---
OA_type: closed access
_id: '17928'
abstract:
- lang: eng
text: We study the single-molecule transport properties of small bandgap diketopyrrolopyrrole
oligomers (DPPn, n = 1–4) with lengths varying from 1 to 5 nm. At a low bias voltage,
the conductance decays exponentially as a function of length indicative of nonresonant
transport. However, at a high bias voltage, we observe a remarkably high conductance
close to 10–2 G0 with currents reaching over 0.1 μA across all four oligomers.
These unique transport properties, together with density functional theory-based
transport calculations, suggest a mechanism of resonant transport across the highly
delocalized DPP backbones in the high bias regime. This study thus demonstrates
the unique properties of diketopyrrolopyrrole derivatives in achieving highly
efficient long-range charge transport in single-molecule devices.
article_processing_charge: No
article_type: original
author:
- first_name: Yaping
full_name: Zang, Yaping
last_name: Zang
- first_name: Suman
full_name: Ray, Suman
last_name: Ray
- first_name: E-Dean
full_name: Fung, E-Dean
last_name: Fung
- first_name: Anders
full_name: Borges, Anders
last_name: Borges
- first_name: Marc H.
full_name: Garner, Marc H.
last_name: Garner
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Gemma C.
full_name: Solomon, Gemma C.
last_name: Solomon
- first_name: Satish
full_name: Patil, Satish
last_name: Patil
- 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, Ray S, Fung E-D, et al. Resonant transport in single diketopyrrolopyrrole
junctions. Journal of the American Chemical Society. 2018;140(41):13167-13170.
doi:10.1021/jacs.8b06964
apa: Zang, Y., Ray, S., Fung, E.-D., Borges, A., Garner, M. H., Steigerwald, M.
L., … Venkataraman, L. (2018). Resonant transport in single diketopyrrolopyrrole
junctions. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.8b06964
chicago: Zang, Yaping, Suman Ray, E-Dean Fung, Anders Borges, Marc H. Garner, Michael
L. Steigerwald, Gemma C. Solomon, Satish Patil, and Latha Venkataraman. “Resonant
Transport in Single Diketopyrrolopyrrole Junctions.” Journal of the American
Chemical Society. American Chemical Society, 2018. https://doi.org/10.1021/jacs.8b06964.
ieee: Y. Zang et al., “Resonant transport in single diketopyrrolopyrrole
junctions,” Journal of the American Chemical Society, vol. 140, no. 41.
American Chemical Society, pp. 13167–13170, 2018.
ista: Zang Y, Ray S, Fung E-D, Borges A, Garner MH, Steigerwald ML, Solomon GC,
Patil S, Venkataraman L. 2018. Resonant transport in single diketopyrrolopyrrole
junctions. Journal of the American Chemical Society. 140(41), 13167–13170.
mla: Zang, Yaping, et al. “Resonant Transport in Single Diketopyrrolopyrrole Junctions.”
Journal of the American Chemical Society, vol. 140, no. 41, American Chemical
Society, 2018, pp. 13167–70, doi:10.1021/jacs.8b06964.
short: Y. Zang, S. Ray, E.-D. Fung, A. Borges, M.H. Garner, M.L. Steigerwald, G.C.
Solomon, S. Patil, L. Venkataraman, Journal of the American Chemical Society 140
(2018) 13167–13170.
date_created: 2024-09-09T07:55:19Z
date_published: 2018-10-03T00:00:00Z
date_updated: 2024-12-11T08:36:50Z
day: '03'
doi: 10.1021/jacs.8b06964
extern: '1'
external_id:
pmid:
- '30280891'
intvolume: ' 140'
issue: '41'
language:
- iso: eng
month: '10'
oa_version: None
page: 13167-13170
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: Resonant transport in single diketopyrrolopyrrole junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2018'
...
---
OA_type: closed access
_id: '17929'
abstract:
- lang: eng
text: Polymethine dyes are linear π-conjugated compounds with an odd number of carbons
that display a much greater delocalization in comparison to polyenes that have
an even number of carbon atoms in their main chain. Herein, we perform scanning
tunneling microscope based break-junction measurements on a series of three cyanine
dyes of increasing length. We demonstrate, at the single molecule level, that
these short chain polymethine systems exhibit a substantially smaller decay in
conductance with length (attenuation factor β = 0.04 Å–1) compared to traditional
polyenes (β ≈ 0.2 Å–1). Furthermore, we show that by changing solvent we are able
to shift the β value, demonstrating a remarkable negative β value, with conductance
increasing with molecular length. First principle calculations provide support
for the experimentally observed near-uniform length dependent conductance and
further suggest that the variations in β with solvent are due to solvent-induced
changes in the alignment of the frontier molecular orbitals relative to the Fermi
energy of the leads. A simplified Hückel model suggests that the smaller decay
in conductance correlates with the smaller degree of bond order alternation present
in polymethine compounds compared to polyenes. These findings may enable the design
of molecular wires without a length-dependent decay for efficient electron transport
at the nanoscale.
article_processing_charge: No
article_type: original
author:
- first_name: Suman
full_name: Gunasekaran, Suman
last_name: Gunasekaran
- first_name: Daniel
full_name: Hernangómez-Pérez, Daniel
last_name: Hernangómez-Pérez
- first_name: Iryna
full_name: Davydenko, Iryna
last_name: Davydenko
- first_name: Seth
full_name: Marder, Seth
last_name: Marder
- 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: Gunasekaran S, Hernangómez-Pérez D, Davydenko I, Marder S, Evers F, Venkataraman
L. Near length-independent conductance in polymethine molecular wires. Nano
Letters. 2018;18(10):6387-6391. doi:10.1021/acs.nanolett.8b02743
apa: Gunasekaran, S., Hernangómez-Pérez, D., Davydenko, I., Marder, S., Evers, F.,
& Venkataraman, L. (2018). Near length-independent conductance in polymethine
molecular wires. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b02743
chicago: Gunasekaran, Suman, Daniel Hernangómez-Pérez, Iryna Davydenko, Seth Marder,
Ferdinand Evers, and Latha Venkataraman. “Near Length-Independent Conductance
in Polymethine Molecular Wires.” Nano Letters. American Chemical Society,
2018. https://doi.org/10.1021/acs.nanolett.8b02743.
ieee: S. Gunasekaran, D. Hernangómez-Pérez, I. Davydenko, S. Marder, F. Evers, and
L. Venkataraman, “Near length-independent conductance in polymethine molecular
wires,” Nano Letters, vol. 18, no. 10. American Chemical Society, pp. 6387–6391,
2018.
ista: Gunasekaran S, Hernangómez-Pérez D, Davydenko I, Marder S, Evers F, Venkataraman
L. 2018. Near length-independent conductance in polymethine molecular wires. Nano
Letters. 18(10), 6387–6391.
mla: Gunasekaran, Suman, et al. “Near Length-Independent Conductance in Polymethine
Molecular Wires.” Nano Letters, vol. 18, no. 10, American Chemical Society,
2018, pp. 6387–91, doi:10.1021/acs.nanolett.8b02743.
short: S. Gunasekaran, D. Hernangómez-Pérez, I. Davydenko, S. Marder, F. Evers,
L. Venkataraman, Nano Letters 18 (2018) 6387–6391.
date_created: 2024-09-09T08:05:20Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-12-11T08:39:06Z
day: '01'
doi: 10.1021/acs.nanolett.8b02743
extern: '1'
external_id:
pmid:
- '30187756'
intvolume: ' 18'
issue: '10'
language:
- iso: eng
month: '09'
oa_version: None
page: 6387-6391
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Near length-independent conductance in polymethine molecular wires
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2018'
...
---
OA_place: publisher
OA_type: free access
_id: '17930'
abstract:
- lang: eng
text: Self-assembled monolayers (SAMs) formed using N-heterocyclic carbenes (NHCs)
have recently emerged as thermally and chemically ultrastable alternatives to
those formed from thiols. The rich chemistry and strong σ-donating ability of
NHCs offer unique prospects for applications in nanoelectronics, sensing, and
electrochemistry. Although stable in SAMs, free carbenes are notoriously reactive,
making their electronic characterization challenging. Here we report the first
investigation of electron transport across single NHC-bound molecules using the
scanning tunneling microscope-based break junction (STM-BJ) technique. We develop
a series of air-stable metal NHC complexes that can be electrochemically reduced
in situ to form NHC–electrode contacts, enabling reliable single-molecule conductance
measurements of NHCs under ambient conditions. Using this approach, we show that
the conductance of an NHC depends on the identity of the single metal atom to
which it is coordinated in the junction. Our observations are supported by density
functional theory (DFT) calculations, which also firmly establish the contributions
of the NHC linker to the junction transport characteristics. Our work demonstrates
a powerful method to probe electron transfer across NHC–electrode interfaces;
more generally, it opens the door to the exploitation of surface-bound NHCs in
constructing novel, functionalized electrodes and/or nanoelectronic devices.
article_processing_charge: No
article_type: original
author:
- first_name: Evan A.
full_name: Doud, Evan A.
last_name: Doud
- first_name: Michael S.
full_name: Inkpen, Michael S.
last_name: Inkpen
- first_name: Giacomo
full_name: Lovat, Giacomo
last_name: Lovat
- first_name: Enrique
full_name: Montes, Enrique
last_name: Montes
- 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: Héctor
full_name: Vázquez, Héctor
last_name: Vázquez
- 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: Doud EA, Inkpen MS, Lovat G, et al. In situ formation of N-heterocyclic carbene-bound
single-molecule junctions. Journal of the American Chemical Society. 2018;140(28):8944-8949.
doi:10.1021/jacs.8b05184
apa: Doud, E. A., Inkpen, M. S., Lovat, G., Montes, E., Paley, D. W., Steigerwald,
M. L., … Roy, X. (2018). In situ formation of N-heterocyclic carbene-bound single-molecule
junctions. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.8b05184
chicago: Doud, Evan A., Michael S. Inkpen, Giacomo Lovat, Enrique Montes, Daniel
W. Paley, Michael L. Steigerwald, Héctor Vázquez, Latha Venkataraman, and Xavier
Roy. “In Situ Formation of N-Heterocyclic Carbene-Bound Single-Molecule Junctions.”
