---
_id: '6733'
abstract:
- lang: eng
text: 'The question whether RM codes are capacity-achieving is a long-standing open
problem in coding theory that was recently answered in the affirmative for transmission
over erasure channels [1], [2]. Remarkably, the proof does not rely on specific
properties of RM codes, apart from their symmetry. Indeed, the main technical
result consists in showing that any sequence of linear codes, with doubly-transitive
permutation groups, achieves capacity on the memoryless erasure channel under
bit-MAP decoding. Thus, a natural question is what happens under block-MAP decoding.
In [1], [2], by exploiting further symmetries of the code, the bit-MAP threshold
was shown to be sharp enough so that the block erasure probability also converges
to 0. However, this technique relies heavily on the fact that the transmission
is over an erasure channel. We present an alternative approach to strengthen results
regarding the bit-MAP threshold to block-MAP thresholds. This approach is based
on a careful analysis of the weight distribution of RM codes. In particular, the
flavor of the main result is the following: assume that the bit-MAP error probability
decays as N -δ , for some δ > 0. Then, the block-MAP error probability also converges
to 0. This technique applies to transmission over any binary memoryless symmetric
channel. Thus, it can be thought of as a first step in extending the proof that
RM codes are capacity-achieving to the general case.'
arxiv: 1
author:
- first_name: Shrinivas
full_name: Kudekar, Shrinivas
last_name: Kudekar
- first_name: Santhosh
full_name: Kumar, Santhosh
last_name: Kumar
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Henry D.
full_name: Pfister, Henry D.
last_name: Pfister
- first_name: Rudiger
full_name: Urbankez, Rudiger
last_name: Urbankez
citation:
ama: 'Kudekar S, Kumar S, Mondelli M, Pfister HD, Urbankez R. Comparing the bit-MAP
and block-MAP decoding thresholds of Reed-Muller codes on BMS channels. In: 2016
IEEE International Symposium on Information Theory . IEEE; 2016:1755-1759.
doi:10.1109/isit.2016.7541600'
apa: 'Kudekar, S., Kumar, S., Mondelli, M., Pfister, H. D., & Urbankez, R. (2016).
Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on
BMS channels. In 2016 IEEE International Symposium on Information Theory
(pp. 1755–1759). Barcelona, Spain: IEEE. https://doi.org/10.1109/isit.2016.7541600'
chicago: Kudekar, Shrinivas, Santhosh Kumar, Marco Mondelli, Henry D. Pfister, and
Rudiger Urbankez. “Comparing the Bit-MAP and Block-MAP Decoding Thresholds of
Reed-Muller Codes on BMS Channels.” In 2016 IEEE International Symposium on
Information Theory , 1755–59. IEEE, 2016. https://doi.org/10.1109/isit.2016.7541600.
ieee: S. Kudekar, S. Kumar, M. Mondelli, H. D. Pfister, and R. Urbankez, “Comparing
the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels,”
in 2016 IEEE International Symposium on Information Theory , Barcelona,
Spain, 2016, pp. 1755–1759.
ista: 'Kudekar S, Kumar S, Mondelli M, Pfister HD, Urbankez R. 2016. Comparing the
bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels.
2016 IEEE International Symposium on Information Theory . ISIT: International
Symposium on Information Theory, 1755–1759.'
mla: Kudekar, Shrinivas, et al. “Comparing the Bit-MAP and Block-MAP Decoding Thresholds
of Reed-Muller Codes on BMS Channels.” 2016 IEEE International Symposium on
Information Theory , IEEE, 2016, pp. 1755–59, doi:10.1109/isit.2016.7541600.
short: S. Kudekar, S. Kumar, M. Mondelli, H.D. Pfister, R. Urbankez, in:, 2016 IEEE
International Symposium on Information Theory , IEEE, 2016, pp. 1755–1759.
conference:
end_date: 2016-07-15
location: Barcelona, Spain
name: 'ISIT: International Symposium on Information Theory'
start_date: 2016-07-10
date_created: 2019-07-31T06:36:16Z
date_published: 2016-08-11T00:00:00Z
date_updated: 2021-01-12T08:08:44Z
day: '11'
doi: 10.1109/isit.2016.7541600
extern: '1'
external_id:
arxiv:
- '1601.06048'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.06048
month: '08'
oa: 1
oa_version: Preprint
page: 1755-1759
publication: '2016 IEEE International Symposium on Information Theory '
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes
on BMS channels
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '6770'
abstract:
- lang: eng
text: "We describe a new method to compare the bit-MAP and block-MAP decoding thresholds
of Reed-Muller (RM) codes for transmission over a binary memoryless symmetric
channel. The question whether RM codes are capacity-achieving is a long-standing
open problem in coding theory and it has recently been answered in the affirmative
for transmission over\r\nerasure channels. Remarkably, the proof does not rely
on specific properties of RM codes, apart from their symmetry. Indeed, the main
technical result consists in showing that any sequence of linear codes, with doubly-transitive
permutation groups, achieves capacity on the memoryless erasure channel under
bit-MAP decoding. A natural question is what happens under block-MAP decoding.
If the minimum distance of the code family is close to linear (e.g., of order
N/ log(N)), then one can combine an upper bound on the bit-MAP error probability
with a lower bound on the minimum distance to show that the code family is also
capacity-achieving under block-MAP decoding. This strategy is successful for BCH
codes. Unfortunately, the minimum distance of RM codes scales only as √N, which
does not suffice to obtain the desired result. Then, one can exploit further symmetries
of RM codes to show that the bit-MAP threshold is sharp enough so that the block
erasure probability also tends to 0. However, this technique relies heavily on
the fact that the transmission is over an erasure channel.\r\nWe present an alternative
approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds.
This approach is based on a careful analysis of the weight distribution of RM
codes. In particular, the flavor of the main result is the following: assume that
the bit-MAP error probability decays as N−δ, for some δ > 0. Then, the block-MAP\r\nerror
probability also converges to 0. This technique applies to the transmission over
any binary memoryless symmetric channel. Thus, it can be thought of as a first
step in extending the proof that RM codes are capacity-achieving to the general
case."
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Shrinivas
full_name: Kudekar, Shrinivas
last_name: Kudekar
- first_name: Santosh
full_name: Kumar, Santosh
last_name: Kumar
- first_name: Henry D.
full_name: Pfister, Henry D.
last_name: Pfister
- first_name: Eren
full_name: Şaşoğlu, Eren
last_name: Şaşoğlu
- first_name: Rüdiger
full_name: Urbanke, Rüdiger
last_name: Urbanke
citation:
ama: 'Mondelli M, Kudekar S, Kumar S, Pfister HD, Şaşoğlu E, Urbanke R. Reed-Muller
codes: Thresholds and weight distribution. In: 24th International Zurich Seminar
on Communications. ETH Zürich; 2016:50. doi:10.3929/ETHZ-A-010646484'
apa: 'Mondelli, M., Kudekar, S., Kumar, S., Pfister, H. D., Şaşoğlu, E., & Urbanke,
R. (2016). Reed-Muller codes: Thresholds and weight distribution. In 24th International
Zurich Seminar on Communications (p. 50). Zurich, Switzerland: ETH Zürich.
https://doi.org/10.3929/ETHZ-A-010646484'
chicago: 'Mondelli, Marco, Shrinivas Kudekar, Santosh Kumar, Henry D. Pfister, Eren
Şaşoğlu, and Rüdiger Urbanke. “Reed-Muller Codes: Thresholds and Weight Distribution.”
