews M, et al. Time-resolved x-ray absorption spectroscopy
with a water window high-harmonic source. Science. 2017;355(6322):264-267.
doi:10.1126/science.aah6114
apa: Pertot, Y., Schmidt, C., Matthews, M., Chauvet, A., Huppert, M., Svoboda, V.,
… Wörner, H. J. (2017). Time-resolved x-ray absorption spectroscopy with a water
window high-harmonic source. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aah6114
chicago: Pertot, Yoann, Cédric Schmidt, Mary Matthews, Adrien Chauvet, Martin Huppert,
Vit Svoboda, Aaron von Conta, et al. “Time-Resolved x-Ray Absorption Spectroscopy
with a Water Window High-Harmonic Source.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aah6114.
ieee: Y. Pertot et al., “Time-resolved x-ray absorption spectroscopy with
a water window high-harmonic source,” Science, vol. 355, no. 6322. American
Association for the Advancement of Science, pp. 264–267, 2017.
ista: Pertot Y, Schmidt C, Matthews M, Chauvet A, Huppert M, Svoboda V, von Conta
A, Tehlar A, Baykusheva DR, Wolf J-P, Wörner HJ. 2017. Time-resolved x-ray absorption
spectroscopy with a water window high-harmonic source. Science. 355(6322), 264–267.
mla: Pertot, Yoann, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water
Window High-Harmonic Source.” Science, vol. 355, no. 6322, American Association
for the Advancement of Science, 2017, pp. 264–67, doi:10.1126/science.aah6114.
short: Y. Pertot, C. Schmidt, M. Matthews, A. Chauvet, M. Huppert, V. Svoboda, A.
von Conta, A. Tehlar, D.R. Baykusheva, J.-P. Wolf, H.J. Wörner, Science 355 (2017)
264–267.
date_created: 2023-08-10T06:36:39Z
date_published: 2017-01-05T00:00:00Z
date_updated: 2023-08-22T08:34:38Z
day: '05'
doi: 10.1126/science.aah6114
extern: '1'
external_id:
pmid:
- '28059713'
intvolume: ' 355'
issue: '6322'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa_version: None
page: 264-267
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Time-resolved x-ray absorption spectroscopy with a water window high-harmonic
source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '14009'
abstract:
- lang: eng
text: Attosecond delays between photoelectron wave packets emitted from different
electronic shells are now well established. Is there any delay between electrons
originating from the same electronic shell but leaving the cation in different
fine-structure states? This question is relevant for all attosecond photoemission
studies involving heavy elements, be it atoms, molecules or solids. We answer
this fundamental question by measuring energy-dependent delays between photoelectron
wave packets associated with the 2P3/2 and 2P1/2 components of the electronic
groundstates of Xe+ and Kr+. We observe delays reaching up to 33±6 as in the case
of Xe. Our results are compared with two state-of-the-art theories. Whereas both
theories quantitatively agree with the results obtained for Kr, neither of them
fully reproduces the experimental results in Xe. Performing delay measurements
very close to the ionization thresholds, we compare the agreement of several analytical
formulas for the continuum-continuum delays with experimental data. Our results
show an important influence of spin-orbit coupling on attosecond photoionization
delays, highlight the requirement for additional theory development, and offer
a precision benchmark for such work.
article_number: '013404'
article_processing_charge: No
article_type: original
author:
- first_name: I.
full_name: Jordan, I.
last_name: Jordan
- first_name: M.
full_name: Huppert, M.
last_name: Huppert
- first_name: S.
full_name: Pabst, S.
last_name: Pabst
- first_name: A. S.
full_name: Kheifets, A. S.
last_name: Kheifets
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. Spin-orbit
delays in photoemission. Physical Review A. 2017;95(1). doi:10.1103/physreva.95.013404
apa: Jordan, I., Huppert, M., Pabst, S., Kheifets, A. S., Baykusheva, D. R., &
Wörner, H. J. (2017). Spin-orbit delays in photoemission. Physical Review A.
American Physical Society. https://doi.org/10.1103/physreva.95.013404
chicago: Jordan, I., M. Huppert, S. Pabst, A. S. Kheifets, Denitsa Rangelova Baykusheva,
and H. J. Wörner. “Spin-Orbit Delays in Photoemission.” Physical Review A.
American Physical Society, 2017. https://doi.org/10.1103/physreva.95.013404.
ieee: I. Jordan, M. Huppert, S. Pabst, A. S. Kheifets, D. R. Baykusheva, and H.
J. Wörner, “Spin-orbit delays in photoemission,” Physical Review A, vol.
95, no. 1. American Physical Society, 2017.
ista: Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. 2017.
Spin-orbit delays in photoemission. Physical Review A. 95(1), 013404.
mla: Jordan, I., et al. “Spin-Orbit Delays in Photoemission.” Physical Review
A, vol. 95, no. 1, 013404, American Physical Society, 2017, doi:10.1103/physreva.95.013404.
short: I. Jordan, M. Huppert, S. Pabst, A.S. Kheifets, D.R. Baykusheva, H.J. Wörner,
Physical Review A 95 (2017).
date_created: 2023-08-10T06:36:58Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2023-08-22T08:38:17Z
day: '10'
doi: 10.1103/physreva.95.013404
extern: '1'
intvolume: ' 95'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-orbit delays in photoemission
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2017'
...
---
_id: '14031'
abstract:
- lang: eng
text: High-harmonic spectroscopy driven by circularly polarized laser pulses and
their counterrotating second harmonic is a new branch of attosecond science which
currently lacks quantitative interpretations. We extend this technique to the
midinfrared regime and record detailed high-harmonic spectra of several rare-gas
atoms. These results are compared with the solution of the Schrödinger equation
in three dimensions and calculations based on the strong-field approximation that
incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit
analysis of these results provides a transparent interpretation of the measured
intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set
of propensity rules related to the angular momentum of the atomic orbitals, (ii)
atom-specific matrix elements related to their electronic structure, and (iii)
the interference of the emissions associated with electrons in orbitals corotating
or counterrotating with the laser fields. These results provide the foundation
for a quantitative understanding of bicircular high-harmonic spectroscopy.
article_number: '203201'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Simon
full_name: Brennecke, Simon
last_name: Brennecke
- first_name: Manfred
full_name: Lein, Manfred
last_name: Lein
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure
in bicircular high-harmonic spectroscopy. Physical Review Letters. 2017;119(20).