Journal of the American Chemical Society. American Chemical Society, 2018.
https://doi.org/10.1021/jacs.8b05184.
ieee: E. A. Doud et al., “In situ formation of N-heterocyclic carbene-bound
single-molecule junctions,” Journal of the American Chemical Society, vol.
140, no. 28. American Chemical Society, pp. 8944–8949, 2018.
ista: Doud EA, Inkpen MS, Lovat G, Montes E, Paley DW, Steigerwald ML, Vázquez H,
Venkataraman L, Roy X. 2018. In situ formation of N-heterocyclic carbene-bound
single-molecule junctions. Journal of the American Chemical Society. 140(28),
8944–8949.
mla: Doud, Evan A., et al. “In Situ Formation of N-Heterocyclic Carbene-Bound Single-Molecule
Junctions.” Journal of the American Chemical Society, vol. 140, no. 28,
American Chemical Society, 2018, pp. 8944–49, doi:10.1021/jacs.8b05184.
short: E.A. Doud, M.S. Inkpen, G. Lovat, E. Montes, D.W. Paley, M.L. Steigerwald,
H. Vázquez, L. Venkataraman, X. Roy, Journal of the American Chemical Society
140 (2018) 8944–8949.
date_created: 2024-09-09T08:14:38Z
date_published: 2018-07-03T00:00:00Z
date_updated: 2024-12-11T08:42:51Z
day: '03'
doi: 10.1021/jacs.8b05184
extern: '1'
external_id:
pmid:
- '29969027'
intvolume: ' 140'
issue: '28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/jacs.8b05184
month: '07'
oa: 1
oa_version: Published Version
page: 8944-8949
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: In situ formation of N-heterocyclic carbene-bound single-molecule junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2018'
...
---
OA_type: closed access
_id: '17931'
abstract:
- lang: eng
text: 'The tunnelling of electrons through molecules (and through any nanoscale
insulating and dielectric material1) shows exponential attenuation with increasing
length2, a length dependence that is reflected in the ability of the electrons
to carry an electrical current. It was recently demonstrated3,4,5 that coherent
tunnelling through a molecular junction can also be suppressed by destructive
quantum interference6, a mechanism that is not length-dependent. For the carbon-based
molecules studied previously, cancelling all transmission channels would involve
the suppression of contributions to the current from both the π-orbital and σ-orbital
systems. Previous reports of destructive interference have demonstrated a decrease
in transmission only through the π-channel. Here we report a saturated silicon-based
molecule with a functionalized bicyclo[2.2.2]octasilane moiety that exhibits destructive
quantum interference in its σ-system. Although molecular silicon typically forms
conducting wires7, we use a combination of conductance measurements and ab initio
calculations to show that destructive σ-interference, achieved here by locking
the silicon–silicon bonds into eclipsed conformations within a bicyclic molecular
framework, can yield extremely insulating molecules less than a nanometre in length.
Our molecules also exhibit an unusually high thermopower (0.97 millivolts per
kelvin), which is a further experimental signature of the suppression of all tunnelling
paths by destructive interference: calculations indicate that the central bicyclo[2.2.2]octasilane
unit is rendered less conductive than the empty space it occupies. The molecular
design presented here provides a proof-of-concept for a quantum-interference-based
approach to single-molecule insulators.'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Marc H.
full_name: Garner, Marc H.
last_name: Garner
- first_name: Haixing
full_name: Li, Haixing
last_name: Li
- first_name: Yan
full_name: Chen, Yan
last_name: Chen
- first_name: Timothy A.
full_name: Su, Timothy A.
last_name: Su
- first_name: Zhichun
full_name: Shangguan, Zhichun
last_name: Shangguan
- first_name: Daniel W.
full_name: Paley, Daniel W.
last_name: Paley
- first_name: Taifeng
full_name: Liu, Taifeng
last_name: Liu
- first_name: Fay
full_name: Ng, Fay
last_name: Ng
- first_name: Hexing
full_name: Li, Hexing
last_name: Li
- first_name: Shengxiong
full_name: Xiao, Shengxiong
last_name: Xiao
- first_name: Colin
full_name: Nuckolls, Colin
last_name: Nuckolls
- 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
citation:
ama: Garner MH, Li H, Chen Y, et al. Comprehensive suppression of single-molecule
conductance using destructive σ-interference. Nature. 2018;558(7710):415-419.
doi:10.1038/s41586-018-0197-9
apa: Garner, M. H., Li, H., Chen, Y., Su, T. A., Shangguan, Z., Paley, D. W., …
Solomon, G. C. (2018). Comprehensive suppression of single-molecule conductance
using destructive σ-interference. Nature. Springer Nature. https://doi.org/10.1038/s41586-018-0197-9
chicago: Garner, Marc H., Haixing Li, Yan Chen, Timothy A. Su, Zhichun Shangguan,
Daniel W. Paley, Taifeng Liu, et al. “Comprehensive Suppression of Single-Molecule
Conductance Using Destructive σ-Interference.” Nature. Springer Nature,
2018. https://doi.org/10.1038/s41586-018-0197-9.
ieee: M. H. Garner et al., “Comprehensive suppression of single-molecule
conductance using destructive σ-interference,” Nature, vol. 558, no. 7710.
Springer Nature, pp. 415–419, 2018.
ista: Garner MH, Li H, Chen Y, Su TA, Shangguan Z, Paley DW, Liu T, Ng F, Li H,
Xiao S, Nuckolls C, Venkataraman L, Solomon GC. 2018. Comprehensive suppression
of single-molecule conductance using destructive σ-interference. Nature. 558(7710),
415–419.
mla: Garner, Marc H., et al. “Comprehensive Suppression of Single-Molecule Conductance
Using Destructive σ-Interference.” Nature, vol. 558, no. 7710, Springer
Nature, 2018, pp. 415–19, doi:10.1038/s41586-018-0197-9.
short: M.H. Garner, H. Li, Y. Chen, T.A. Su, Z. Shangguan, D.W. Paley, T. Liu, F.
Ng, H. Li, S. Xiao, C. Nuckolls, L. Venkataraman, G.C. Solomon, Nature 558 (2018)
415–419.
date_created: 2024-09-09T08:17:04Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2024-12-11T08:51:55Z
day: '06'
doi: 10.1038/s41586-018-0197-9
extern: '1'
external_id:
pmid:
- '29875407'
intvolume: ' 558'
issue: '7710'
language:
- iso: eng
month: '06'
oa_version: None
page: 415-419
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: Comprehensive suppression of single-molecule conductance using destructive
σ-interference
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 558
year: '2018'
...
---
OA_type: closed access
_id: '17932'
abstract:
- lang: eng
text: We compare the ultrafast charge transfer dynamics of molecules on epitaxial
graphene and bilayer graphene grown on Ni(111) interfaces through first principles
calculations and X-ray resonant photoemission spectroscopy. We use 4,4′-bipyridine
as a prototypical molecule for these explorations as the energy level alignment
of core-excited molecular orbitals allows ultrafast injection of electrons from
a substrate to a molecule on a femtosecond timescale. We show that the ultrafast
injection of electrons from the substrate to the molecule is ∼4 times slower on
weakly coupled bilayer graphene than on epitaxial graphene. Through our experiments
and calculations, we can attribute this to a difference in the density of states
close to the Fermi level between graphene and bilayer graphene. We therefore show
how graphene coupling with the substrate influences charge transfer dynamics between
organic molecules and graphene interfaces.
article_processing_charge: No
article_type: original
author:
- first_name: Abhilash
full_name: Ravikumar, Abhilash
last_name: Ravikumar
- first_name: Gregor
full_name: Kladnik, Gregor
last_name: Kladnik
- first_name: Moritz
full_name: Müller, Moritz
last_name: Müller
- first_name: Albano
full_name: Cossaro, Albano
last_name: Cossaro
- first_name: Gregor
full_name: Bavdek, Gregor
last_name: Bavdek
- first_name: Laerte L.
full_name: Patera, Laerte L.
last_name: Patera
- first_name: Daniel
full_name: Sánchez-Portal, Daniel
last_name: Sánchez-Portal
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
- first_name: Alberto
full_name: Morgante, Alberto
last_name: Morgante
- first_name: Gian Paolo
full_name: Brivio, Gian Paolo
last_name: Brivio
- first_name: Dean
full_name: Cvetko, Dean
last_name: Cvetko
- first_name: Guido
full_name: Fratesi, Guido
last_name: Fratesi
citation:
ama: Ravikumar A, Kladnik G, Müller M, et al. Tuning ultrafast electron injection
dynamics at organic-graphene/metal interfaces. Nanoscale. 2018;10(17):8014-8022.
doi:10.1039/c7nr08737c
apa: Ravikumar, A., Kladnik, G., Müller, M., Cossaro, A., Bavdek, G., Patera, L.