In 24th International Zurich Seminar on Communications, 50. ETH Zürich,
2016. https://doi.org/10.3929/ETHZ-A-010646484.'
ieee: 'M. Mondelli, S. Kudekar, S. Kumar, H. D. Pfister, E. Şaşoğlu, and R. Urbanke,
“Reed-Muller codes: Thresholds and weight distribution,” in 24th International
Zurich Seminar on Communications, Zurich, Switzerland, 2016, p. 50.'
ista: 'Mondelli M, Kudekar S, Kumar S, Pfister HD, Şaşoğlu E, Urbanke R. 2016. Reed-Muller
codes: Thresholds and weight distribution. 24th International Zurich Seminar on
Communications. IZS: International Zurich Seminar on Communications, 50.'
mla: 'Mondelli, Marco, et al. “Reed-Muller Codes: Thresholds and Weight Distribution.”
24th International Zurich Seminar on Communications, ETH Zürich, 2016,
p. 50, doi:10.3929/ETHZ-A-010646484.'
short: M. Mondelli, S. Kudekar, S. Kumar, H.D. Pfister, E. Şaşoğlu, R. Urbanke,
in:, 24th International Zurich Seminar on Communications, ETH Zürich, 2016, p.
50.
conference:
end_date: 2016-03-04
location: Zurich, Switzerland
name: 'IZS: International Zurich Seminar on Communications'
start_date: 2016-03-02
date_created: 2019-08-05T12:43:48Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T08:08:57Z
day: '01'
doi: 10.3929/ETHZ-A-010646484
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: '50'
publication: 24th International Zurich Seminar on Communications
publication_status: published
publisher: ETH Zürich
quality_controlled: '1'
status: public
title: 'Reed-Muller codes: Thresholds and weight distribution'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '100'
abstract:
- lang: eng
text: We introduce a scheme for preparation, manipulation, and read out of Majorana
zero modes in semiconducting wires with mesoscopic superconducting islands. Our
approach synthesizes recent advances in materials growth with tools commonly used
in quantum-dot experiments, including gate control of tunnel barriers and Coulomb
effects, charge sensing, and charge pumping. We outline a sequence of milestones
interpolating between zero-mode detection and quantum computing that includes
(1) detection of fusion rules for non-Abelian anyons using either proximal charge
sensors or pumped current, (2) validation of a prototype topological qubit, and
(3) demonstration of non-Abelian statistics by braiding in a branched geometry.
The first two milestones require only a single wire with two islands, and additionally
enable sensitive measurements of the system\'s excitation gap, quasiparticle poisoning
rates, residual Majorana zero-mode splittings, and topological-qubit coherence
times. These pre-braiding experiments can be adapted to other manipulation and
read out schemes as well.
acknowledgement: We acknowledge support from Microsoft Research, the National Science
Foundation through Grant No. DMR-1341822 (J. A.); the Alfred P. Sloan Foundation
(J. A.); the Caltech Institute for Quantum Information and Matter, an NSF Physics
Frontiers Center with support of the Gordon and Betty Moore Foundation through Grant
No. GBMF1250; the Walter Burke Institute for Theoretical Physics at Caltech; the
NSERC PGSD program (D. A.); the Crafoord Foundation (M. L. and M. H.) and the Swedish
Research Council (M. L.); The Danish National Research Foundation, and the Villum
Foundation (C. M.); The Danish Council for Independent Research/Natural Sciences,
and Danmarks Nationalbank (J. F.). Part of this work was performed at the Aspen
Center for Physics, which is supported by National Science Foundation Grant No.
PHY-1066293 (R. V. M.).
article_number: '031016'
author:
- first_name: David
full_name: Aasen, David
last_name: Aasen
- first_name: Michael
full_name: Hell, Michael
last_name: Hell
- first_name: Ryan
full_name: Mishmash, Ryan
last_name: Mishmash
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Joshua
full_name: Folk, Joshua
last_name: Folk
- first_name: Charles
full_name: Marcs, Charles
last_name: Marcs
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Jason
full_name: Alicea, Jason
last_name: Alicea
citation:
ama: Aasen D, Hell M, Mishmash R, et al. Milestones toward Majorana-based quantum
computing. Physical Review X. 2016;6(3). doi:10.1103/PhysRevX.6.031016
apa: Aasen, D., Hell, M., Mishmash, R., Higginbotham, A. P., Danon, J., Leijnse,
M., … Alicea, J. (2016). Milestones toward Majorana-based quantum computing. Physical
Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.031016
chicago: Aasen, David, Michael Hell, Ryan Mishmash, Andrew P Higginbotham, Jeroen
Danon, Martin Leijnse, Thomas Jespersen, et al. “Milestones toward Majorana-Based
Quantum Computing.” Physical Review X. American Physical Society, 2016.
https://doi.org/10.1103/PhysRevX.6.031016.
ieee: D. Aasen et al., “Milestones toward Majorana-based quantum computing,”
Physical Review X, vol. 6, no. 3. American Physical Society, 2016.
ista: Aasen D, Hell M, Mishmash R, Higginbotham AP, Danon J, Leijnse M, Jespersen
T, Folk J, Marcs C, Flensberg K, Alicea J. 2016. Milestones toward Majorana-based
quantum computing. Physical Review X. 6(3), 031016.
mla: Aasen, David, et al. “Milestones toward Majorana-Based Quantum Computing.”
Physical Review X, vol. 6, no. 3, 031016, American Physical Society, 2016,
doi:10.1103/PhysRevX.6.031016.
short: D. Aasen, M. Hell, R. Mishmash, A.P. Higginbotham, J. Danon, M. Leijnse,
T. Jespersen, J. Folk, C. Marcs, K. Flensberg, J. Alicea, Physical Review X 6
(2016).
date_created: 2018-12-11T11:44:37Z
date_published: 2016-08-03T00:00:00Z
date_updated: 2021-01-12T06:47:33Z
day: '03'
ddc:
- '530'
doi: 10.1103/PhysRevX.6.031016
extern: '1'
file:
- access_level: open_access
content_type: application/pdf
creator: kschuh
date_created: 2019-05-15T14:12:31Z
date_updated: 2019-05-15T14:12:31Z
file_id: '6458'
file_name: 2016_PhysRevX_Aasen.pdf
file_size: 2142676
relation: main_file
success: 1
file_date_updated: 2019-05-15T14:12:31Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '7954'
quality_controlled: '1'
status: public
title: Milestones toward Majorana-based quantum computing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1008'
abstract:
- lang: eng
text: Feedback loops in biological networks, among others, enable differentiation
and cell cycle progression, and increase robustness in signal transduction. In
natural networks, feedback loops are often complex and intertwined, making it
challenging to identify which loops are mainly responsible for an observed behavior.
However, minimal synthetic replicas could allow for such identification. Here,
we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae
to analyze if a transport-mediated positive feedback loop could be a core mechanism
for the switch-like behavior in the regulation of metabolic gene networks such
as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized
the synthetic circuit using deterministic and stochastic mathematical models.