doi:10.1103/physrevlett.119.203201
apa: Baykusheva, D. R., Brennecke, S., Lein, M., & Wörner, H. J. (2017). Signatures
of electronic structure in bicircular high-harmonic spectroscopy. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.119.203201
chicago: Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans
Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic
Spectroscopy.” Physical Review Letters. American Physical Society, 2017.
https://doi.org/10.1103/physrevlett.119.203201.
ieee: D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of
electronic structure in bicircular high-harmonic spectroscopy,” Physical Review
Letters, vol. 119, no. 20. American Physical Society, 2017.
ista: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic
structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20),
203201.
mla: Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in
Bicircular High-Harmonic Spectroscopy.” Physical Review Letters, vol. 119,
no. 20, 203201, American Physical Society, 2017, doi:10.1103/physrevlett.119.203201.
short: D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters
119 (2017).
date_created: 2023-08-10T06:48:12Z
date_published: 2017-11-17T00:00:00Z
date_updated: 2023-08-22T06:48:28Z
day: '17'
doi: 10.1103/physrevlett.119.203201
extern: '1'
external_id:
arxiv:
- '1710.04474'
pmid:
- '29219334'
intvolume: ' 119'
issue: '20'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.04474
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Signatures of electronic structure in bicircular high-harmonic spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '1407'
abstract:
- lang: eng
text: We consider the problem of computing the set of initial states of a dynamical
system such that there exists a control strategy to ensure that the trajectories
satisfy a temporal logic specification with probability 1 (almost-surely). We
focus on discrete-time, stochastic linear dynamics and specifications given as
formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over
linear predicates in the states of the system. We propose a solution based on
iterative abstraction-refinement, and turn-based 2-player probabilistic games.
While the theoretical guarantee of our algorithm after any finite number of iterations
is only a partial solution, we show that if our algorithm terminates, then the
result is the set of all satisfying initial states. Moreover, for any (partial)
solution our algorithm synthesizes witness control strategies to ensure almost-sure
satisfaction of the temporal logic specification. While the proposed algorithm
guarantees progress and soundness in every iteration, it is computationally demanding.
We offer an alternative, more efficient solution for the reachability properties
that decomposes the problem into a series of smaller problems of the same type.
All algorithms are demonstrated on an illustrative case study.
article_processing_charge: No
arxiv: 1
author:
- first_name: Mária
full_name: Svoreňová, Mária
last_name: Svoreňová
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ivana
full_name: Cěrná, Ivana
last_name: Cěrná
- first_name: Cǎlin
full_name: Belta, Cǎlin
last_name: Belta
citation:
ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal
logic control for stochastic linear systems using abstraction refinement of probabilistic
games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006'
apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &
Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction
refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems.
Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006'
chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee,
Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.'
ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta,
“Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no.
2. Elsevier, pp. 230–253, 2017.'
ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017.
Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.'
mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.'
short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta,
Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.'
date_created: 2018-12-11T11:51:50Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2025-06-11T06:33:00Z
day: '01'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1016/j.nahs.2016.04.006
ec_funded: 1
external_id:
arxiv:
- '1410.5387'
isi:
- '000390637000014'
intvolume: ' 23'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.5387
month: '02'
oa: 1
oa_version: Preprint
page: 230 - 253
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_status: published
publisher: Elsevier
publist_id: '5800'
quality_controlled: '1'
related_material:
record:
- id: '1689'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2017'
...
---
_id: '14205'
abstract:
- lang: eng
text: Two of the most fundamental prototypes of greedy optimization are the matching
pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both
classes of methods, leading to the first explicit convergence rates of matching
pursuit methods in an optimization sense, for general sets of atoms. We derive
sublinear (1/t) convergence for both classes on general smooth objectives, and
linear convergence on strongly convex objectives, as well as a clear correspondence
of algorithm variants. Our presented algorithms and rates are affine invariant,
and do not need any incoherence or sparsity assumptions.
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on
generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International
Conference on Artificial Intelligence and Statistics. Vol 54. ML Research
Press; 2017:860-868.'
apa: 'Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified
optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings
of the 20th International Conference on Artificial Intelligence and Statistics
(Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.'
chicago: Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi.
“A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.”
In Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics, 54:860–68. ML Research Press, 2017.
ieee: F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization
view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, Fort
Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.
ista: 'Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization
view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th
International Conference on Artificial Intelligence and Statistics. AISTATS: Conference
on Artificial Intelligence and Statistics vol. 54, 860–868.'
mla: Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching
Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference
on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017,
pp. 860–68.
short: F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, ML Research
Press, 2017, pp. 860–868.
conference:
end_date: 2017-04-22
location: Fort Lauderdale, FL, United States
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2017-04-20
date_created: 2023-08-22T14:17:19Z
date_published: 2017-02-21T00:00:00Z
date_updated: 2023-09-13T09:49:10Z
day: '21'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1702.06457'
intvolume: ' 54'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1702.06457
month: '02'
oa: 1
oa_version: Preprint
page: 860-868
publication: Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: A unified optimization view on generalized matching pursuit and Frank-Wolfe
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '14206'
abstract:
- lang: eng
text: Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe
(FW) algorithms regained popularity in recent years due to their simplicity, effectiveness
and theoretical guarantees. MP and FW address optimization over the linear span
and the convex hull of a set of atoms, respectively. In this paper, we consider
the intermediate case of optimization over the convex cone, parametrized as the
conic hull of a generic atom set, leading to the first principled definitions
of non-negative MP algorithms for which we give explicit convergence rates and
demonstrate excellent empirical performance. In particular, we derive sublinear
(O(1/t)) convergence on general smooth and convex objectives, and linear convergence
(O(e−t)) on strongly convex objectives, in both cases for general sets of atoms.
Furthermore, we establish a clear correspondence of our algorithms to known algorithms
from the MP and FW literature. Our novel algorithms and analyses target general
atom sets and general objective functions, and hence are directly applicable to
a large variety of learning settings.
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained
optimization with convergence guarantees. In: Advances in Neural Information
Processing Systems. ; 2017.'
apa: Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms
for cone constrained optimization with convergence guarantees. In Advances
in Neural Information Processing Systems. Long Beach, CA, United States.
chicago: Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi.
“Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.”