L., … Fratesi, G. (2018). Tuning ultrafast electron injection dynamics at organic-graphene/metal
interfaces. Nanoscale. Royal Society of Chemistry. https://doi.org/10.1039/c7nr08737c
chicago: Ravikumar, Abhilash, Gregor Kladnik, Moritz Müller, Albano Cossaro, Gregor
Bavdek, Laerte L. Patera, Daniel Sánchez-Portal, et al. “Tuning Ultrafast Electron
Injection Dynamics at Organic-Graphene/Metal Interfaces.” Nanoscale. Royal
Society of Chemistry, 2018. https://doi.org/10.1039/c7nr08737c.
ieee: A. Ravikumar et al., “Tuning ultrafast electron injection dynamics
at organic-graphene/metal interfaces,” Nanoscale, vol. 10, no. 17. Royal
Society of Chemistry, pp. 8014–8022, 2018.
ista: Ravikumar A, Kladnik G, Müller M, Cossaro A, Bavdek G, Patera LL, Sánchez-Portal
D, Venkataraman L, Morgante A, Brivio GP, Cvetko D, Fratesi G. 2018. Tuning ultrafast
electron injection dynamics at organic-graphene/metal interfaces. Nanoscale. 10(17),
8014–8022.
mla: Ravikumar, Abhilash, et al. “Tuning Ultrafast Electron Injection Dynamics at
Organic-Graphene/Metal Interfaces.” Nanoscale, vol. 10, no. 17, Royal Society
of Chemistry, 2018, pp. 8014–22, doi:10.1039/c7nr08737c.
short: A. Ravikumar, G. Kladnik, M. Müller, A. Cossaro, G. Bavdek, L.L. Patera,
D. Sánchez-Portal, L. Venkataraman, A. Morgante, G.P. Brivio, D. Cvetko, G. Fratesi,
Nanoscale 10 (2018) 8014–8022.
date_created: 2024-09-09T08:19:10Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2024-12-11T08:56:09Z
day: '26'
doi: 10.1039/c7nr08737c
extern: '1'
external_id:
pmid:
- '29667672'
intvolume: ' 10'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 8014-8022
pmid: 1
publication: Nanoscale
publication_identifier:
eissn:
- 2040-3372
issn:
- 2040-3364
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tuning ultrafast electron injection dynamics at organic-graphene/metal interfaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2018'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17933'
abstract:
- lang: eng
text: Break-junction measurements are typically aimed at characterizing electronic
properties of single molecules bound between two metal electrodes. Although these
measurements have provided structure–function relationships for such devices,
there is little work that studies the impact of molecule-molecule interactions
on junction characteristics. Here, we use a scanning tunneling microscope based
break-junction technique to study pi-stacked dimer junctions formed with two amine-terminated
conjugated molecules. We show that the conductance, force and flicker noise of
such dimers differ dramatically when compared with the corresponding monomer junctions
and discuss the implications of these results on intra- and inter-molecular charge
transport.
article_processing_charge: No
article_type: original
author:
- first_name: András
full_name: Magyarkuti, András
last_name: Magyarkuti
- first_name: Olgun
full_name: Adak, Olgun
last_name: Adak
- first_name: Andras
full_name: Halbritter, Andras
last_name: Halbritter
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Magyarkuti A, Adak O, Halbritter A, Venkataraman L. Electronic and mechanical
characteristics of stacked dimer molecular junctions. Nanoscale. 2018;10(7):3362-3368.
doi:10.1039/c7nr08354h
apa: Magyarkuti, A., Adak, O., Halbritter, A., & Venkataraman, L. (2018). Electronic
and mechanical characteristics of stacked dimer molecular junctions. Nanoscale.
Royal Society of Chemistry. https://doi.org/10.1039/c7nr08354h
chicago: Magyarkuti, András, Olgun Adak, Andras Halbritter, and Latha Venkataraman.
“Electronic and Mechanical Characteristics of Stacked Dimer Molecular Junctions.”
Nanoscale. Royal Society of Chemistry, 2018. https://doi.org/10.1039/c7nr08354h.
ieee: A. Magyarkuti, O. Adak, A. Halbritter, and L. Venkataraman, “Electronic and
mechanical characteristics of stacked dimer molecular junctions,” Nanoscale,
vol. 10, no. 7. Royal Society of Chemistry, pp. 3362–3368, 2018.
ista: Magyarkuti A, Adak O, Halbritter A, Venkataraman L. 2018. Electronic and mechanical
characteristics of stacked dimer molecular junctions. Nanoscale. 10(7), 3362–3368.
mla: Magyarkuti, András, et al. “Electronic and Mechanical Characteristics of Stacked
Dimer Molecular Junctions.” Nanoscale, vol. 10, no. 7, Royal Society of
Chemistry, 2018, pp. 3362–68, doi:10.1039/c7nr08354h.
short: A. Magyarkuti, O. Adak, A. Halbritter, L. Venkataraman, Nanoscale 10 (2018)
3362–3368.
date_created: 2024-09-09T08:30:14Z
date_published: 2018-01-09T00:00:00Z
date_updated: 2024-12-17T10:00:20Z
day: '09'
doi: 10.1039/c7nr08354h
extern: '1'
external_id:
pmid:
- '29388658'
intvolume: ' 10'
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/3.0/
main_file_link:
- open_access: '1'
url: "DOI\thttps://doi.org/10.1039/C7NR08354H"
month: '01'
oa: 1
oa_version: Published Version
page: 3362-3368
pmid: 1
publication: Nanoscale
publication_identifier:
eissn:
- 2040-3372
issn:
- 2040-3364
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electronic and mechanical characteristics of stacked dimer molecular junctions
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2018'
...
---
OA_place: repository
OA_type: green
_id: '17934'
abstract:
- lang: eng
text: We measure the conductance of unmodified peptides at the single-molecule level
using the scanning tunneling microscope-based break-junction method, utilizing
the N-terminal amine group and the C-terminal carboxyl group as gold metal-binding
linkers. Our conductance measurements of oligoglycine and oligoalanine backbones
do not rely on peptide side-chain linkers. We compare our results with alkanes
terminated asymmetrically with an amine group on one end and a carboxyl group
on the other to show that peptide bonds decrease the conductance of an otherwise
saturated carbon chain. Using a newly developed first-principles approach, we
attribute the decrease in conductance to charge localization at the peptide bond,
which reduces the energy of the frontier orbitals relative to the Fermi energy
and the electronic coupling to the leads, lowering the tunneling probability.
Crucially, this manifests as an increase in conductance decay of peptide backbones
with increasing length when compared with alkanes.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Joseph M.
full_name: Brisendine, Joseph M.
last_name: Brisendine
- first_name: Sivan
full_name: Refaely-Abramson, Sivan
last_name: Refaely-Abramson
- first_name: Zhen-Fei
full_name: Liu, Zhen-Fei
last_name: Liu
- first_name: Jing
full_name: Cui, Jing
last_name: Cui
- first_name: Fay
full_name: Ng, Fay
last_name: Ng
- first_name: Jeffrey B.
full_name: Neaton, Jeffrey B.
last_name: Neaton
- first_name: Ronald L.
full_name: Koder, Ronald L.
last_name: Koder
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Brisendine JM, Refaely-Abramson S, Liu Z-F, et al. Probing charge transport
through peptide bonds. The Journal of Physical Chemistry Letters. 2018;9(4):763-767.
doi:10.1021/acs.jpclett.8b00176
apa: Brisendine, J. M., Refaely-Abramson, S., Liu, Z.-F., Cui, J., Ng, F., Neaton,
J. B., … Venkataraman, L. (2018). Probing charge transport through peptide bonds.
The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00176
chicago: Brisendine, Joseph M., Sivan Refaely-Abramson, Zhen-Fei Liu, Jing Cui,
Fay Ng, Jeffrey B. Neaton, Ronald L. Koder, and Latha Venkataraman. “Probing Charge
Transport through Peptide Bonds.” The Journal of Physical Chemistry Letters.