Similar to its natural counterparts, our synthetic system shows bistable and hysteretic
behavior, and the inducer concentration range for bistability as well as the switching
rates between the two stable states depend on the repressor concentration. Our
results indicate that a generic permease–inducer–repressor circuit with a single
feedback loop is sufficient to explain the experimentally observed bistable behavior
of the natural systems. We anticipate that the approach of reimplementing natural
systems with orthogonal parts to identify crucial network components is applicable
to other natural systems such as signaling pathways.
acknowledgement: We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı
́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor
W. Schmidt for provision of and support with the micro fl uidic device, Markus Du
̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using
“ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions,
comments, and support.
author:
- first_name: Robert
full_name: Gnügge, Robert
last_name: Gnügge
- first_name: Lekshmi
full_name: Dharmarajan, Lekshmi
last_name: Dharmarajan
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Jörg
full_name: Stelling, Jörg
last_name: Stelling
citation:
ama: Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor
feedback loop shows bistability. ACS Synthetic Biology. 2016;5(10):1098-1107.
doi:10.1021/acssynbio.6b00013
apa: Gnügge, R., Dharmarajan, L., Lang, M., & Stelling, J. (2016). An orthogonal
permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology.
American Chemical Society. https://doi.org/10.1021/acssynbio.6b00013
chicago: Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An
Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS
Synthetic Biology. American Chemical Society, 2016. https://doi.org/10.1021/acssynbio.6b00013.
ieee: R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor
feedback loop shows bistability,” ACS Synthetic Biology, vol. 5, no. 10.
American Chemical Society, pp. 1098–1107, 2016.
ista: Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor
feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.
mla: Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop
Shows Bistability.” ACS Synthetic Biology, vol. 5, no. 10, American Chemical
Society, 2016, pp. 1098–107, doi:10.1021/acssynbio.6b00013.
short: R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5
(2016) 1098–1107.
date_created: 2018-12-11T11:49:40Z
date_published: 2016-05-05T00:00:00Z
date_updated: 2021-01-12T06:47:37Z
day: '05'
department:
- _id: CaGu
doi: 10.1021/acssynbio.6b00013
intvolume: ' 5'
issue: '10'
language:
- iso: eng
month: '05'
oa_version: None
page: 1098 - 1107
publication: ACS Synthetic Biology
publication_status: published
publisher: American Chemical Society
publist_id: '6390'
quality_controlled: '1'
status: public
title: An orthogonal permease–inducer–repressor feedback loop shows bistability
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2016'
...
---
_id: '101'
abstract:
- lang: eng
text: Majorana zero modes are quasiparticle excitations in condensed matter systems
that have been proposed as building blocks of fault-tolerant quantum computers.
They are expected to exhibit non-Abelian particle statistics, in contrast to the
usual statistics of fermions and bosons, enabling quantum operations to be performed
by braiding isolated modes around one another. Quantum braiding operations are
topologically protected insofar as these modes are pinned near zero energy, with
the departure from zero expected to be exponentially small as the modes become
spatially separated. Following theoretical proposals, several experiments have
identified signatures of Majorana modes in nanowires with proximity-induced superconductivity
and atomic chains, with small amounts of mode splitting potentially explained
by hybridization of Majorana modes. Here, we use Coulomb-blockade spectroscopy
in an InAs nanowire segment with epitaxial aluminium, which forms a proximity-induced
superconducting Coulomb island (a â ∼ Majorana islandâ (tm)) that is isolated
from normal-metal leads by tunnel barriers, to measure the splitting of near-zero-energy
Majorana modes. We observe exponential suppression of energy splitting with increasing
wire length. For short devices of a few hundred nanometres, sub-gap state energies
oscillate as the magnetic field is varied, as is expected for hybridized Majorana
modes. Splitting decreases by a factor of about ten for each half a micrometre
of increased wire length. For devices longer than about one micrometre, transport
in strong magnetic fields occurs through a zero-energy state that is energetically
isolated from a continuum, yielding uniformly spaced Coulomb-blockade conductance
peaks, consistent with teleportation via Majorana modes. Our results help to explain
the trivial-to-topological transition in finite systems and to quantify the scaling
of topological protection with end-mode separation.
acknowledgement: This research was supported by Microsoft Project Q, the Danish National
Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation and the European
Commission. C.M.M. acknowledges support from the Villum Foundation.
arxiv: 1
author:
- first_name: S M
full_name: Albrecht, S M
last_name: Albrecht
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Morten
full_name: Madsen, Morten
last_name: Madsen
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Jesper
full_name: Nygård, Jesper
last_name: Nygård
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Albrecht SM, Higginbotham AP, Jespersen T, et al. Exponential protection of
zero modes in Majorana islands. Nature. 2016;531(7593):206-209. doi:10.1038/nature17162
apa: Albrecht, S. M., Higginbotham, A. P., Jespersen, T., Madsen, M., Kuemmeth,
F., Nygård, J., … Marcus, C. (2016). Exponential protection of zero modes in Majorana
islands. Nature. Nature Publishing Group. https://doi.org/10.1038/nature17162
chicago: Albrecht, S M, Andrew P Higginbotham, Thomas Jespersen, Morten Madsen,
Ferdinand Kuemmeth, Jesper Nygård, Peter Krogstrup, and Charles Marcus. “Exponential
Protection of Zero Modes in Majorana Islands.” Nature. Nature Publishing
Group, 2016. https://doi.org/10.1038/nature17162.
ieee: S. M. Albrecht et al., “Exponential protection of zero modes in Majorana
islands,” Nature, vol. 531, no. 7593. Nature Publishing Group, pp. 206–209,
2016.
ista: Albrecht SM, Higginbotham AP, Jespersen T, Madsen M, Kuemmeth F, Nygård J,
Krogstrup P, Marcus C. 2016. Exponential protection of zero modes in Majorana
islands. Nature. 531(7593), 206–209.
mla: Albrecht, S. M., et al. “Exponential Protection of Zero Modes in Majorana Islands.”
Nature, vol. 531, no. 7593, Nature Publishing Group, 2016, pp. 206–09,
doi:10.1038/nature17162.
short: S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J.
Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.
date_created: 2018-12-11T11:44:38Z
date_published: 2016-03-10T00:00:00Z
date_updated: 2021-01-12T06:47:37Z
day: '10'
doi: 10.1038/nature17162
extern: '1'
external_id:
arxiv:
- '1603.03217'
intvolume: ' 531'
issue: '7593'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.03217
month: '03'
oa: 1
oa_version: Submitted Version
page: 206 - 209
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7953'
quality_controlled: '1'
status: public
title: Exponential protection of zero modes in Majorana islands
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 531
year: '2016'
...
---
_id: '102'
abstract:
- lang: eng
text: 'Recent experiments have produced mounting evidence of Majorana zero modes
in nanowire-superconductor hybrids. Signatures of an expected topological phase
transition accompanying the onset of these modes nevertheless remain elusive.
We investigate a fundamental question concerning this issue: Do well-formed Majorana
modes necessarily entail a sharp phase transition in these setups? Assuming reasonable
parameters, we argue that finite-size effects can dramatically smooth this putative
transition into a crossover, even in systems large enough to support well-localized
Majorana modes. We propose overcoming such finite-size effects by examining the
behavior of low-lying excited states through tunneling spectroscopy. In particular,
the excited-state energies exhibit characteristic field and density dependence,
and scaling with system size, that expose an approaching topological phase transition.