In Advances in Neural Information Processing Systems, 2017.
ieee: F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for
cone constrained optimization with convergence guarantees,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017.
ista: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for
cone constrained optimization with convergence guarantees. Advances in Neural
Information Processing Systems. NeurIPS: Neural Information Processing Systems.'
mla: Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization
with Convergence Guarantees.” Advances in Neural Information Processing Systems,
2017.
short: F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural
Information Processing Systems, 2017.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2017-12-04
date_created: 2023-08-22T14:17:38Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2024-10-14T12:29:50Z
day: '31'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1705.11041'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.11041
month: '05'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781510860964'
publication_status: published
quality_controlled: '1'
status: public
title: Greedy algorithms for cone constrained optimization with convergence guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '14286'
abstract:
- lang: eng
text: 'The bacteriophage M13 has found frequent applications in nanobiotechnology
due to its chemically and genetically tunable protein surface and its ability
to self-assemble into colloidal membranes. Additionally, its single-stranded (ss)
genome is commonly used as scaffold for DNA origami. Despite the manifold uses
of M13, upstream production methods for phage and scaffold ssDNA are underexamined
with respect to future industrial usage. Here, the high-cell-density phage production
with Escherichia coli as host organism was studied in respect of medium composition,
infection time, multiplicity of infection, and specific growth rate. The specific
growth rate and the multiplicity of infection were identified as the crucial state
variables that influence phage amplification rate on one hand and the concentration
of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity
of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration
of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced
by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial
uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784.'
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin
full_name: Kick, Benjamin
last_name: Kick
- first_name: Samantha
full_name: Hensler, Samantha
last_name: Hensler
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Dirk
full_name: Weuster-Botz, Dirk
last_name: Weuster-Botz
citation:
ama: Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth
rate and multiplicity of infection affect high-cell-density fermentation with
bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering.
2017;114(4):777-784. doi:10.1002/bit.26200
apa: Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., & Weuster-Botz, D.
(2017). Specific growth rate and multiplicity of infection affect high-cell-density
fermentation with bacteriophage M13 for ssDNA production. Biotechnology and
Bioengineering. Wiley. https://doi.org/10.1002/bit.26200
chicago: Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz,
and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect
High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” Biotechnology
and Bioengineering. Wiley, 2017. https://doi.org/10.1002/bit.26200.
ieee: B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific
growth rate and multiplicity of infection affect high-cell-density fermentation
with bacteriophage M13 for ssDNA production,” Biotechnology and Bioengineering,
vol. 114, no. 4. Wiley, pp. 777–784, 2017.
ista: Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific
growth rate and multiplicity of infection affect high-cell-density fermentation
with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering.
114(4), 777–784.
mla: Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection
Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.”
Biotechnology and Bioengineering, vol. 114, no. 4, Wiley, 2017, pp. 777–84,
doi:10.1002/bit.26200.
short: B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology
and Bioengineering 114 (2017) 777–784.
date_created: 2023-09-06T12:08:29Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-11-07T12:36:20Z
day: '01'
doi: 10.1002/bit.26200
extern: '1'
external_id:
pmid:
- '27748519'
intvolume: ' 114'
issue: '4'
keyword:
- Applied Microbiology and Biotechnology
- Bioengineering
- Biotechnology
language:
- iso: eng
month: '04'
oa_version: None
page: 777-784
pmid: 1
publication: Biotechnology and Bioengineering
publication_identifier:
issn:
- 0006-3592
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specific growth rate and multiplicity of infection affect high-cell-density
fermentation with bacteriophage M13 for ssDNA production
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '14287'
abstract:
- lang: eng
text: We describe an approach to bottom-up fabrication that allows integration of
the functional diversity of proteins into designed three-dimensional structural
frameworks. A set of custom staple proteins based on transcription activator–like
effector proteins folds a double-stranded DNA template into a user-defined shape.
Each staple protein is designed to recognize and closely link two distinct double-helical
DNA sequences at separate positions on the template. We present design rules for
constructing megadalton-scale DNA-protein hybrid shapes; introduce various structural
motifs, such as custom curvature, corners, and vertices; and describe principles
for creating multilayer DNA-protein objects with enhanced rigidity. We demonstrate
self-assembly of our hybrid nanostructures in one-pot mixtures that include the
genetic information for the designed proteins, the template DNA, RNA polymerase,
ribosomes, and cofactors for transcription and translation.
article_number: eaam5488
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Praetorius FM, Dietz H. Self-assembly of genetically encoded DNA-protein hybrid
nanoscale shapes. Science. 2017;355(6331). doi:10.1126/science.aam5488
apa: Praetorius, F. M., & Dietz, H. (2017). Self-assembly of genetically encoded
DNA-protein hybrid nanoscale shapes. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aam5488
chicago: Praetorius, Florian M, and Hendrik Dietz. “Self-Assembly of Genetically
Encoded DNA-Protein Hybrid Nanoscale Shapes.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5488.
ieee: F. M. Praetorius and H. Dietz, “Self-assembly of genetically encoded DNA-protein
hybrid nanoscale shapes,” Science, vol. 355, no. 6331. American Association
for the Advancement of Science, 2017.
ista: Praetorius FM, Dietz H. 2017. Self-assembly of genetically encoded DNA-protein
hybrid nanoscale shapes. Science. 355(6331), eaam5488.
mla: Praetorius, Florian M., and Hendrik Dietz. “Self-Assembly of Genetically Encoded
DNA-Protein Hybrid Nanoscale Shapes.” Science, vol. 355, no. 6331, eaam5488,
American Association for the Advancement of Science, 2017, doi:10.1126/science.aam5488.
short: F.M. Praetorius, H. Dietz, Science 355 (2017).
date_created: 2023-09-06T12:08:55Z
date_published: 2017-03-24T00:00:00Z
date_updated: 2023-11-07T12:33:05Z
day: '24'
doi: 10.1126/science.aam5488
extern: '1'
external_id:
pmid:
- '28336611'
intvolume: ' 355'
issue: '6331'
language:
- iso: eng
month: '03'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '14290'
abstract:
- lang: eng
text: DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly
of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12.
These structures are customizable in that they can be site-specifically functionalized13
or constructed to exhibit machine-like14,15 or logic-gating behaviour16. Their
use has been limited to applications that require only small amounts of material
(of the order of micrograms), owing to the limitations of current production methods.
But many proposed applications, for example as therapeutic agents or in complex
materials3,16,17,18,19,20,21,22, could be realized if more material could be used.
In DNA origami, a nanostructure is assembled from a very long single-stranded
scaffold molecule held in place by many short single-stranded staple oligonucleotides.