American Chemical Society, 2018. https://doi.org/10.1021/acs.jpclett.8b00176.
ieee: J. M. Brisendine et al., “Probing charge transport through peptide
bonds,” The Journal of Physical Chemistry Letters, vol. 9, no. 4. American
Chemical Society, pp. 763–767, 2018.
ista: Brisendine JM, Refaely-Abramson S, Liu Z-F, Cui J, Ng F, Neaton JB, Koder
RL, Venkataraman L. 2018. Probing charge transport through peptide bonds. The
Journal of Physical Chemistry Letters. 9(4), 763–767.
mla: Brisendine, Joseph M., et al. “Probing Charge Transport through Peptide Bonds.”
The Journal of Physical Chemistry Letters, vol. 9, no. 4, American Chemical
Society, 2018, pp. 763–67, doi:10.1021/acs.jpclett.8b00176.
short: J.M. Brisendine, S. Refaely-Abramson, Z.-F. Liu, J. Cui, F. Ng, J.B. Neaton,
R.L. Koder, L. Venkataraman, The Journal of Physical Chemistry Letters 9 (2018)
763–767.
date_created: 2024-09-09T08:34:32Z
date_published: 2018-01-27T00:00:00Z
date_updated: 2024-12-17T09:41:02Z
day: '27'
doi: 10.1021/acs.jpclett.8b00176
extern: '1'
external_id:
pmid:
- '29376375'
intvolume: ' 9'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://europepmc.org/article/med/29376375#free-full-text
month: '01'
oa: 1
oa_version: Submitted Version
page: 763-767
pmid: 1
publication: The Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probing charge transport through peptide bonds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '18'
abstract:
- lang: eng
text: An N-superconcentrator is a directed, acyclic graph with N input nodes and
N output nodes such that every subset of the inputs and every subset of the outputs
of same cardinality can be connected by node-disjoint paths. It is known that
linear-size and bounded-degree superconcentrators exist. We prove the existence
of such superconcentrators with asymptotic density 25.3 (where the density is
the number of edges divided by N). The previously best known densities were 28
[12] and 27.4136 [17].
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. Ars Combinatoria.
2018;141(10):269-304.
apa: Kolmogorov, V., & Rolinek, M. (2018). Superconcentrators of density 25.3.
Ars Combinatoria. Charles Babbage Research Centre.
chicago: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density
25.3.” Ars Combinatoria. Charles Babbage Research Centre, 2018.
ieee: V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” Ars
Combinatoria, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304,
2018.
ista: Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria.
141(10), 269–304.
mla: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.”
Ars Combinatoria, vol. 141, no. 10, Charles Babbage Research Centre, 2018,
pp. 269–304.
short: V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.
date_created: 2018-12-11T11:44:11Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-19T14:46:18Z
day: '01'
department:
- _id: VlKo
external_id:
arxiv:
- '1405.7828'
isi:
- '000446809500022'
intvolume: ' 141'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.7828
month: '10'
oa: 1
oa_version: Preprint
page: 269 - 304
publication: Ars Combinatoria
publication_identifier:
issn:
- 0381-7032
publication_status: published
publisher: Charles Babbage Research Centre
publist_id: '8037'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superconcentrators of density 25.3
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 141
year: '2018'
...
---
_id: '180'
abstract:
- lang: eng
text: In this paper we define and study the classical Uniform Electron Gas (UEG),
a system of infinitely many electrons whose density is constant everywhere in
space. The UEG is defined differently from Jellium, which has a positive constant
background but no constraint on the density. We prove that the UEG arises in Density
Functional Theory in the limit of a slowly varying density, minimizing the indirect
Coulomb energy. We also construct the quantum UEG and compare it to the classical
UEG at low density.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme
(grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by
the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National
Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mathieu
full_name: Lewi, Mathieu
last_name: Lewi
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron
gas. Journal de l’Ecole Polytechnique - Mathematiques. 2018;5:79-116. doi:10.5802/jep.64
apa: Lewi, M., Lieb, É., & Seiringer, R. (2018). Statistical mechanics of the
uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques.
Ecole Polytechnique. https://doi.org/10.5802/jep.64
chicago: Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics
of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques.
Ecole Polytechnique, 2018. https://doi.org/10.5802/jep.64.
ieee: M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform
electron gas,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5.
Ecole Polytechnique, pp. 79–116, 2018.
ista: Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron
gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.
mla: Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.”
Journal de l’Ecole Polytechnique - Mathematiques, vol. 5, Ecole Polytechnique,
2018, pp. 79–116, doi:10.5802/jep.64.
short: M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques
5 (2018) 79–116.
date_created: 2018-12-11T11:45:03Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2025-04-14T07:26:59Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.5802/jep.64
ec_funded: 1
external_id:
arxiv:
- '1705.10676'
file:
- access_level: open_access
checksum: 1ba7cccdf3900f42c4f715ae75d6813c
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:38:18Z
date_updated: 2020-07-14T12:45:16Z
file_id: '5726'
file_name: 2018_JournaldeLecoleMath_Lewi.pdf
file_size: 843938
relation: main_file
file_date_updated: 2020-07-14T12:45:16Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 79 - 116
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Journal de l'Ecole Polytechnique - Mathematiques
publication_identifier:
eissn:
- 2270-518X
issn:
- 2429-7100
publication_status: published
publisher: Ecole Polytechnique
publist_id: '7741'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical mechanics of the uniform electron gas
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...
---
_id: '181'
abstract:
- lang: eng
text: We consider large random matrices X with centered, independent entries but
possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for
f, g functions analytic on the spectrum of X. We use these results to compute
the long time asymptotics for systems of coupled di erential equations with random
coe cients. We show that when the coupling is critical, the norm squared of the
solution decays like t−1/2.
acknowledgement: The work of the second author was also partially supported by the
Hausdorff Center of Mathematics.
article_processing_charge: No
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: David T
full_name: Renfrew, David T
id: 4845BF6A-F248-11E8-B48F-1D18A9856A87
last_name: Renfrew
orcid: 0000-0003-3493-121X
citation:
ama: Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled
differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290.
doi:10.1137/17M1143125
apa: Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for
systems of randomly coupled differential equations. SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125
chicago: Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for
Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.
ieee: L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of
randomly coupled differential equations,” SIAM Journal on Mathematical Analysis,
vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290,
2018.
ista: Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly
coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3),
3271–3290.
mla: Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential
Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society
for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.
short: L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis
50 (2018) 3271–3290.
date_created: 2018-12-11T11:45:03Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-04-15T08:05:02Z
day: '01'
department:
- _id: LaEr
doi: 10.1137/17M1143125
ec_funded: 1
external_id:
arxiv:
- '1708.01546'
isi:
- '000437018500032'
intvolume: ' 50'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.01546
month: '01'
oa: 1
oa_version: Published Version
page: 3271 - 3290
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 258F40A4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02080
name: Structured Non-Hermitian Random Matrices
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7740'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Power law decay for systems of randomly coupled differential equations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '18197'
abstract:
- lang: eng
text: Controlling matter to simultaneously support coupled properties is of fundamental
and technological importance1 (for example, in multiferroics2,3,4,5 or high-temperature
superconductors6,7,8,9). However, determining the microscopic mechanisms responsible
for the simultaneous presence of different orders is difficult, making it hard
to predict material phenomenology10,11 or modify properties12,13,14,15,16. Here,
using a quantum gas to engineer an adjustable interaction at the microscopic level,
we demonstrate scenarios of competition, coexistence and mutual enhancement of
two orders. For the enhancement scenario, the presence of one order lowers the
critical point of the other. Our system is realized by a Bose–Einstein condensate
that can undergo self-organization phase transitions in two optical resonators17,
resulting in two distinct crystalline density orders. We characterize the coupling
between these orders by measuring the composite order parameter and the elementary
excitations and explain our results with a mean-field free-energy model derived
from a microscopic Hamiltonian. Our system is ideally suited to explore quantum
tricritical points18 and can be extended to study the interplay of spin and density
orders19 as a function of temperature20.
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Andrea
full_name: Morales, Andrea
last_name: Morales
- first_name: Philip
full_name: Zupancic, Philip
last_name: Zupancic
- first_name: Julian
full_name: Leonard, Julian
id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577
last_name: Leonard
- first_name: Tilman
full_name: Esslinger, Tilman
last_name: Esslinger
- first_name: Tobias
full_name: Donner, Tobias
last_name: Donner
citation:
ama: Morales A, Zupancic P, Leonard J, Esslinger T, Donner T. Coupling two order
parameters in a quantum gas. Nature Materials. 2018;17(8):686-690. doi:10.1038/s41563-018-0118-1
apa: Morales, A., Zupancic, P., Leonard, J., Esslinger, T., & Donner, T. (2018).
Coupling two order parameters in a quantum gas. Nature Materials. Springer
Nature. https://doi.org/10.1038/s41563-018-0118-1
chicago: Morales, Andrea, Philip Zupancic, Julian Leonard, Tilman Esslinger, and
Tobias Donner. “Coupling Two Order Parameters in a Quantum Gas.” Nature Materials.
Springer Nature, 2018. https://doi.org/10.1038/s41563-018-0118-1.
ieee: A. Morales, P. Zupancic, J. Leonard, T. Esslinger, and T. Donner, “Coupling
two order parameters in a quantum gas,” Nature Materials, vol. 17, no.