We suggest several experiments for extracting the predicted behavior. As a useful
byproduct, the protocols also allow one to measure the wire''s spin-orbit coupling
directly in its superconducting environment.'
article_number: '245404'
arxiv: 1
author:
- first_name: Ryan
full_name: Mishmash, Ryan
last_name: Mishmash
- first_name: David
full_name: Aasen, David
last_name: Aasen
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Jason
full_name: Alicea, Jason
last_name: Alicea
citation:
ama: Mishmash R, Aasen D, Higginbotham AP, Alicea J. Approaching a topological phase
transition in Majorana nanowires. Physical Review B. 2016;93(24). doi:10.1103/PhysRevB.93.245404
apa: Mishmash, R., Aasen, D., Higginbotham, A. P., & Alicea, J. (2016). Approaching
a topological phase transition in Majorana nanowires. Physical Review B.
American Physical Society. https://doi.org/10.1103/PhysRevB.93.245404
chicago: Mishmash, Ryan, David Aasen, Andrew P Higginbotham, and Jason Alicea. “Approaching
a Topological Phase Transition in Majorana Nanowires.” Physical Review B.
American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.245404.
ieee: R. Mishmash, D. Aasen, A. P. Higginbotham, and J. Alicea, “Approaching a topological
phase transition in Majorana nanowires,” Physical Review B, vol. 93, no.
24. American Physical Society, 2016.
ista: Mishmash R, Aasen D, Higginbotham AP, Alicea J. 2016. Approaching a topological
phase transition in Majorana nanowires. Physical Review B. 93(24), 245404.
mla: Mishmash, Ryan, et al. “Approaching a Topological Phase Transition in Majorana
Nanowires.” Physical Review B, vol. 93, no. 24, 245404, American Physical
Society, 2016, doi:10.1103/PhysRevB.93.245404.
short: R. Mishmash, D. Aasen, A.P. Higginbotham, J. Alicea, Physical Review B 93
(2016).
date_created: 2018-12-11T11:44:38Z
date_published: 2016-06-08T00:00:00Z
date_updated: 2021-01-12T06:47:42Z
day: '08'
doi: 10.1103/PhysRevB.93.245404
extern: '1'
external_id:
arxiv:
- '1601.07908'
intvolume: ' 93'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.07908
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '7952'
quality_controlled: '1'
status: public
title: Approaching a topological phase transition in Majorana nanowires
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '10376'
abstract:
- lang: eng
text: Nucleation processes are at the heart of a large number of phenomena, from
cloud formation to protein crystallization. A recently emerging area where nucleation
is highly relevant is the initiation of filamentous protein self-assembly, a process
that has broad implications in many research areas ranging from medicine to nanotechnology.
As such, spontaneous nucleation of protein fibrils has received much attention
in recent years with many theoretical and experimental studies focusing on the
underlying physical principles. In this paper we make a step forward in this direction
and explore the early time behaviour of filamentous protein growth in the context
of nucleation theory. We first provide an overview of the thermodynamics and kinetics
of spontaneous nucleation of protein filaments in the presence of one relevant
degree of freedom, namely the cluster size. In this case, we review how key kinetic
observables, such as the reaction order of spontaneous nucleation, are directly
related to the physical size of the critical nucleus. We then focus on the increasingly
prominent case of filament nucleation that includes a conformational conversion
of the nucleating building-block as an additional slow step in the nucleation
process. Using computer simulations, we study the concentration dependence of
the nucleation rate. We find that, under these circumstances, the reaction order
of spontaneous nucleation with respect to the free monomer does no longer relate
to the overall physical size of the nucleating aggregate but rather to the portion
of the aggregate that actively participates in the conformational conversion.
Our results thus provide a novel interpretation of the common kinetic descriptors
of protein filament formation, including the reaction order of the nucleation
step or the scaling exponent of lag times, and put into perspective current theoretical
descriptions of protein aggregation.
acknowledgement: We acknowledge support from the Human Frontier Science Program and
Emmanuel College (A.Š.), St John’s and Peterhouse Colleges (T.C.T.M.), the Swiss
National Science Foundation (T.C.T.M.), the Biotechnology and Biological Sciences
Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.),
the European Research Council (T.C.T.M., T.P.J.K., and D.F.), and the Engineering
and Physical Sciences Research Council (D.F.).
article_number: '211926'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Alessio
full_name: Zaccone, Alessio
last_name: Zaccone
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous
filament nucleation via oligomers: Insights from theory and simulation. The
Journal of Chemical Physics. 2016;145(21). doi:10.1063/1.4965040'
apa: 'Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., & Frenkel,
D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights
from theory and simulation. The Journal of Chemical Physics. American Institute
of Physics. https://doi.org/10.1063/1.4965040'
chicago: 'Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles,
and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics.
American Institute of Physics, 2016. https://doi.org/10.1063/1.4965040.'
ieee: 'A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel,
“Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation,” The Journal of Chemical Physics, vol. 145, no. 21. American
Institute of Physics, 2016.'
ista: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics
of spontaneous filament nucleation via oligomers: Insights from theory and simulation.
The Journal of Chemical Physics. 145(21), 211926.'
mla: 'Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics,
vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:10.1063/1.4965040.'
short: A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal
of Chemical Physics 145 (2016).
date_created: 2021-11-29T10:01:57Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-11-29T10:33:11Z
day: '01'
doi: 10.1063/1.4965040
extern: '1'
external_id:
arxiv:
- '1610.02320'
pmid:
- '28799382'
intvolume: ' 145'
issue: '21'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02320
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 145
year: '2016'
...
---
_id: '10377'
abstract:
- lang: eng
text: The interplay of membrane proteins is vital for many biological processes,
such as cellular transport, cell division, and signal transduction between nerve
cells. Theoretical considerations have led to the idea that the membrane itself
mediates protein self-organization in these processes through minimization of
membrane curvature energy. Here, we present a combined experimental and numerical
study in which we quantify these interactions directly for the first time. In
our experimental model system we control the deformation of a lipid membrane by
adhering colloidal particles. Using confocal microscopy, we establish that these
membrane deformations cause an attractive interaction force leading to reversible
binding. The attraction extends over 2.5 times the particle diameter and has a
strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo
simulations of the system are in excellent agreement with the experimental results
and prove that the measured interaction is independent of length scale. Our combined
experimental and numerical results reveal membrane curvature as a common physical
origin for interactions between any membrane-deforming objects, from nanometre-sized
proteins to micrometre-sized particles.
acknowledgement: This work was supported by the Netherlands Organisation for Scientific
Research (NWO/OCW), as part of the Frontiers of Nanoscience program and VENI grant
680-47-431. We thank Jeroen Appel and Wim Pomp for advice on the protocol design
and Marcel Winter and Ruben Verweij for experimental support.
article_number: '32825'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Casper
full_name: van der Wel, Casper
last_name: van der Wel
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Doris
full_name: Heinrich, Doris
last_name: Heinrich
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated
attraction between curvature inducing objects. Scientific Reports. 2016;6(1).
doi:10.1038/srep32825
apa: van der Wel, C., Vahid, A., Šarić, A., Idema, T., Heinrich, D., & Kraft,
D. J. (2016). Lipid membrane-mediated attraction between curvature inducing objects.
Scientific Reports. Springer Nature. https://doi.org/10.1038/srep32825
chicago: Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich,
and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing
Objects.” Scientific Reports. Springer Nature, 2016. https://doi.org/10.1038/srep32825.
ieee: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft,
“Lipid membrane-mediated attraction between curvature inducing objects,” Scientific
Reports, vol. 6, no. 1. Springer Nature, 2016.
ista: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. 2016. Lipid
membrane-mediated attraction between curvature inducing objects. Scientific Reports.