Only the bacteriophage-derived scaffold molecules are amenable to scalable and
efficient mass production23; the shorter staple strands are obtained through costly
solid-phase synthesis24 or enzymatic processes25. Here we show that single strands
of DNA of virtually arbitrary length and with virtually arbitrary sequences can
be produced in a scalable and cost-efficient manner by using bacteriophages to
generate single-stranded precursor DNA that contains target strand sequences interleaved
with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent
DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA
for several DNA origami using shaker-flask cultures, and demonstrate end-to-end
production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank
bioreactor. Our method is compatible with existing DNA origami design frameworks
and retains the modularity and addressability of DNA origami objects that are
necessary for implementing custom modifications using functional groups. With
all of the production and purification steps amenable to scaling, we expect that
our method will expand the scope of DNA nanotechnology in many areas of science
and technology.
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Benjamin
full_name: Kick, Benjamin
last_name: Kick
- first_name: Karl L.
full_name: Behler, Karl L.
last_name: Behler
- first_name: Maximilian N.
full_name: Honemann, Maximilian N.
last_name: Honemann
- first_name: Dirk
full_name: Weuster-Botz, Dirk
last_name: Weuster-Botz
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. Biotechnological
mass production of DNA origami. Nature. 2017;552(7683):84-87. doi:10.1038/nature24650
apa: Praetorius, F. M., Kick, B., Behler, K. L., Honemann, M. N., Weuster-Botz,
D., & Dietz, H. (2017). Biotechnological mass production of DNA origami. Nature.
Springer Nature. https://doi.org/10.1038/nature24650
chicago: Praetorius, Florian M, Benjamin Kick, Karl L. Behler, Maximilian N. Honemann,
Dirk Weuster-Botz, and Hendrik Dietz. “Biotechnological Mass Production of DNA
Origami.” Nature. Springer Nature, 2017. https://doi.org/10.1038/nature24650.
ieee: F. M. Praetorius, B. Kick, K. L. Behler, M. N. Honemann, D. Weuster-Botz,
and H. Dietz, “Biotechnological mass production of DNA origami,” Nature,
vol. 552, no. 7683. Springer Nature, pp. 84–87, 2017.
ista: Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. 2017.
Biotechnological mass production of DNA origami. Nature. 552(7683), 84–87.
mla: Praetorius, Florian M., et al. “Biotechnological Mass Production of DNA Origami.”
Nature, vol. 552, no. 7683, Springer Nature, 2017, pp. 84–87, doi:10.1038/nature24650.
short: F.M. Praetorius, B. Kick, K.L. Behler, M.N. Honemann, D. Weuster-Botz, H.
Dietz, Nature 552 (2017) 84–87.
date_created: 2023-09-06T12:14:20Z
date_published: 2017-12-07T00:00:00Z
date_updated: 2023-11-07T12:24:49Z
day: '07'
doi: 10.1038/nature24650
extern: '1'
external_id:
pmid:
- '29219963'
intvolume: ' 552'
issue: '7683'
language:
- iso: eng
month: '12'
oa_version: None
page: 84-87
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Biotechnological mass production of DNA origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 552
year: '2017'
...
---
_id: '14308'
abstract:
- lang: eng
text: Here we describe an approach to bottom-up fabrication with nanometer-precision
that allows integrating the functional diversity of proteins in designed three-dimensional
structural frameworks. We reimagined the successful DNA origami design principle
using a set of custom staple proteins to fold a double-stranded DNA template into
a user-defined shape. Each staple protein recognizes two distinct double-helical
DNA sequences and can carry additional functionalities. The staple proteins we
present here are based on the transcription activator-like (TAL) effector proteins.
Due to their repetitive structure these proteins offer a unique programmability
that enables us to construct numerous staple proteins targeting any desired DNA
sequence. Our approach is general, meaning that many different objects may be
created using the same set of rules, and it is modular, because components can
be modified or exchanged individually. We present rules for constructing megadalton-scale
DNA-protein hybrid nanostructures; introduce important structural motifs, such
as curvature, corners, and vertices; describe principles for creating multi-layer
DNA-protein objects with enhanced rigidity; and demonstrate the possibility to
combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since
all components can be encoded genetically, our structures should be amenable to
biotechnological mass-production. Moreover, since the target objects can self-assemble
at room temperature in near-physiological buffer, our hybrid origami may also
provide an attractive method to realize positioning and scaffolding tasks in vivo.
We expect our method to find application both in scaffolding protein functionalities
and in manipulating the spatial arrangement of genomic DNA.
article_number: 25a
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. Biophysical
Journal. 2017;112(3). doi:10.1016/j.bpj.2016.11.171
apa: Praetorius, F. M., & Dietz, H. (2017). Genetically encoded DNA-protein
hybrid origami. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2016.11.171
chicago: Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein
Hybrid Origami.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2016.11.171.
ieee: F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,”
Biophysical Journal, vol. 112, no. 3. Elsevier, 2017.
ista: Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami.
Biophysical Journal. 112(3), 25a.
mla: Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein
Hybrid Origami.” Biophysical Journal, vol. 112, no. 3, 25a, Elsevier, 2017,
doi:10.1016/j.bpj.2016.11.171.
short: F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).
date_created: 2023-09-06T13:19:10Z
date_published: 2017-02-03T00:00:00Z
date_updated: 2024-10-14T12:31:35Z
day: '03'
doi: 10.1016/j.bpj.2016.11.171
extern: '1'
intvolume: ' 112'
issue: '3'
keyword:
- Biophysics
language:
- iso: eng
month: '02'
oa_version: None
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encoded DNA-protein hybrid origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2017'
...
---
_id: '14309'
abstract:
- lang: eng
text: Establishing precise control over the shape and the interactions of the microscopic
building blocks is essential for design of macroscopic soft materials with novel
structural, optical and mechanical properties. Here, we demonstrate robust assembly
of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular
twisted ribbons and two-dimensional colloidal membranes. The exquisite control
afforded by the DNA origami technology establishes a quantitative relationship
between the microscopic filament structure and the macroscopic cholesteric pitch.