8. Springer Nature, pp. 686–690, 2018.
ista: Morales A, Zupancic P, Leonard J, Esslinger T, Donner T. 2018. Coupling two
order parameters in a quantum gas. Nature Materials. 17(8), 686–690.
mla: Morales, Andrea, et al. “Coupling Two Order Parameters in a Quantum Gas.” Nature
Materials, vol. 17, no. 8, Springer Nature, 2018, pp. 686–90, doi:10.1038/s41563-018-0118-1.
short: A. Morales, P. Zupancic, J. Leonard, T. Esslinger, T. Donner, Nature Materials
17 (2018) 686–690.
date_created: 2024-10-07T11:48:59Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2024-10-07T12:15:41Z
day: '01'
doi: 10.1038/s41563-018-0118-1
extern: '1'
external_id:
arxiv:
- '1711.07988'
intvolume: ' 17'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1711.07988
month: '08'
oa: 1
oa_version: Preprint
page: 686-690
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: Coupling two order parameters in a quantum gas
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2018'
...
---
_id: '182'
abstract:
- lang: eng
text: We describe a new algorithm for the parametric identification problem for
signal temporal logic (STL), stated as follows. Given a densetime real-valued
signal w and a parameterized temporal logic formula φ, compute the subset of the
parameter space that renders the formula satisfied by the signal. Unlike previous
solutions, which were based on search in the parameter space or quantifier elimination,
our procedure works recursively on φ and computes the evolution over time of the
set of valid parameter assignments. This procedure is similar to that of monitoring
or computing the robustness of φ relative to w. Our implementation and experiments
demonstrate that this approach can work well in practice.
alternative_title:
- HSCC Proceedings
article_processing_charge: No
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
citation:
ama: 'Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL.
In: Proceedings of the 21st International Conference on Hybrid Systems.
ACM; 2018:177-186. doi:10.1145/3178126.3178132'
apa: 'Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification
for STL. In Proceedings of the 21st International Conference on Hybrid Systems
(pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132'
chicago: Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric
Identification for STL.” In Proceedings of the 21st International Conference
on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132.
ieee: A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification
for STL,” in Proceedings of the 21st International Conference on Hybrid Systems,
Porto, Portugal, 2018, pp. 177–186.
ista: 'Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification
for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC:
Hybrid Systems - Computation and Control, HSCC Proceedings, , 177–186.'
mla: Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings
of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86,
doi:10.1145/3178126.3178132.
short: A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International
Conference on Hybrid Systems, ACM, 2018, pp. 177–186.
conference:
end_date: 2018-04-13
location: Porto, Portugal
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2018-04-11
date_created: 2018-12-11T11:45:04Z
date_published: 2018-04-11T00:00:00Z
date_updated: 2025-07-10T11:51:21Z
day: '11'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3178126.3178132
external_id:
isi:
- '000474781600020'
file:
- access_level: open_access
checksum: 81eabc96430e84336ea88310ac0a1ad0
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:18:29Z
date_updated: 2020-07-14T12:45:17Z
file_id: '7833'
file_name: 2018_HSCC_Bakhirkin.pdf
file_size: 5900421
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 177 - 186
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the 21st International Conference on Hybrid Systems
publication_identifier:
isbn:
- '978-1-4503-5642-8 '
publication_status: published
publisher: ACM
publist_id: '7739'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient parametric identification for STL
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '18270'
abstract:
- lang: eng
text: The availability of affordable and portable depth sensors has made scanning
objects and people simpler than ever. However, dealing with occlusions and missing
parts is still a significant challenge. The problem of reconstructing a (possibly
non-rigidly moving) 3D object from a single or multiple partial scans has received
increasing attention in recent years. In this work, we propose a novel learning-based
method for the completion of partial shapes. Unlike the majority of existing approaches,
our method focuses on objects that can undergo non-rigid deformations. The core
of our method is a variational autoencoder with graph convolutional operations
that learns a latent space for complete realistic shapes. At inference, we optimize
to find the representation in this latent space that best fits the generated shape
to the known partial input. The completed shape exhibits a realistic appearance
on the unknown part. We show promising results towards the completion of synthetic
and real scans of human body and face meshes exhibiting different styles of articulation
and partiality.
article_number: '8578300'
article_processing_charge: No
arxiv: 1
author:
- first_name: Or
full_name: Litany, Or
last_name: Litany
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Michael
full_name: Bronstein, Michael
last_name: Bronstein
- first_name: Ameesh
full_name: Makadia, Ameesh
last_name: Makadia
citation:
ama: 'Litany O, Bronstein AM, Bronstein M, Makadia A. Deformable shape completion
with graph convolutional autoencoders. In: 2018 IEEE/CVF Conference on Computer
Vision and Pattern Recognition. IEEE; 2018. doi:10.1109/cvpr.2018.00202'
apa: 'Litany, O., Bronstein, A. M., Bronstein, M., & Makadia, A. (2018). Deformable
shape completion with graph convolutional autoencoders. In 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition. Salt Lake City, UT, United States:
IEEE. https://doi.org/10.1109/cvpr.2018.00202'
chicago: Litany, Or, Alex M. Bronstein, Michael Bronstein, and Ameesh Makadia. “Deformable
Shape Completion with Graph Convolutional Autoencoders.” In 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00202.
ieee: O. Litany, A. M. Bronstein, M. Bronstein, and A. Makadia, “Deformable shape
completion with graph convolutional autoencoders,” in 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition, Salt Lake City, UT, United States,
2018.
ista: Litany O, Bronstein AM, Bronstein M, Makadia A. 2018. Deformable shape completion
with graph convolutional autoencoders. 2018 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. 31st Meeting of the IEEE/CVF Conference on Computer Vision
and Pattern Recognition, 8578300.
mla: Litany, Or, et al. “Deformable Shape Completion with Graph Convolutional Autoencoders.”
2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 8578300,
IEEE, 2018, doi:10.1109/cvpr.2018.00202.
short: O. Litany, A.M. Bronstein, M. Bronstein, A. Makadia, in:, 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition, IEEE, 2018.
conference:
end_date: 2018-06-23
location: Salt Lake City, UT, United States
name: 31st Meeting of the IEEE/CVF Conference on Computer Vision and Pattern Recognition
start_date: 2018-06-18
date_created: 2024-10-09T07:41:53Z
date_published: 2018-12-16T00:00:00Z
date_updated: 2024-12-05T14:40:39Z
day: '16'
doi: 10.1109/cvpr.2018.00202
extern: '1'
external_id:
arxiv:
- '1712.00268'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1712.00268
month: '12'
oa: 1
oa_version: Preprint
publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
eissn:
- 2575-7075
isbn:
- '9781538664216'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deformable shape completion with graph convolutional autoencoders
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
OA_place: repository
OA_type: green
_id: '18271'
abstract:
- lang: eng
text: We propose a fully convolutional neural-network architecture for image denoising
which is simple yet powerful. Its structure allows to exploit the gradual nature
of the denoising process, in which the shallow layers handle local noise statistics,
while deeper layers recover edges and enhance textures. Our method advances the
state of the art when trained for different noise levels and distributions (both
Gaussian and Poisson). In addition, we show that making the denoiser class-aware
by exploiting semantic class information boosts the performance, enhances the
textures, and reduces the artifacts.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Tal
full_name: Remez, Tal
last_name: Remez
- first_name: Or
full_name: Litany, Or
last_name: Litany
- first_name: Raja
full_name: Giryes, Raja
last_name: Giryes
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: Remez T, Litany O, Giryes R, Bronstein AM. Class-aware fully convolutional
Gaussian and Poisson denoising. IEEE Transactions on Image Processing.
2018;27(11):5707-5722. doi:10.1109/tip.2018.2859044
apa: Remez, T., Litany, O., Giryes, R., & Bronstein, A. M. (2018). Class-aware
fully convolutional Gaussian and Poisson denoising. IEEE Transactions on Image
Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tip.2018.2859044
chicago: Remez, Tal, Or Litany, Raja Giryes, and Alex M. Bronstein. “Class-Aware
Fully Convolutional Gaussian and Poisson Denoising.” IEEE Transactions on Image
Processing. Institute of Electrical and Electronics Engineers, 2018. https://doi.org/10.1109/tip.2018.2859044.
ieee: T. Remez, O. Litany, R. Giryes, and A. M. Bronstein, “Class-aware fully convolutional
Gaussian and Poisson denoising,” IEEE Transactions on Image Processing,
vol. 27, no. 11. Institute of Electrical and Electronics Engineers, pp. 5707–5722,
2018.
ista: Remez T, Litany O, Giryes R, Bronstein AM. 2018. Class-aware fully convolutional
Gaussian and Poisson denoising. IEEE Transactions on Image Processing. 27(11),
5707–5722.
mla: Remez, Tal, et al. “Class-Aware Fully Convolutional Gaussian and Poisson Denoising.”