6(1), 32825.
mla: van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature
Inducing Objects.” Scientific Reports, vol. 6, no. 1, 32825, Springer Nature,
2016, doi:10.1038/srep32825.
short: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific
Reports 6 (2016).
date_created: 2021-11-29T10:34:08Z
date_published: 2016-09-13T00:00:00Z
date_updated: 2021-11-29T11:08:15Z
day: '13'
ddc:
- '540'
doi: 10.1038/srep32825
extern: '1'
external_id:
arxiv:
- '1603.04644'
pmid:
- '27618764'
file:
- access_level: open_access
checksum: d6cf16dd511e15726b001e7cc287cf1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T10:50:00Z
date_updated: 2021-11-29T10:50:00Z
file_id: '10379'
file_name: 2016_SciRep_vanderWel.pdf
file_size: 1598289
relation: main_file
success: 1
file_date_updated: 2021-11-29T10:50:00Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.nature.com/articles/srep32825
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/srep37382
scopus_import: '1'
status: public
title: Lipid membrane-mediated attraction between curvature inducing objects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2016'
...
---
_id: '10378'
abstract:
- lang: eng
text: The ability of biological molecules to replicate themselves is the foundation
of life, requiring a complex cellular machinery. However, a range of aberrant
processes involve the self-replication of pathological protein structures without
any additional assistance. One example is the autocatalytic generation of pathological
protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders.
Here, we use computer simulations to identify the necessary requirements for the
self-replication of fibrillar assemblies of proteins. We establish that a key
physical determinant for this process is the affinity of proteins for the surfaces
of fibrils. We find that self-replication can take place only in a very narrow
regime of inter-protein interactions, implying a high level of sensitivity to
system parameters and experimental conditions. We then compare our theoretical
predictions with kinetic and biosensor measurements of fibrils formed from the
Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative
connection between the kinetics of self-replication and the surface coverage of
fibrils by monomeric proteins. These findings reveal the fundamental physical
requirements for the formation of supra-molecular structures able to replicate
themselves, and shed light on mechanisms in play in the proliferation of protein
aggregates in nature.
acknowledgement: We acknowledge support from the Human Frontier Science Program and
Emmanuel College (A.Š.), the Leverhulme Trust and Magdalene College (A.K.B.), St
John’s College (T.C.T.M.), the Biotechnology and Biological Sciences Research Council
(T.P.J.K. and C.M.D.), the Frances and Augustus Newman Foundation (T.P.J.K.), the
European Research Council (T.P.J.K., T.C.T.M., S.L. and D.F.), and the Engineering
and Physical Sciences Research Council (D.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Buell AK, Meisl G, et al. Physical determinants of the self-replication
of protein fibrils. Nature Physics. 2016;12(9):874-880. doi:10.1038/nphys3828
apa: Šarić, A., Buell, A. K., Meisl, G., Michaels, T. C. T., Dobson, C. M., Linse,
S., … Frenkel, D. (2016). Physical determinants of the self-replication of protein
fibrils. Nature Physics. Springer Nature. https://doi.org/10.1038/nphys3828
chicago: Šarić, Anđela, Alexander K. Buell, Georg Meisl, Thomas C. T. Michaels,
Christopher M. Dobson, Sara Linse, Tuomas P. J. Knowles, and Daan Frenkel. “Physical
Determinants of the Self-Replication of Protein Fibrils.” Nature Physics.
Springer Nature, 2016. https://doi.org/10.1038/nphys3828.
ieee: A. Šarić et al., “Physical determinants of the self-replication of
protein fibrils,” Nature Physics, vol. 12, no. 9. Springer Nature, pp.
874–880, 2016.
ista: Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ,
Frenkel D. 2016. Physical determinants of the self-replication of protein fibrils.
Nature Physics. 12(9), 874–880.
mla: Šarić, Anđela, et al. “Physical Determinants of the Self-Replication of Protein
Fibrils.” Nature Physics, vol. 12, no. 9, Springer Nature, 2016, pp. 874–80,
doi:10.1038/nphys3828.
short: A. Šarić, A.K. Buell, G. Meisl, T.C.T. Michaels, C.M. Dobson, S. Linse, T.P.J.
Knowles, D. Frenkel, Nature Physics 12 (2016) 874–880.
date_created: 2021-11-29T10:36:11Z
date_published: 2016-07-18T00:00:00Z
date_updated: 2021-11-29T11:07:25Z
day: '18'
doi: 10.1038/nphys3828
extern: '1'
external_id:
pmid:
- '31031819'
intvolume: ' 12'
issue: '9'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://discovery.ucl.ac.uk/id/eprint/1517406/
month: '07'
oa: 1
oa_version: Preprint
page: 874-880
pmid: 1
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physical determinants of the self-replication of protein fibrils
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2016'
...
---
_id: '10380'
abstract:
- lang: eng
text: Using non-equilibrium molecular dynamics simulations, it has been recently
demonstrated that water molecules align in response to an imposed temperature
gradient, resulting in an effective electric field. Here, we investigate how thermally
induced fields depend on the underlying treatment of long-ranged interactions.
For the short-ranged Wolf method and Ewald summation, we find the peak strength
of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient
of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower
than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139,
014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show
that this discrepancy can be traced back to the use of an incorrect kernel in
the calculation of the electrostatic field. More seriously, we find that the Wolf
method fails to predict correct molecular orientations, resulting in dipole densities
with opposite sign to those computed using Ewald summation. By considering two
different multipole expansions, we show that, for inhomogeneous polarisations,
the quadrupole contribution can be significant and even outweigh the dipole contribution
to the field. Finally, we propose a more accurate way of calculating the electrostatic
potential and the field. In particular, we show that averaging the microscopic
field analytically to obtain the macroscopic Maxwell field reduces the error bars
by up to an order of magnitude. As a consequence, the simulation times required
to reach a given statistical accuracy decrease by up to two orders of magnitude.
acknowledgement: The authors should like to dedicate this paper to the memory of Simon
de Leeuw, who was a pioneer in the calculation of Coulomb effects in simulations.
P.W. would like to thank the Austrian Academy of Sciences for financial support
through a DOC Fellowship, and for covering the travel expenses for the CECAM workshop
in Zaragoza in May 2015, where these results were first presented. P.W. would also
like to thank Chao Zhang for pointing out the equivalence of the two expressions
for the electric field discussed in Sec. VI D, Michiel Sprik for emphasising the
importance of the quadrupole contribution in experimental studies of interfacial
systems, as well as Aleks Reinhardt and other members of the Frenkel and Dellago
groups for their advice. We further acknowledge support from the Federation of Austrian
Industry (IV) Carinthia (P.W.), the University of Zagreb and Erasmus SMP (D. Fijan),
the Human Frontier Science Program and Emmanuel College (A.Š.), the Austrian Science
Fund FWF within the SFB Vicom project F41 (C.D.), and the Engineering and Physical
Sciences Research Council Programme Grant No. EP/I001352/1 (D.F.). Additional data
related to this publication are available at the University of Cambridge data repository
(http://dx.doi.org/10.17863/CAM.118).
article_number: '224102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: P.
full_name: Wirnsberger, P.
last_name: Wirnsberger
- first_name: D.
full_name: Fijan, D.
last_name: Fijan
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: M.
full_name: Neumann, M.
last_name: Neumann
- first_name: C.
full_name: Dellago, C.
last_name: Dellago
- first_name: D.
full_name: Frenkel, D.