Furthermore, it also enables robust assembly of one-dimensional twisted ribbons,
which behave as effective supramolecular polymers whose structure and elastic
properties can be precisely tuned by controlling the geometry of the elemental
building blocks. Our results demonstrate the potential synergy between DNA origami
technology and colloidal science, in which the former allows for rapid and robust
synthesis of complex particles, and the latter can be used to assemble such particles
into bulk materials.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M
full_name: Siavashpouri, M
last_name: Siavashpouri
- first_name: CH
full_name: Wachauf, CH
last_name: Wachauf
- first_name: MJ
full_name: Zakhary, MJ
last_name: Zakhary
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: H
full_name: Dietz, H
last_name: Dietz
- first_name: Z
full_name: Dogic, Z
last_name: Dogic
citation:
ama: Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular
engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials.
2017;16(8):849-856. doi:10.1038/nmat4909
apa: Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &
Dogic, Z. (2017). Molecular engineering of chiral colloidal liquid crystals using
DNA origami. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat4909
chicago: Siavashpouri, M, CH Wachauf, MJ Zakhary, Florian M Praetorius, H Dietz,
and Z Dogic. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using
DNA Origami.” Nature Materials. Springer Nature, 2017. https://doi.org/10.1038/nmat4909.
ieee: M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z.
Dogic, “Molecular engineering of chiral colloidal liquid crystals using DNA origami,”
Nature Materials, vol. 16, no. 8. Springer Nature, pp. 849–856, 2017.
ista: Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017.
Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature
Materials. 16(8), 849–856.
mla: Siavashpouri, M., et al. “Molecular Engineering of Chiral Colloidal Liquid
Crystals Using DNA Origami.” Nature Materials, vol. 16, no. 8, Springer
Nature, 2017, pp. 849–56, doi:10.1038/nmat4909.
short: M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic,
Nature Materials 16 (2017) 849–856.
date_created: 2023-09-06T13:37:27Z
date_published: 2017-05-22T00:00:00Z
date_updated: 2023-11-07T11:40:00Z
day: '22'
doi: 10.1038/nmat4909
extern: '1'
external_id:
arxiv:
- '1705.08944'
pmid:
- '28530665'
intvolume: ' 16'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1705.08944'
month: '05'
oa: 1
oa_version: Preprint
page: 849-856
pmid: 1
publication: Nature Materials
publication_identifier:
eissn:
- 1476-4660
issn:
- 1476-1122
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular engineering of chiral colloidal liquid crystals using DNA origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2017'
...
---
_id: '14310'
article_processing_charge: No
author:
- first_name: Mahsa
full_name: Siavashpouri, Mahsa
last_name: Siavashpouri
- first_name: Christian
full_name: Wachauf, Christian
last_name: Wachauf
- first_name: Mark
full_name: Zakhary, Mark
last_name: Zakhary
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Zvonimir
full_name: Dogic, Zvonimir
last_name: Dogic
citation:
ama: 'Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular
engineering of colloidal liquid crystals using DNA origami. In: APS March Meeting
2017. APS; 2017.'
apa: Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &
Dogic, Z. (2017). Molecular engineering of colloidal liquid crystals using DNA
origami. In APS March Meeting 2017. APS.
chicago: Siavashpouri, Mahsa, Christian Wachauf, Mark Zakhary, Florian M Praetorius,
Hendrik Dietz, and Zvonimir Dogic. “Molecular Engineering of Colloidal Liquid
Crystals Using DNA Origami.” In APS March Meeting 2017. APS, 2017.
ieee: M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z.
Dogic, “Molecular engineering of colloidal liquid crystals using DNA origami,”
in APS March Meeting 2017, 2017.
ista: Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017.
Molecular engineering of colloidal liquid crystals using DNA origami. APS March
Meeting 2017. .
mla: Siavashpouri, Mahsa, et al. “Molecular Engineering of Colloidal Liquid Crystals
Using DNA Origami.” APS March Meeting 2017, APS, 2017.
short: M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic,
in:, APS March Meeting 2017, APS, 2017.
date_created: 2023-09-06T13:40:20Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-11-07T11:36:15Z
day: '01'
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
publication: APS March Meeting 2017
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: Molecular engineering of colloidal liquid crystals using DNA origami
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
OA_type: free access
_id: '1433'
abstract:
- lang: eng
text: Phat is an open-source C. ++ library for the computation of persistent homology
by matrix reduction, targeted towards developers of software for topological data
analysis. We aim for a simple generic design that decouples algorithms from data
structures without sacrificing efficiency or user-friendliness. We provide numerous
different reduction strategies as well as data types to store and manipulate the
boundary matrix. We compare the different combinations through extensive experimental
evaluation and identify optimization techniques that work well in practical situations.
We also compare our software with various other publicly available libraries for
persistent homology.
acknowledgement: Michael Kerber acknowledges support by the Max Planck Center for
Visual Computing and Communications (FKZ-01IMC01 and FKZ-01IM10001). Ulrich Bauer,
Jan Reininghaus, and Hubert Wagner acknowledge support by the EU Project TOPOSYS
(FP7-ICT-318493-STREP).
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
last_name: Bauer
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Jan
full_name: Reininghaus, Jan
last_name: Reininghaus
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms
toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008
apa: Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent
homology algorithms toolbox. Journal of Symbolic Computation. Academic
Press. https://doi.org/10.1016/j.jsc.2016.03.008
chicago: Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat
- Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation.
Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008.
ieee: U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology
algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic
Press, pp. 76–90, 2017.
ista: Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology
algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.
mla: Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal
of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008.
short: U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation
78 (2017) 76–90.
corr_author: '1'
date_created: 2018-12-11T11:51:59Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-10-01T07:39:51Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jsc.2016.03.008
ec_funded: 1
external_id:
isi:
- '000384396000005'
intvolume: ' 78'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jsc.2016.03.008
month: '01'
oa: 1
oa_version: Published Version
page: 76 - 90
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Symbolic Computation
publication_identifier:
issn:
- ' 0747-7171'
publication_status: published
publisher: Academic Press
publist_id: '5765'
quality_controlled: '1'
related_material:
record:
- id: '10894'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Phat - Persistent homology algorithms toolbox
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2017'
...