IEEE Transactions on Image Processing, vol. 27, no. 11, Institute of Electrical
and Electronics Engineers, 2018, pp. 5707–22, doi:10.1109/tip.2018.2859044.
short: T. Remez, O. Litany, R. Giryes, A.M. Bronstein, IEEE Transactions on Image
Processing 27 (2018) 5707–5722.
date_created: 2024-10-09T07:42:49Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2024-10-16T13:00:30Z
day: '01'
doi: 10.1109/tip.2018.2859044
extern: '1'
external_id:
arxiv:
- '1808.06562'
intvolume: ' 27'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1808.06562
month: '11'
oa: 1
oa_version: Preprint
page: 5707-5722
publication: IEEE Transactions on Image Processing
publication_identifier:
eissn:
- 1941-0042
issn:
- 1057-7149
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Class-aware fully convolutional Gaussian and Poisson denoising
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2018'
...
---
_id: '18272'
abstract:
- lang: eng
text: Accelerating iterative algorithms for solving inverse problems using neural
networks have become a very popular strategy in the recent years. In this work,
we propose a theoretical analysis that may provide an explanation for its success.
Our theory relies on the usage of inexact projections with the projected gradient
descent (PGD) method. It is demonstrated in various problems including image super-resolution.
article_number: '8462136'
article_processing_charge: No
author:
- first_name: Raja
full_name: Giryes, Raja
last_name: Giryes
- first_name: Yonina C.
full_name: Eldar, Yonina C.
last_name: Eldar
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Guillermo
full_name: Sapiro, Guillermo
last_name: Sapiro
citation:
ama: 'Giryes R, Eldar YC, Bronstein AM, Sapiro G. The learned inexact project gradient
descent algorithm. In: 2018 IEEE International Conference on Acoustics, Speech
and Signal Processing (ICASSP). IEEE; 2018. doi:10.1109/icassp.2018.8462136'
apa: 'Giryes, R., Eldar, Y. C., Bronstein, A. M., & Sapiro, G. (2018). The learned
inexact project gradient descent algorithm. In 2018 IEEE International Conference
on Acoustics, Speech and Signal Processing (ICASSP). Calgary, AB, Canada:
IEEE. https://doi.org/10.1109/icassp.2018.8462136'
chicago: Giryes, Raja, Yonina C. Eldar, Alex M. Bronstein, and Guillermo Sapiro.
“The Learned Inexact Project Gradient Descent Algorithm.” In 2018 IEEE International
Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE, 2018.
https://doi.org/10.1109/icassp.2018.8462136.
ieee: R. Giryes, Y. C. Eldar, A. M. Bronstein, and G. Sapiro, “The learned inexact
project gradient descent algorithm,” in 2018 IEEE International Conference
on Acoustics, Speech and Signal Processing (ICASSP), Calgary, AB, Canada,
2018.
ista: Giryes R, Eldar YC, Bronstein AM, Sapiro G. 2018. The learned inexact project
gradient descent algorithm. 2018 IEEE International Conference on Acoustics, Speech
and Signal Processing (ICASSP). IEEE International Conference on Acoustics, Speech,
and Signal Processing, 8462136.
mla: Giryes, Raja, et al. “The Learned Inexact Project Gradient Descent Algorithm.”
2018 IEEE International Conference on Acoustics, Speech and Signal Processing
(ICASSP), 8462136, IEEE, 2018, doi:10.1109/icassp.2018.8462136.
short: R. Giryes, Y.C. Eldar, A.M. Bronstein, G. Sapiro, in:, 2018 IEEE International
Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2018.
conference:
end_date: 2018-04-20
location: Calgary, AB, Canada
name: IEEE International Conference on Acoustics, Speech, and Signal Processing
start_date: 2018-04-15
date_created: 2024-10-09T07:43:07Z
date_published: 2018-09-13T00:00:00Z
date_updated: 2024-12-05T14:33:48Z
day: '13'
doi: 10.1109/icassp.2018.8462136
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
publication: 2018 IEEE International Conference on Acoustics, Speech and Signal Processing
(ICASSP)
publication_identifier:
eisbn:
- '9781538646588'
eissn:
- 2379-190X
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: The learned inexact project gradient descent algorithm
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '18273'
abstract:
- lang: eng
text: Deep neural networks (DNNs) are used by different applications that are executed
on a range of computer architectures, from IoT devices to supercomputers. The
footprint of these networks is huge as well as their computational and communication
needs. In order to ease the pressure on resources, research indicates that in
many cases a low precision representation (1-2 bit per parameter) of weights and
other parameters can achieve similar accuracy while requiring less resources.
Using quantized values enables the use of FPGAs to run NNs, since FPGAs are well
fitted to these primitives; e.g., FPGAs provide efficient support for bitwise
operations and can work with arbitrary-precision representation of numbers. This
paper presents a new streaming architecture for running QNNs on FPGAs. The proposed
architecture scales out better than alternatives, allowing us to take advantage
of systems with multiple FPGAs. We also included support for skip connections,
that are used in state-of-the art NNs, and shown that our architecture allows
to add those connections almost for free. All this allowed us to implement an
18-layer ResNet for 224×224 images classification, achieving 57.5% top-1 accuracy.
In addition, we implemented a full-sized quantized AlexNet. In contrast to previous
works, we use 2-bit activations instead of 1-bit ones, which improves AlexNet's
top-1 accuracy from 41.8% to 51.03% for the ImageNet classification. Both AlexNet
and ResNet can handle 1000-class real-time classification on an FPGA. Our implementation
of ResNet-18 consumes 5× less power and is 4× slower for ImageNet, when compared
to the same NN on the latest Nvidia GPUs. Smaller NNs, that fit a single FPGA,
are running faster then on GPUs on small (32×32) inputs, while consuming up to
20× less energy and power.
article_number: '8425399'
article_processing_charge: No
arxiv: 1
author:
- first_name: Chaim
full_name: Baskin, Chaim
last_name: Baskin
- first_name: Natan
full_name: Liss, Natan
last_name: Liss
- first_name: Evgenii
full_name: Zheltonozhskii, Evgenii
last_name: Zheltonozhskii
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Avi
full_name: Mendelson, Avi
last_name: Mendelson
citation:
ama: 'Baskin C, Liss N, Zheltonozhskii E, Bronstein AM, Mendelson A. Streaming architecture
for large-scale quantized neural networks on an FPGA-based dataflow platform.
In: 2018 IEEE International Parallel and Distributed Processing Symposium Workshops
(IPDPSW). IEEE; 2018. doi:10.1109/ipdpsw.2018.00032'
apa: 'Baskin, C., Liss, N., Zheltonozhskii, E., Bronstein, A. M., & Mendelson,
A. (2018). Streaming architecture for large-scale quantized neural networks on
an FPGA-based dataflow platform. In 2018 IEEE International Parallel and Distributed
Processing Symposium Workshops (IPDPSW). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/ipdpsw.2018.00032'
chicago: Baskin, Chaim, Natan Liss, Evgenii Zheltonozhskii, Alex M. Bronstein, and
Avi Mendelson. “Streaming Architecture for Large-Scale Quantized Neural Networks
on an FPGA-Based Dataflow Platform.” In 2018 IEEE International Parallel and
Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2018. https://doi.org/10.1109/ipdpsw.2018.00032.
ieee: C. Baskin, N. Liss, E. Zheltonozhskii, A. M. Bronstein, and A. Mendelson,
“Streaming architecture for large-scale quantized neural networks on an FPGA-based
dataflow platform,” in 2018 IEEE International Parallel and Distributed Processing
Symposium Workshops (IPDPSW), Vancouver, BC, Canada, 2018.
ista: Baskin C, Liss N, Zheltonozhskii E, Bronstein AM, Mendelson A. 2018. Streaming
architecture for large-scale quantized neural networks on an FPGA-based dataflow
platform. 2018 IEEE International Parallel and Distributed Processing Symposium
Workshops (IPDPSW). 32nd IEEE International Parallel and Distributed Processing
Symposium Workshops, 8425399.
mla: Baskin, Chaim, et al. “Streaming Architecture for Large-Scale Quantized Neural
Networks on an FPGA-Based Dataflow Platform.” 2018 IEEE International Parallel
and Distributed Processing Symposium Workshops (IPDPSW), 8425399, IEEE, 2018,
doi:10.1109/ipdpsw.2018.00032.
short: C. Baskin, N. Liss, E. Zheltonozhskii, A.M. Bronstein, A. Mendelson, in:,
2018 IEEE International Parallel and Distributed Processing Symposium Workshops
(IPDPSW), IEEE, 2018.