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 2016;144(22). doi:10.1063/1.4953036
apa: Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., & Frenkel,
D. (2016). Non-equilibrium simulations of thermally induced electric fields in
water. The Journal of Chemical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4953036
chicago: Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D.
Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in
Water.” The Journal of Chemical Physics. American Institute of Physics,
2016. https://doi.org/10.1063/1.4953036.
ieee: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel,
“Non-equilibrium simulations of thermally induced electric fields in water,” The
Journal of Chemical Physics, vol. 144, no. 22. American Institute of Physics,
2016.
ista: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 144(22), 224102.
mla: Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric
Fields in Water.” The Journal of Chemical Physics, vol. 144, no. 22, 224102,
American Institute of Physics, 2016, doi:10.1063/1.4953036.
short: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The
Journal of Chemical Physics 144 (2016).
date_created: 2021-11-29T11:08:52Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-11-29T13:09:08Z
day: '10'
doi: 10.1063/1.4953036
extern: '1'
external_id:
arxiv:
- '1602.02734'
pmid:
- '27305991'
intvolume: ' 144'
issue: '22'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02734
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium simulations of thermally induced electric fields in water
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 144
year: '2016'
...
---
_id: '10381'
abstract:
- lang: eng
text: We study phase behaviour of lipid-bilayer vesicles functionalised by ligand–receptor
complexes made of synthetic DNA by introducing a modelling framework and a dedicated
experimental platform. In particular, we perform Monte Carlo simulations that
combine a coarse grained description of the lipid bilayer with state of art analytical
models for multivalent ligand–receptor interactions. Using density of state calculations,
we derive the partition function in pairs of vesicles and compute the number of
ligand–receptor bonds as a function of temperature. Numerical results are compared
to microscopy and fluorimetry experiments on large unilamellar vesicles decorated
by DNA linkers carrying complementary overhangs. We find that vesicle aggregation
is suppressed when the total number of linkers falls below a threshold value.
Within the model proposed here, this is due to the higher configurational costs
required to form inter-vesicle bridges as compared to intra-vesicle loops, which
are in turn related to membrane deformability. Our findings and our numerical/experimental
methodologies are applicable to the rational design of liposomes used as functional
materials and drug delivery applications, as well as to study inter-membrane interactions
in living systems, such as cell adhesion.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stephan Jan
full_name: Bachmann, Stephan Jan
last_name: Bachmann
- first_name: Jurij
full_name: Kotar, Jurij
last_name: Kotar
- first_name: Lucia
full_name: Parolini, Lucia
last_name: Parolini
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Pietro
full_name: Cicuta, Pietro
last_name: Cicuta
- first_name: Lorenzo
full_name: Di Michele, Lorenzo
last_name: Di Michele
- first_name: Bortolo Matteo
full_name: Mognetti, Bortolo Matteo
last_name: Mognetti
citation:
ama: Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles
functionalised by mobile DNA linkers. Soft Matter. 2016;12(37):7804-7817.
doi:10.1039/c6sm01515h
apa: Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele,
L., & Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised
by mobile DNA linkers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c6sm01515h
chicago: Bachmann, Stephan Jan, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro
Cicuta, Lorenzo Di Michele, and Bortolo Matteo Mognetti. “Melting Transition in
Lipid Vesicles Functionalised by Mobile DNA Linkers.” Soft Matter. Royal
Society of Chemistry, 2016. https://doi.org/10.1039/c6sm01515h.
ieee: S. J. Bachmann et al., “Melting transition in lipid vesicles functionalised
by mobile DNA linkers,” Soft Matter, vol. 12, no. 37. Royal Society of
Chemistry, pp. 7804–7817, 2016.
ista: Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti
BM. 2016. Melting transition in lipid vesicles functionalised by mobile DNA linkers.
Soft Matter. 12(37), 7804–7817.
mla: Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised
by Mobile DNA Linkers.” Soft Matter, vol. 12, no. 37, Royal Society of
Chemistry, 2016, pp. 7804–17, doi:10.1039/c6sm01515h.
short: S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele,
B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.
date_created: 2021-11-29T11:09:55Z
date_published: 2016-08-19T00:00:00Z
date_updated: 2021-11-29T13:09:00Z
day: '19'
doi: 10.1039/c6sm01515h
extern: '1'
external_id:
arxiv:
- '1608.05788'
pmid:
- '27722701'
intvolume: ' 12'
issue: '37'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05788
month: '08'
oa: 1
oa_version: Preprint
page: 7804-7817
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Melting transition in lipid vesicles functionalised by mobile DNA linkers
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2016'
...
---
_id: '1057'
abstract:
- lang: eng
text: Far-field super-resolution fluorescence microscopy discerns fluorophores residing
closer than the diffraction barrier by briefly transferring them in different
(typically ON and OFF) states before detection. In coordinate-targeted super-resolution
variants, such as stimulated emission depletion (STED) microscopy, this state
difference is created by the intensity minima and maxima of an optical pattern,
causing all fluorophores to assume the off state, for instance, except at the
minima. Although strong spatial confinement of the on state enables high resolution,
it also subjects the fluorophores to excess intensities and state cycles at the
maxima. Here, we address these issues by driving the fluorophores into a second
off state that is inert to the excess light. By using reversibly switchable fluorescent
proteins as labels, our approach reduces bleaching and enhances resolution and
contrast in live-cell STED microscopy. Using two or more transitions to off states
is a useful strategy for augmenting the power of coordinate-targeted super-resolution
microscopy.
acknowledgement: We thank T. Gilat and E. Rothermel (both MPI) for help with preparing
samples, and J. Keller for discussion. J.G.D. acknowledges support by the European
Union through a Marie Curie fellowship PIEF-GA-2011-299283. S.W.H. acknowledges
support by the Körber Foundation.
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Carola
full_name: Gregor, Carola
last_name: Gregor
- first_name: Nicolai
full_name: Urban, Nicolai
last_name: Urban
- first_name: Peter
full_name: Ilgen, Peter
last_name: Ilgen
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Danzl JG, Sidenstein S, Gregor C, et al. Coordinate-targeted fluorescence nanoscopy
with multiple off states. Nature Photonics. 2016;10(2):122-128. doi:10.1038/nphoton.2015.266
apa: Danzl, J. G., Sidenstein, S., Gregor, C., Urban, N., Ilgen, P., Jakobs, S.,
& Hell, S. (2016). Coordinate-targeted fluorescence nanoscopy with multiple
off states. Nature Photonics. Nature Publishing Group. https://doi.org/10.1038/nphoton.2015.266
chicago: Danzl, Johann G, Sven Sidenstein, Carola Gregor, Nicolai Urban, Peter Ilgen,
Stefan Jakobs, and Stefan Hell. “Coordinate-Targeted Fluorescence Nanoscopy with
Multiple off States.” Nature Photonics. Nature Publishing Group, 2016.
https://doi.org/10.1038/nphoton.2015.266.
ieee: J. G. Danzl et al., “Coordinate-targeted fluorescence nanoscopy with
multiple off states,” Nature Photonics, vol. 10, no. 2. Nature Publishing
Group, pp. 122–128, 2016.
ista: Danzl JG, Sidenstein S, Gregor C, Urban N, Ilgen P, Jakobs S, Hell S. 2016.