---
OA_type: closed access
_id: '17936'
abstract:
- lang: eng
text: We report that the single‐molecule junction conductance of thiol‐terminated
silanes with Ag electrodes are higher than the conductance of those formed with
Au electrodes. These results are in contrast to the trends in the metal work function
Φ(Ag)<Φ(Au). As such, a better alignment of the Au Fermi level to the molecular
orbital of silane that mediates charge transport would be expected. This conductance
trend is reversed when we replace the thiols with amines, highlighting the impact
of metal–S covalent and metal–NH2 dative bonds in controlling
the molecular conductance. Density functional theory calculations elucidate the
crucial role of the chemical linkers in determining the level alignment when molecules
are attached to different metal contacts. We also demonstrate that conductance
of thiol‐terminated silanes with Pt electrodes is lower than the ones formed with
Au and Ag electrodes, again in contrast to the trends in the metal work‐functions.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Haixing
full_name: Li, Haixing
last_name: Li
- first_name: Timothy A.
full_name: Su, Timothy A.
last_name: Su
- first_name: María
full_name: Camarasa‐Gómez, María
last_name: Camarasa‐Gómez
- first_name: Daniel
full_name: Hernangómez‐Pérez, Daniel
last_name: Hernangómez‐Pérez
- first_name: Simon E.
full_name: Henn, Simon E.
last_name: Henn
- first_name: Vladislav
full_name: Pokorný, Vladislav
last_name: Pokorný
- first_name: Caravaggio D.
full_name: Caniglia, Caravaggio D.
last_name: Caniglia
- first_name: Michael S.
full_name: Inkpen, Michael S.
last_name: Inkpen
- first_name: Richard
full_name: Korytár, Richard
last_name: Korytár
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Colin
full_name: Nuckolls, Colin
last_name: Nuckolls
- first_name: Ferdinand
full_name: Evers, Ferdinand
last_name: Evers
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Li H, Su TA, Camarasa‐Gómez M, et al. Silver makes better eElectrical contacts
to thiol‐terminated silanes than Gold. Angewandte Chemie International Edition.
2017;56(45):14145-14148. doi:10.1002/anie.201708524
apa: Li, H., Su, T. A., Camarasa‐Gómez, M., Hernangómez‐Pérez, D., Henn, S. E.,
Pokorný, V., … Venkataraman, L. (2017). Silver makes better eElectrical contacts
to thiol‐terminated silanes than Gold. Angewandte Chemie International Edition.
Wiley. https://doi.org/10.1002/anie.201708524
chicago: Li, Haixing, Timothy A. Su, María Camarasa‐Gómez, Daniel Hernangómez‐Pérez,
Simon E. Henn, Vladislav Pokorný, Caravaggio D. Caniglia, et al. “Silver Makes
Better EElectrical Contacts to Thiol‐terminated Silanes than Gold.” Angewandte
Chemie International Edition. Wiley, 2017. https://doi.org/10.1002/anie.201708524.
ieee: H. Li et al., “Silver makes better eElectrical contacts to thiol‐terminated
silanes than Gold,” Angewandte Chemie International Edition, vol. 56, no.
45. Wiley, pp. 14145–14148, 2017.
ista: Li H, Su TA, Camarasa‐Gómez M, Hernangómez‐Pérez D, Henn SE, Pokorný V, Caniglia
CD, Inkpen MS, Korytár R, Steigerwald ML, Nuckolls C, Evers F, Venkataraman L.
2017. Silver makes better eElectrical contacts to thiol‐terminated silanes than
Gold. Angewandte Chemie International Edition. 56(45), 14145–14148.
mla: Li, Haixing, et al. “Silver Makes Better EElectrical Contacts to Thiol‐terminated
Silanes than Gold.” Angewandte Chemie International Edition, vol. 56, no.
45, Wiley, 2017, pp. 14145–48, doi:10.1002/anie.201708524.
short: H. Li, T.A. Su, M. Camarasa‐Gómez, D. Hernangómez‐Pérez, S.E. Henn, V. Pokorný,
C.D. Caniglia, M.S. Inkpen, R. Korytár, M.L. Steigerwald, C. Nuckolls, F. Evers,
L. Venkataraman, Angewandte Chemie International Edition 56 (2017) 14145–14148.
date_created: 2024-09-09T08:45:32Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2024-12-17T10:06:36Z
day: '06'
doi: 10.1002/anie.201708524
extern: '1'
intvolume: ' 56'
issue: '45'
language:
- iso: eng
month: '11'
oa_version: None
page: 14145-14148
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Silver makes better eElectrical contacts to thiol‐terminated silanes than Gold
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2017'
...
---
OA_type: closed access
_id: '17937'
abstract:
- lang: eng
text: Fabricating nanoscopic devices capable of manipulating and processing single
units of charge is an essential step towards creating functional devices where
quantum effects dominate transport characteristics. The archetypal single-electron
transistor comprises a small conducting or semiconducting island separated from
two metallic reservoirs by insulating barriers1,2,3,4,5. By enabling the transfer
of a well-defined number of charge carriers between the island and the reservoirs,
such a device may enable discrete single-electron operations6,7,8,9. Here, we
describe a single-molecule junction comprising a redox-active, atomically precise
cobalt chalcogenide cluster wired between two nanoscopic electrodes10,11. We observe
current blockade at room temperature in thousands of single-cluster junctions.
Below a threshold voltage, charge transfer across the junction is suppressed.
The device is turned on when the temporary occupation of the core states by a
transiting carrier is energetically enabled, resulting in a sequential tunnelling
process and an increase in current by a factor of ∼600. We perform in situ and
ex situ cyclic voltammetry as well as density functional theory calculations to
unveil a two-step process mediated by an orbital localized on the core of the
cluster in which charge carriers reside before tunnelling to the collector reservoir.
As the bias window of the junction is opened wide enough to include one of the
cluster frontier orbitals, the current blockade is lifted and charge carriers
can tunnel sequentially across the junction.
article_processing_charge: No
article_type: original
author:
- first_name: Giacomo
full_name: Lovat, Giacomo
last_name: Lovat
- first_name: Bonnie
full_name: Choi, Bonnie
last_name: Choi
- first_name: Daniel W.
full_name: Paley, Daniel W.
last_name: Paley
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
- first_name: Xavier
full_name: Roy, Xavier
last_name: Roy
citation:
ama: Lovat G, Choi B, Paley DW, Steigerwald ML, Venkataraman L, Roy X. Room-temperature
current blockade in atomically defined single-cluster junctions. Nature Nanotechnology.
2017;12:1050-1054. doi:10.1038/nnano.2017.156
apa: Lovat, G., Choi, B., Paley, D. W., Steigerwald, M. L., Venkataraman, L., &
Roy, X. (2017). Room-temperature current blockade in atomically defined single-cluster
junctions. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2017.156
chicago: Lovat, Giacomo, Bonnie Choi, Daniel W. Paley, Michael L. Steigerwald, Latha
Venkataraman, and Xavier Roy. “Room-Temperature Current Blockade in Atomically
Defined Single-Cluster Junctions.” Nature Nanotechnology. Springer Nature,
2017. https://doi.org/10.1038/nnano.2017.156.
ieee: G. Lovat, B. Choi, D. W. Paley, M. L. Steigerwald, L. Venkataraman, and X.