conference:
end_date: 2018-05-25
location: Vancouver, BC, Canada
name: 32nd IEEE International Parallel and Distributed Processing Symposium Workshops
start_date: 2018-05-21
date_created: 2024-10-09T07:43:30Z
date_published: 2018-08-06T00:00:00Z
date_updated: 2024-12-05T14:25:32Z
day: '06'
doi: 10.1109/ipdpsw.2018.00032
extern: '1'
external_id:
arxiv:
- '1708.00052'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1708.00052
month: '08'
oa: 1
oa_version: Preprint
publication: 2018 IEEE International Parallel and Distributed Processing Symposium
Workshops (IPDPSW)
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Streaming architecture for large-scale quantized neural networks on an FPGA-based
dataflow platform
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
OA_place: repository
OA_type: green
_id: '18274'
abstract:
- lang: eng
text: 'Comparison among graphs is ubiquitous in graph analytics. However, it is
a hard task in terms of the expressiveness of the employed similarity measure
and the efficiency of its computation. Ideally, graph comparison should be invariant
to the order of nodes and the sizes of compared graphs, adaptive to the scale
of graph patterns, and scalable. Unfortunately, these properties have not been
addressed together. Graph comparisons still rely on direct approaches, graph kernels,
or representation-based methods, which are all inefficient and impractical for
large graph collections. In this paper, we propose the Network Laplacian Spectral
Descriptor (NetLSD): the first, to our knowledge, permutation- and size-invariant,
scale-adaptive, and efficiently computable graph representation method that allows
for straightforward comparisons of large graphs. NetLSD extracts a compact signature
that inherits the formal properties of the Laplacian spectrum, specifically its
heat or wave kernel; thus, it \em hears the shape of a graph. Our evaluation on
a variety of real-world graphs demonstrates that it outperforms previous works
in both expressiveness and efficiency.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Anton
full_name: Tsitsulin, Anton
last_name: Tsitsulin
- first_name: Davide
full_name: Mottin, Davide
last_name: Mottin
- first_name: Panagiotis
full_name: Karras, Panagiotis
last_name: Karras
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Emmanuel
full_name: Müller, Emmanuel
last_name: Müller
citation:
ama: 'Tsitsulin A, Mottin D, Karras P, Bronstein AM, Müller E. NetLSD: Hearing the
shape of a graph. In: ACM SIGKDD International Conference on Knowledge Discovery
and Data Mining. ACM; 2018:2347-2356. doi:10.1145/3219819.3219991'
apa: 'Tsitsulin, A., Mottin, D., Karras, P., Bronstein, A. M., & Müller, E.
(2018). NetLSD: Hearing the shape of a graph. In ACM SIGKDD International Conference
on Knowledge Discovery and Data Mining (pp. 2347–2356). London, United Kingdom:
ACM. https://doi.org/10.1145/3219819.3219991'
chicago: 'Tsitsulin, Anton, Davide Mottin, Panagiotis Karras, Alex M. Bronstein,
and Emmanuel Müller. “NetLSD: Hearing the Shape of a Graph.” In ACM SIGKDD
International Conference on Knowledge Discovery and Data Mining, 2347–56.
ACM, 2018. https://doi.org/10.1145/3219819.3219991.'
ieee: 'A. Tsitsulin, D. Mottin, P. Karras, A. M. Bronstein, and E. Müller, “NetLSD:
Hearing the shape of a graph,” in ACM SIGKDD International Conference on Knowledge
Discovery and Data Mining, London, United Kingdom, 2018, pp. 2347–2356.'
ista: 'Tsitsulin A, Mottin D, Karras P, Bronstein AM, Müller E. 2018. NetLSD: Hearing
the shape of a graph. ACM SIGKDD International Conference on Knowledge Discovery
and Data Mining. KDD: ACM SIGKDD International Conference on Knowledge Discovery
and Data Mining, 2347–2356.'
mla: 'Tsitsulin, Anton, et al. “NetLSD: Hearing the Shape of a Graph.” ACM SIGKDD
International Conference on Knowledge Discovery and Data Mining, ACM, 2018,
pp. 2347–56, doi:10.1145/3219819.3219991.'
short: A. Tsitsulin, D. Mottin, P. Karras, A.M. Bronstein, E. Müller, in:, ACM SIGKDD
International Conference on Knowledge Discovery and Data Mining, ACM, 2018, pp.
2347–2356.
conference:
end_date: 2018-08-23
location: London, United Kingdom
name: 'KDD: ACM SIGKDD International Conference on Knowledge Discovery and Data
Mining'
start_date: 2018-08-19
date_created: 2024-10-09T07:43:50Z
date_published: 2018-07-19T00:00:00Z
date_updated: 2025-02-04T14:59:22Z
day: '19'
doi: 10.1145/3219819.3219991
extern: '1'
external_id:
arxiv:
- '1805.10712'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1805.10712
month: '07'
oa: 1
oa_version: Preprint
page: 2347 - 2356
publication: ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'NetLSD: Hearing the shape of a graph'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
DOAJ_listed: '1'
_id: '18275'
abstract:
- lang: eng
text: "Homologous recombination (HR) is a mechanism that repairs a variety of DNA
lesions. Under certain circumstances, however, HR can generate intermediates that
can interfere with other cellular processes such as DNA transcription or replication.
Cells have therefore developed pathways that abolish undesirable HR intermediates.
The Saccharomyces cerevisiae yeast Srs2 helicase has a major role in one of these
pathways. Srs2 also works during DNA replication and interacts with the clamp
PCNA. The relative importance of Srs2’s helicase activity, Rad51 removal function,
and PCNA interaction in genome stability remains unclear. We created a new SRS2
allele [srs2(1-850)] that lacks the whole C terminus, containing the interaction
site for Rad51 and PCNA and interactions with many other proteins. Thus, the new
allele encodes an Srs2 protein bearing only the activity of the DNA helicase.
We find that the interactions of Srs2 with Rad51 and PCNA are dispensable for
the main role of Srs2 in the repair of DNA damage in vegetative cells and for
proper completion of meiosis. On the other hand, it has been shown that in cells
impaired for the DNA damage tolerance (DDT) pathways, Srs2 generates toxic intermediates
that lead to DNA damage sensitivity; we show that this negative Srs2 activity
requires the C terminus of Srs2. Dissection of the genetic interactions of the
srs2(1-850) allele suggest a role for Srs2’s helicase activity in sister chromatid
cohesion. Our results also indicate that Srs2’s function becomes more central
in diploid cells.\r\nIMPORTANCE Homologous recombination (HR) is a key mechanism
that repairs damaged DNA. However, this process has to be tightly regulated; failure
to regulate it can lead to genome instability. The Srs2 helicase is considered
a regulator of HR; it was shown to be able to evict the recombinase Rad51 from
DNA. Cells lacking Srs2 exhibit sensitivity to DNA-damaging agents, and in some
cases, they display defects in DNA replication. The relative roles of the helicase
and Rad51 removal activities of Srs2 in genome stability remain unclear. To address
this question, we created a new Srs2 mutant which has only the DNA helicase domain.
Our study shows that only the DNA helicase domain is needed to deal with DNA damage
and assist in DNA replication during vegetative growth and in meiosis. Thus, our
findings shift the view on the role of Srs2 in the maintenance of genome integrity."
article_number: e01192-18
article_processing_charge: No
author:
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Lihi
full_name: Gershon, Lihi
last_name: Gershon
- first_name: Gilad
full_name: Grinberg, Gilad
last_name: Grinberg
- first_name: Elisa
full_name: Alonso-Perez, Elisa
last_name: Alonso-Perez
- first_name: Martin
full_name: Kupiec, Martin
last_name: Kupiec
citation:
ama: Bronstein AM, Gershon L, Grinberg G, Alonso-Perez E, Kupiec M. The main role
of Srs2 in DNA repair depends on its helicase activity, rather than on its interactions
with PCNA or Rad51. mBio. 2018;9(4). doi:10.1128/mbio.01192-18
apa: Bronstein, A. M., Gershon, L., Grinberg, G., Alonso-Perez, E., & Kupiec,
M. (2018). The main role of Srs2 in DNA repair depends on its helicase activity,
rather than on its interactions with PCNA or Rad51. MBio. American Society
for Microbiology. https://doi.org/10.1128/mbio.01192-18
chicago: Bronstein, Alex M., Lihi Gershon, Gilad Grinberg, Elisa Alonso-Perez, and
Martin Kupiec. “The Main Role of Srs2 in DNA Repair Depends on Its Helicase Activity,
Rather than on Its Interactions with PCNA or Rad51.” MBio. American Society
for Microbiology, 2018. https://doi.org/10.1128/mbio.01192-18.
ieee: A. M. Bronstein, L. Gershon, G. Grinberg, E. Alonso-Perez, and M. Kupiec,
“The main role of Srs2 in DNA repair depends on its helicase activity, rather
than on its interactions with PCNA or Rad51,” mBio, vol. 9, no. 4. American
Society for Microbiology, 2018.
ista: Bronstein AM, Gershon L, Grinberg G, Alonso-Perez E, Kupiec M. 2018. The main
role of Srs2 in DNA repair depends on its helicase activity, rather than on its
interactions with PCNA or Rad51. mBio. 9(4), e01192-18.
mla: Bronstein, Alex M., et al. “The Main Role of Srs2 in DNA Repair Depends on
Its Helicase Activity, Rather than on Its Interactions with PCNA or Rad51.” MBio,
vol. 9, no. 4, e01192-18, American Society for Microbiology, 2018, doi:10.1128/mbio.01192-18.
short: A.M. Bronstein, L. Gershon, G. Grinberg, E. Alonso-Perez, M. Kupiec, MBio
9 (2018).