Roy, “Room-temperature current blockade in atomically defined single-cluster junctions,”
Nature Nanotechnology, vol. 12. Springer Nature, pp. 1050–1054, 2017.
ista: Lovat G, Choi B, Paley DW, Steigerwald ML, Venkataraman L, Roy X. 2017. Room-temperature
current blockade in atomically defined single-cluster junctions. Nature Nanotechnology.
12, 1050–1054.
mla: Lovat, Giacomo, et al. “Room-Temperature Current Blockade in Atomically Defined
Single-Cluster Junctions.” Nature Nanotechnology, vol. 12, Springer Nature,
2017, pp. 1050–54, doi:10.1038/nnano.2017.156.
short: G. Lovat, B. Choi, D.W. Paley, M.L. Steigerwald, L. Venkataraman, X. Roy,
Nature Nanotechnology 12 (2017) 1050–1054.
date_created: 2024-09-09T08:46:15Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2024-12-17T10:09:35Z
day: '01'
doi: 10.1038/nnano.2017.156
extern: '1'
external_id:
pmid:
- '28805817'
intvolume: ' 12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1050-1054
pmid: 1
publication: Nature Nanotechnology
publication_identifier:
eissn:
- 1748-3395
issn:
- 1748-3387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Room-temperature current blockade in atomically defined single-cluster junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2017'
...
---
OA_type: closed access
_id: '17939'
abstract:
- lang: eng
text: We report a series of single-molecule transport measurements carried out in
an ionic environment with oligophenylenediamine wires. These molecules exhibit
three discrete conducting states accessed by electrochemically modifying the contacts.
Transport in these junctions is defined by the oligophenylene backbone, but the
conductance is increased by factors of ∼20 and ∼400 when compared to traditional
dative junctions. We propose that the higher-conducting states arise from in situ
electrochemical conversion of the dative Au←N bond into a new type of Au–N contact.
Density functional theory-based transport calculations establish that the new
contacts dramatically increase the electronic coupling of the oligophenylene backbone
to the Au electrodes, consistent with experimental transport data. The resulting
contact resistance is the lowest reported to date; more generally, our work demonstrates
a facile method for creating electronically transparent metal–organic interfaces.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Yaping
full_name: Zang, Yaping
last_name: Zang
- first_name: Andrew
full_name: Pinkard, Andrew
last_name: Pinkard
- first_name: Zhen-Fei
full_name: Liu, Zhen-Fei
last_name: Liu
- first_name: Jeffrey B.
full_name: Neaton, Jeffrey B.
last_name: Neaton
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Xavier
full_name: Roy, Xavier
last_name: Roy
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Zang Y, Pinkard A, Liu Z-F, et al. Electronically transparent Au–N bonds for
molecular junctions. Journal of the American Chemical Society. 2017;139(42):14845-14848.
doi:10.1021/jacs.7b08370
apa: Zang, Y., Pinkard, A., Liu, Z.-F., Neaton, J. B., Steigerwald, M. L., Roy,
X., & Venkataraman, L. (2017). Electronically transparent Au–N bonds for molecular
junctions. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.7b08370
chicago: Zang, Yaping, Andrew Pinkard, Zhen-Fei Liu, Jeffrey B. Neaton, Michael
L. Steigerwald, Xavier Roy, and Latha Venkataraman. “Electronically Transparent
Au–N Bonds for Molecular Junctions.” Journal of the American Chemical Society.
American Chemical Society, 2017. https://doi.org/10.1021/jacs.7b08370.
ieee: Y. Zang et al., “Electronically transparent Au–N bonds for molecular
junctions,” Journal of the American Chemical Society, vol. 139, no. 42.
American Chemical Society, pp. 14845–14848, 2017.
ista: Zang Y, Pinkard A, Liu Z-F, Neaton JB, Steigerwald ML, Roy X, Venkataraman
L. 2017. Electronically transparent Au–N bonds for molecular junctions. Journal
of the American Chemical Society. 139(42), 14845–14848.
mla: Zang, Yaping, et al. “Electronically Transparent Au–N Bonds for Molecular Junctions.”
Journal of the American Chemical Society, vol. 139, no. 42, American Chemical
Society, 2017, pp. 14845–48, doi:10.1021/jacs.7b08370.
short: Y. Zang, A. Pinkard, Z.-F. Liu, J.B. Neaton, M.L. Steigerwald, X. Roy, L.
Venkataraman, Journal of the American Chemical Society 139 (2017) 14845–14848.
date_created: 2024-09-09T08:47:04Z
date_published: 2017-10-05T00:00:00Z
date_updated: 2024-12-17T10:13:56Z
day: '05'
doi: 10.1021/jacs.7b08370
extern: '1'
external_id:
pmid:
- '28981277'
intvolume: ' 139'
issue: '42'
language:
- iso: eng
month: '10'
oa_version: None
page: 14845-14848
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electronically transparent Au–N bonds for molecular junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2017'
...
---
OA_type: closed access
_id: '17940'
abstract:
- lang: eng
text: Single-molecule conductance studies have traditionally focused on creating
highly conducting molecular wires. However, progress in nanoscale electronics
demands insulators just as it needs conductors. Here we describe the single-molecule
length-dependent conductance properties of the classic silicon dioxide insulator.
We synthesize molecular wires consisting of Si–O repeat units and measure their
conductance through the scanning tunneling microscope-based break-junction method.
These molecules yield conductance lower than alkanes of the same length and the
largest length-dependent conductance decay of any molecular systems measured to
date. We calculate single-molecule junction transmission and the complex band
structure of the infinite 1D material for siloxane, in comparison with silane
and alkane, and show that the large conductance decay is intrinsic to the nature
of the Si–O bond. This work highlights the potential for siloxanes to function
as molecular insulators in electronics.
article_processing_charge: No
article_type: original
author:
- first_name: Haixing
full_name: Li, Haixing
last_name: Li
- first_name: Marc H.
full_name: Garner, Marc H.
last_name: Garner
- first_name: Timothy A.
full_name: Su, Timothy A.
last_name: Su
- first_name: Anders
full_name: Jensen, Anders
last_name: Jensen
- first_name: Michael S.
full_name: Inkpen, Michael S.
last_name: Inkpen
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
- first_name: Gemma C.
full_name: Solomon, Gemma C.
last_name: Solomon
- first_name: Colin
full_name: Nuckolls, Colin
last_name: Nuckolls
citation:
ama: Li H, Garner MH, Su TA, et al. Extreme conductance suppression in molecular
siloxanes. Journal of the American Chemical Society. 2017;139(30):10212-10215.
doi:10.1021/jacs.7b05599
apa: Li, H., Garner, M. H., Su, T. A., Jensen, A., Inkpen, M. S., Steigerwald, M.
L., … Nuckolls, C. (2017). Extreme conductance suppression in molecular siloxanes.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.7b05599
chicago: Li, Haixing, Marc H. Garner, Timothy A. Su, Anders Jensen, Michael S. Inkpen,
Michael L. Steigerwald, Latha Venkataraman, Gemma C. Solomon, and Colin Nuckolls.
“Extreme Conductance Suppression in Molecular Siloxanes.” Journal of the American
Chemical Society. American Chemical Society, 2017. https://doi.org/10.1021/jacs.7b05599.
ieee: H. Li et al., “Extreme conductance suppression in molecular siloxanes,”
Journal of the American Chemical Society, vol. 139, no. 30. American Chemical
Society, pp. 10212–10215, 2017.
ista: Li H, Garner MH, Su TA, Jensen A, Inkpen MS, Steigerwald ML, Venkataraman
L, Solomon GC, Nuckolls C. 2017. Extreme conductance suppression in molecular
siloxanes. Journal of the American Chemical Society. 139(30), 10212–10215.
mla: Li, Haixing, et al. “Extreme Conductance Suppression in Molecular Siloxanes.”
Journal of the American Chemical Society, vol. 139, no. 30, American Chemical
Society, 2017, pp. 10212–15, doi:10.1021/jacs.7b05599.
short: H. Li, M.H. Garner, T.A. Su, A. Jensen, M.S. Inkpen, M.L. Steigerwald, L.
Venkataraman, G.C. Solomon, C. Nuckolls, Journal of the American Chemical Society
139 (2017) 10212–10215.
date_created: 2024-09-09T08:48:28Z
date_published: 2017-07-13T00:00:00Z
date_updated: 2024-12-18T07:27:18Z
day: '13'
doi: 10.1021/jacs.7b05599
extern: '1'
external_id:
pmid:
- '28702995'
intvolume: ' 139'
issue: '30'
language:
- iso: eng
month: '07'
oa_version: None
page: 10212-10215
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extreme conductance suppression in molecular siloxanes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2017'
...
---
OA_type: closed access
_id: '17941'
abstract:
- lang: eng
text: How heteroatomic substitutions affect electron transport through π-conjugated
hydrocarbons has been the subject of some debate. In this paper we investigate
the effect of heteroatomic linkers in a molecular junction on the electron-transmission
spectrum, focusing on the occurrence of quantum interference (QI) close to the
Fermi level, where conductivity can be significantly suppressed. We find that
the substitution or addition of heteroatoms to a carbon skeleton at the contact
positions does not change the main feature of QI due to the underlying carbon
skeleton. QI in the overall system thus remains a robust feature. This empirical
observation leads us to derive, in two mathematical ways, that these findings
can be generalized. We note that addition or substitution of a carbon atom by
a heteroatom at the contact positions will increase or decrease the number of
electrons in the π-system, which will lead to a change in the alignment of the
molecular orbitals of the isolated system relative to the electrode Fermi level.
Both Hückel and density functional theory calculations on model systems probe
the effect of this Fermi level change and confirm qualitatively the implications
of the underlying mathematical proofs.
article_processing_charge: No
article_type: original
author:
- first_name: Yuta
full_name: Tsuji, Yuta
last_name: Tsuji
- first_name: Thijs
full_name: Stuyver, Thijs
last_name: Stuyver
- first_name: Suman
full_name: Gunasekaran, Suman
last_name: Gunasekaran
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: 'Tsuji Y, Stuyver T, Gunasekaran S, Venkataraman L. The influence of linkers
on quantum interference: A linker theorem. The Journal of Physical Chemistry
C. 2017;121(27):14451-14462. doi:10.1021/acs.jpcc.7b03493'
apa: 'Tsuji, Y., Stuyver, T., Gunasekaran, S., & Venkataraman, L. (2017). The
influence of linkers on quantum interference: A linker theorem. The Journal
of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/acs.jpcc.7b03493'
chicago: 'Tsuji, Yuta, Thijs Stuyver, Suman Gunasekaran, and Latha Venkataraman.
“The Influence of Linkers on Quantum Interference: A Linker Theorem.” The Journal
of Physical Chemistry C. American Chemical Society, 2017. https://doi.org/10.1021/acs.jpcc.7b03493.'
ieee: 'Y. Tsuji, T. Stuyver, S. Gunasekaran, and L. Venkataraman, “The influence
of linkers on quantum interference: A linker theorem,” The Journal of Physical
Chemistry C, vol. 121, no. 27. American Chemical Society, pp. 14451–14462,
2017.'
ista: 'Tsuji Y, Stuyver T, Gunasekaran S, Venkataraman L. 2017. The influence of
linkers on quantum interference: A linker theorem. The Journal of Physical Chemistry
C. 121(27), 14451–14462.'
mla: 'Tsuji, Yuta, et al. “The Influence of Linkers on Quantum Interference: A Linker
Theorem.” The Journal of Physical Chemistry C, vol. 121, no. 27, American
Chemical Society, 2017, pp. 14451–62, doi:10.1021/acs.jpcc.7b03493.'
short: Y. Tsuji, T. Stuyver, S. Gunasekaran, L. Venkataraman, The Journal of Physical
Chemistry C 121 (2017) 14451–14462.
date_created: 2024-09-09T08:49:27Z
date_published: 2017-06-09T00:00:00Z
date_updated: 2024-12-18T07:29:42Z
day: '09'
doi: 10.1021/acs.jpcc.7b03493
extern: '1'
intvolume: ' 121'
issue: '27'
language:
- iso: eng
month: '06'
oa_version: None
page: 14451-14462
publication: The Journal of Physical Chemistry C
publication_identifier:
eissn:
- 1932-7455
issn:
- 1932-7447
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The influence of linkers on quantum interference: A linker theorem'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2017'
...