date_created: 2024-10-09T07:44:09Z
date_published: 2018-07-17T00:00:00Z
date_updated: 2024-12-19T12:43:33Z
day: '17'
doi: 10.1128/mbio.01192-18
extern: '1'
intvolume: ' 9'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1128/mbio.01192-18
month: '07'
oa: 1
oa_version: Published Version
publication: mBio
publication_identifier:
eissn:
- 2150-7511
publication_status: published
publisher: American Society for Microbiology
quality_controlled: '1'
scopus_import: '1'
status: public
title: The main role of Srs2 in DNA repair depends on its helicase activity, rather
than on its interactions with PCNA or Rad51
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '18276'
abstract:
- lang: eng
text: We present a method to match three dimensional shapes under non-isometric
deformations, topology changes and partiality. We formulate the problem as matching
between a set of pair-wise and point-wise descriptors, imposing a continuity prior
on the mapping, and propose a projected descent optimization procedure inspired
by difference of convex functions (DC) programming.
article_processing_charge: No
arxiv: 1
author:
- first_name: Matthias
full_name: Vestner, Matthias
last_name: Vestner
- first_name: Zorah
full_name: Lahner, Zorah
last_name: Lahner
- first_name: Amit
full_name: Boyarski, Amit
last_name: Boyarski
- first_name: Or
full_name: Litany, Or
last_name: Litany
- first_name: Ron
full_name: Slossberg, Ron
last_name: Slossberg
- first_name: Tal
full_name: Remez, Tal
last_name: Remez
- first_name: Emanuele
full_name: Rodola, Emanuele
last_name: Rodola
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Michael
full_name: Bronstein, Michael
last_name: Bronstein
- first_name: Ron
full_name: Kimmel, Ron
last_name: Kimmel
- first_name: Daniel
full_name: Cremers, Daniel
last_name: Cremers
citation:
ama: 'Vestner M, Lahner Z, Boyarski A, et al. Efficient deformable shape correspondence
via kernel matching. In: 2017 International Conference on 3D Vision (3DV).
IEEE; 2018:517-526. doi:10.1109/3dv.2017.00065'
apa: 'Vestner, M., Lahner, Z., Boyarski, A., Litany, O., Slossberg, R., Remez, T.,
… Cremers, D. (2018). Efficient deformable shape correspondence via kernel matching.
In 2017 International Conference on 3D Vision (3DV) (pp. 517–526). Qingdao,
China: IEEE. https://doi.org/10.1109/3dv.2017.00065'
chicago: Vestner, Matthias, Zorah Lahner, Amit Boyarski, Or Litany, Ron Slossberg,
Tal Remez, Emanuele Rodola, et al. “Efficient Deformable Shape Correspondence
via Kernel Matching.” In 2017 International Conference on 3D Vision (3DV),
517–26. IEEE, 2018. https://doi.org/10.1109/3dv.2017.00065.
ieee: M. Vestner et al., “Efficient deformable shape correspondence via kernel
matching,” in 2017 International Conference on 3D Vision (3DV), Qingdao,
China, 2018, pp. 517–526.
ista: Vestner M, Lahner Z, Boyarski A, Litany O, Slossberg R, Remez T, Rodola E,
Bronstein AM, Bronstein M, Kimmel R, Cremers D. 2018. Efficient deformable shape
correspondence via kernel matching. 2017 International Conference on 3D Vision
(3DV). 7th IEEE International Conference on 3D Vision, 517–526.
mla: Vestner, Matthias, et al. “Efficient Deformable Shape Correspondence via Kernel
Matching.” 2017 International Conference on 3D Vision (3DV), IEEE, 2018,
pp. 517–26, doi:10.1109/3dv.2017.00065.
short: M. Vestner, Z. Lahner, A. Boyarski, O. Litany, R. Slossberg, T. Remez, E.
Rodola, A.M. Bronstein, M. Bronstein, R. Kimmel, D. Cremers, in:, 2017 International
Conference on 3D Vision (3DV), IEEE, 2018, pp. 517–526.
conference:
end_date: 2017-10-12
location: Qingdao, China
name: 7th IEEE International Conference on 3D Vision
start_date: 2017-10-10
date_created: 2024-10-09T07:44:28Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2024-12-05T14:21:33Z
day: '07'
doi: 10.1109/3dv.2017.00065
extern: '1'
external_id:
arxiv:
- '1707.08991'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1707.08991
month: '06'
oa: 1
oa_version: Preprint
page: 517 - 526
publication: 2017 International Conference on 3D Vision (3DV)
publication_identifier:
isbn:
- '9781538626115'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient deformable shape correspondence via kernel matching
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
DOAJ_listed: '1'
_id: '18277'
abstract:
- lang: eng
text: Proper DNA damage repair is one of the most vital and fundamental functions
of every cell. Several different repair mechanisms exist to deal with various
types of DNA damage, in various stages of the cell cycle and under different conditions.
Homologous recombination is one of the most important repair mechanisms in all
organisms. Srs2, a regulator of homologous recombination, is a DNA helicase involved
in DNA repair, cell cycle progression and genome integrity. Srs2 can remove Rad51
from ssDNA, and is thought to inhibit unscheduled recombination. However, Srs2
has to be precisely regulated, as failure to do so is toxic and can lead to cell
death. We noticed that a very slight elevation of the levels of Srs2 (by addition
of a single extra copy of the SRS2 gene) leads to hyper-sensitivity of yeast cells
to methyl methanesulfonate (MMS, a DNA damaging agent). This effect is seen in
haploid, but not in diploid, cells. We analyzed the mechanism that controls haploid/diploid
sensitivity and arrived to the conclusion that the sensitivity requires the activity
of RAD59 and RDH54, whose expression in diploid cells is repressed. We carried
out a mutational analysis of Srs2 to determine the regions of the protein required
for the sensitization to genotoxins. Interestingly, Srs2 needs the HR machinery
and its helicase activity for its toxicity, but does not need to dismantle Rad51.
Our work underscores the tight regulation that is required on the levels of Srs2
activity, and the fact that Srs2 helicase activity plays a more central role in
DNA repair than the ability of Srs2 to dismantle Rad51 filaments.
article_processing_charge: No
author:
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Shay
full_name: Bramson, Shay
last_name: Bramson
- first_name: Keren
full_name: Shemesh, Keren
last_name: Shemesh
- first_name: Batia
full_name: Liefshitz, Batia
last_name: Liefshitz
- first_name: Martin
full_name: Kupiec, Martin
last_name: Kupiec
citation:
ama: 'Bronstein AM, Bramson S, Shemesh K, Liefshitz B, Kupiec M. Tight regulation
of Srs2 helicase activity is crucial for proper functioning of DNA Repair mechanisms.
G3: Genes, Genomes, Genetics . 2018;8(5):1615-1626. doi:10.1534/g3.118.200181'
apa: 'Bronstein, A. M., Bramson, S., Shemesh, K., Liefshitz, B., & Kupiec, M.
(2018). Tight regulation of Srs2 helicase activity is crucial for proper functioning
of DNA Repair mechanisms. G3: Genes, Genomes, Genetics . Oxford University
Press (OUP). https://doi.org/10.1534/g3.118.200181'
chicago: 'Bronstein, Alex M., Shay Bramson, Keren Shemesh, Batia Liefshitz, and
Martin Kupiec. “Tight Regulation of Srs2 Helicase Activity Is Crucial for Proper
Functioning of DNA Repair Mechanisms.” G3: Genes, Genomes, Genetics . Oxford
University Press (OUP), 2018. https://doi.org/10.1534/g3.118.200181.'
ieee: 'A. M. Bronstein, S. Bramson, K. Shemesh, B. Liefshitz, and M. Kupiec, “Tight
regulation of Srs2 helicase activity is crucial for proper functioning of DNA
Repair mechanisms,” G3: Genes, Genomes, Genetics , vol. 8, no. 5. Oxford
University Press (OUP), pp. 1615–1626, 2018.'
ista: 'Bronstein AM, Bramson S, Shemesh K, Liefshitz B, Kupiec M. 2018. Tight regulation
of Srs2 helicase activity is crucial for proper functioning of DNA Repair mechanisms.
G3: Genes, Genomes, Genetics . 8(5), 1615–1626.'
mla: 'Bronstein, Alex M., et al. “Tight Regulation of Srs2 Helicase Activity Is
Crucial for Proper Functioning of DNA Repair Mechanisms.” G3: Genes, Genomes,
Genetics , vol. 8, no. 5, Oxford University Press (OUP), 2018, pp. 1615–26,
doi:10.1534/g3.118.200181.'
short: 'A.M. Bronstein, S. Bramson, K. Shemesh, B. Liefshitz, M. Kupiec, G3: Genes,
Genomes, Genetics 8 (2018) 1615–1626.'
date_created: 2024-10-09T07:44:48Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2024-12-19T16:00:24Z
day: '01'
doi: 10.1534/g3.118.200181
extern: '1'
intvolume: ' 8'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/g3.118.200181
month: '05'
oa: 1
oa_version: Published Version
page: 1615-1626
publication: 'G3: Genes, Genomes, Genetics '
publication_identifier:
eissn:
- 2160-1836
publication_status: published
publisher: Oxford University Press (OUP)
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tight regulation of Srs2 helicase activity is crucial for proper functioning
of DNA Repair mechanisms
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2018'
...