Coordinate-targeted fluorescence nanoscopy with multiple off states. Nature Photonics.
10(2), 122–128.
mla: Danzl, Johann G., et al. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple
off States.” Nature Photonics, vol. 10, no. 2, Nature Publishing Group,
2016, pp. 122–28, doi:10.1038/nphoton.2015.266.
short: J.G. Danzl, S. Sidenstein, C. Gregor, N. Urban, P. Ilgen, S. Jakobs, S. Hell,
Nature Photonics 10 (2016) 122–128.
date_created: 2018-12-11T11:49:55Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:47:58Z
day: '01'
doi: 10.1038/nphoton.2015.266
extern: '1'
intvolume: ' 10'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 122 - 128
publication: Nature Photonics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6331'
status: public
title: Coordinate-targeted fluorescence nanoscopy with multiple off states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2016'
...
---
_id: '1059'
abstract:
- lang: eng
text: A range of bright and photostable rhodamines and carbopyronines with absorption
maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling
of cytoskeletal filaments using HaloTag technology followed by staining with 1
μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters,
fluorogenic behavior, and structure-property relationships of the new dyes are
discussed. Light microscopy with stimulated emission depletion (STED) provided
one- and two-color images of living cells with an optical resolution of 40-60
nm.
acknowledgement: We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka,
Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC,
Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC),
Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare
Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS
spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring
fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to
a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium
für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für
Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283).
article_processing_charge: No
author:
- first_name: Alexey
full_name: Butkevich, Alexey
last_name: Butkevich
- first_name: Gyuzel
full_name: Mitronova, Gyuzel
last_name: Mitronova
- first_name: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Jessica
full_name: Klocke, Jessica
last_name: Klocke
- first_name: Dirk
full_name: Kamin, Dirk
last_name: Kamin
- first_name: Dirk
full_name: Meineke, Dirk
last_name: Meineke
- first_name: Elisa
full_name: D'Este, Elisa
last_name: D'Este
- first_name: Philip
full_name: Kraemer, Philip
last_name: Kraemer
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Vladimir
full_name: Belov, Vladimir
last_name: Belov
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic
carbopyronines for super-resolution STED microscopy in living cells. Angewandte
Chemie - International Edition. 2016;55(10):3290-3294. doi:10.1002/anie.201511018
apa: Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke,
D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for
super-resolution STED microscopy in living cells. Angewandte Chemie - International
Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201511018
chicago: Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk
Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic
Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” Angewandte
Chemie - International Edition. Wiley-Blackwell, 2016. https://doi.org/10.1002/anie.201511018.
ieee: A. Butkevich et al., “Fluorescent rhodamines and fluorogenic carbopyronines
for super-resolution STED microscopy in living cells,” Angewandte Chemie -
International Edition, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.
ista: Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este
E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic
carbopyronines for super-resolution STED microscopy in living cells. Angewandte
Chemie - International Edition. 55(10), 3290–3294.
mla: Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines
for Super-Resolution STED Microscopy in Living Cells.” Angewandte Chemie -
International Edition, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94,
doi:10.1002/anie.201511018.
short: A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke,
E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International
Edition 55 (2016) 3290–3294.
date_created: 2018-12-11T11:49:55Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:47:59Z
day: '01'
doi: 10.1002/anie.201511018
extern: '1'
intvolume: ' 55'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa_version: None
page: 3290 - 3294
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6330'
status: public
title: Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution
STED microscopy in living cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1060'
abstract:
- lang: eng
text: Superresolution fluorescence microscopy of multiple fluorophores still requires
development. Here we present simultaneous three-colour stimulated emission depletion
(STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam
between two or more power levels ("multilevelSTEDv) optimizes resolution
and contrast in all colour channels, which are intrinsically co-aligned and well
separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal
organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified
periodic actin/betaII spectrin lattices along dendrites and spines; however, at
presynaptic and postsynaptic sites, these patterns were found to be absent. Both
our multicolour scheme and the 620 nm STED line should be attractive for routine
STED microscopy applications.
acknowledgement: We acknowledge the assistance of I. Herfort with neuron preparation,
and of J. Bienert and K. Müller with analyses of the dye 540R derivatives. We thank
T. Gilat and E. Rothermel for sample preparation as well as J. Keller, F. Winter
(all MPI-BPC) and C.A. Wurm (Abberior Instruments) for helpful discussion, and S.J.
Sahl (MPI-BPC) for a critical reading of the manuscript.
article_processing_charge: No
author:
- first_name: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Elisa
full_name: D'Este, Elisa
last_name: D'Este
- first_name: Marvin
full_name: Böhm, Marvin
last_name: Böhm
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Vladimir
full_name: Belov, Vladimir
last_name: Belov
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. Multicolour multilevel
STED nanoscopy of actin/spectrin organization at synapses. Scientific Reports.
2016;6:1-8. doi:10.1038/srep26725
apa: Sidenstein, S., D’Este, E., Böhm, M., Danzl, J. G., Belov, V., & Hell,
S. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organization
at synapses. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep26725
chicago: Sidenstein, Sven, Elisa D’Este, Marvin Böhm, Johann G Danzl, Vladimir Belov,
and Stefan Hell. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization
at Synapses.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep26725.
ieee: S. Sidenstein, E. D’Este, M. Böhm, J. G. Danzl, V. Belov, and S. Hell, “Multicolour
multilevel STED nanoscopy of actin/spectrin organization at synapses,” Scientific
Reports, vol. 6. Nature Publishing Group, pp. 1–8, 2016.
ista: Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. 2016. Multicolour
multilevel STED nanoscopy of actin/spectrin organization at synapses. Scientific
Reports. 6, 1–8.
mla: Sidenstein, Sven, et al. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin
Organization at Synapses.” Scientific Reports, vol. 6, Nature Publishing
Group, 2016, pp. 1–8, doi:10.1038/srep26725.
short: S. Sidenstein, E. D’Este, M. Böhm, J.G. Danzl, V. Belov, S. Hell, Scientific
Reports 6 (2016) 1–8.
date_created: 2018-12-11T11:49:56Z
date_published: 2016-05-25T00:00:00Z
date_updated: 2021-01-12T06:47:59Z
day: '25'
doi: 10.1038/srep26725
extern: '1'
intvolume: ' 6'
language:
- iso: eng
month: '05'
oa_version: None
page: 1 - 8
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6329'
status: public
title: Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1068'
abstract:
- lang: eng
text: 'Games on graphs provide the appropriate framework to study several central
problems in computer science, such as verification and synthesis of reactive systems.
One of the most basic objectives for games on graphs is the liveness (or Büchi)
objective that given a target set of vertices requires that some vertex in the
target set is visited infinitely often. We study generalized Büchi objectives
(i.e., conjunction of liveness objectives), and implications between two generalized
Büchi objectives (known as GR(1) objectives), that arise in numerous applications
in computer-aided verification. We present improved algorithms and conditional
super-linear lower bounds based on widely believed assumptions about the complexity
of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider
graph games with n vertices, m edges, and generalized Büchi objectives with k
conjunctions. First, we present an algorithm with running time O(k*n^2), improving
the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm
is optimal for dense graphs under (A1). Second, we show that the basic algorithm
for the problem is optimal for sparse graphs when the target sets have constant
size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions
in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1
k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time
algorithm for m > n^{1.5}. '
acknowledgement: K. C., M. H., and W. D. are partially supported by the Vienna Science
and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported
by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC
Start grant (279307
alternative_title:
- LIPIcs
article_number: '25'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Conditionally optimal
algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2016. doi:10.4230/LIPIcs.MFCS.2016.25'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2016).
Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented
at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow, Poland:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.25'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika
Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,”
Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.25.
ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Conditionally
optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical
Foundations of Computer Science (SG), Krakow, Poland, 2016, vol. 58.'
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2016. Conditionally
optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations
of Computer Science (SG), LIPIcs, vol. 58, 25.'
mla: Chatterjee, Krishnendu, et al. Conditionally Optimal Algorithms for Generalized
Büchi Games. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPIcs.MFCS.2016.25.
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Krakow, Poland
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2016-08-22
date_created: 2018-12-11T11:49:58Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-06-02T08:53:50Z
day: '01'
ddc:
- '000'
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2016.25
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:02Z
date_updated: 2018-12-12T10:16:02Z
file_id: '5187'
file_name: IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf
file_size: 632786
relation: main_file
file_date_updated: 2018-12-12T10:16:02Z
has_accepted_license: '1'
intvolume: ' 58'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6317'
pubrep_id: '779'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Conditionally optimal algorithms for generalized Büchi Games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2016'
...
---
_id: '1069'
abstract:
- lang: eng
text: "The Continuous Skolem Problem asks whether a real-valued function satisfying
a linear differen-\r\ntial equation has a zero in a given interval of real numbers.
This is a fundamental reachability\r\nproblem for continuous linear dynamical
systems, such as linear hybrid automata and continuous-\r\ntime Markov chains.
Decidability of the problem is currently open – indeed decidability is open\r\neven
for the sub-problem in which a zero is sought in a bounded interval. In this paper
we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture,
a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse
the unbounded problem in terms of the\r\nfrequencies of the differential equation,
that is, the imaginary parts of the characteristic roots.\r\nWe show that the
unbounded problem can be reduced to the bounded problem if there is at most\r\none
rationally linearly independent frequency, or if there are two rationally linearly
independent\r\nfrequencies and all characteristic roots are simple. We complete
the picture by showing that de-\r\ncidability of the unbounded problem in the
case of two (or more) rationally linearly independent\r\nfrequencies would entail
a major new effectiveness result in Diophantine approximation, namely\r\ncomputability
of the Diophantine-approximation types of all real algebraic numbers."
acknowledgement: 'Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN
Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and ERC
Advanced Grant (267989: QUAREM).'
alternative_title:
- LIPIcs
article_number: '100'
author:
- first_name: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
- first_name: Joël
full_name: Ouaknine, Joël
last_name: Ouaknine
- first_name: James
full_name: Worrell, James
last_name: Worrell
citation:
ama: 'Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear
dynamical systems. In: Vol 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik;
2016. doi:10.4230/LIPIcs.ICALP.2016.100'
apa: 'Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the skolem problem
for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata,
Languages and Programming, Rome, Italy: Schloss Dagstuhl- Leibniz-Zentrum fur
Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2016.100'
chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem
Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik, 2016. https://doi.org/10.4230/LIPIcs.ICALP.2016.100.
ieee: 'V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous
linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming,
Rome, Italy, 2016, vol. 55.'
ista: 'Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous
linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs,
vol. 55, 100.'
mla: Chonev, Ventsislav K., et al. On the Skolem Problem for Continuous Linear
Dynamical Systems. Vol. 55, 100, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016, doi:10.4230/LIPIcs.ICALP.2016.100.
short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik, 2016.
conference:
end_date: 2016-07-15
location: Rome, Italy
name: 'ICALP: Automata, Languages and Programming'
start_date: 2016-07-12
date_created: 2018-12-11T11:49:59Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:48:03Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ICALP.2016.100
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:26Z
date_updated: 2018-12-12T10:16:26Z
file_id: '5213'
file_name: IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf
file_size: 521415
relation: main_file
file_date_updated: 2018-12-12T10:16:26Z
has_accepted_license: '1'
intvolume: ' 55'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik
publist_id: '6314'
pubrep_id: '778'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the skolem problem for continuous linear dynamical systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1070'
abstract:
- lang: eng
text: 'We present a logic that extends CTL (Computation Tree Logic) with operators
that express synchronization properties. A property is synchronized in a system
if it holds in all paths of a certain length. The new logic is obtained by using
the same path quantifiers and temporal operators as in CTL, but allowing a different
order of the quantifiers. This small syntactic variation induces a logic that
can express non-regular properties for which known extensions of MSO with equality
of path length are undecidable. We show that our variant of CTL is decidable and
that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We
analogously consider quantifier exchange in extensions of CTL, and we present
operators defined using basic operators of CTL* that express the occurrence of
infinitely many synchronization points. We show that the model-checking problem
remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide
if the Next operator is allowed in the logics, thus the classical bisimulation
quotient can be used for state-space reduction before model checking. '
acknowledgement: "This research was partially supported by Austrian Science Fund (FWF)
NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna
Science and Technology Fund (WWTF) through project ICT15-003, and European project
Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for
their insightful\r\ncomments and suggestions.\r\n"
alternative_title:
- LIPIcs
article_number: '98'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Computation tree logic for synchronization properties.
In: Vol 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ICALP.2016.98'
apa: 'Chatterjee, K., & Doyen, L. (2016). Computation tree logic for synchronization
properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming,
Rome, Italy: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2016.98'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for
Synchronization Properties,” Vol. 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016. https://doi.org/10.4230/LIPIcs.ICALP.2016.98.
ieee: 'K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,”
presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016,
vol. 55.'
ista: 'Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties.
ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. Computation Tree Logic for Synchronization
Properties. Vol. 55, 98, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016, doi:10.4230/LIPIcs.ICALP.2016.98.
short: K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016.
conference:
end_date: 2016-07-15
location: Rome, Italy
name: 'ICALP: Automata, Languages and Programming'
start_date: 2016-07-12
date_created: 2018-12-11T11:49:59Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:48:03Z
day: '01'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ICALP.2016.98
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:52Z
date_updated: 2018-12-12T10:08:52Z
file_id: '4714'
file_name: IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf
file_size: 546133
relation: main_file
file_date_updated: 2018-12-12T10:08:52Z
has_accepted_license: '1'
intvolume: ' 55'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik
publist_id: '6313'
pubrep_id: '812'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computation tree logic for synchronization properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1071'
abstract:
- lang: eng
text: 'We consider data-structures for answering reachability and distance queries
on constant-treewidth graphs with n nodes, on the standard RAM computational model
with wordsize W=Theta(log n). Our first contribution is a data-structure that
after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time;
and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically)
optimal and is faster than DFS/BFS when answering more than a constant number
of single-source queries. The data-structure uses at all times O(n) space. Our
second contribution is a space-time tradeoff data-structure for distance queries.
For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing
time that allows pair queries in O(n^{1-\epsilon} alpha(n)) time, where alpha
is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space.
The input graph G is not considered in the space complexity. '
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant
(279307: Graph Games).'
alternative_title:
- LIPIcs
article_number: '28'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space
time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ESA.2016.28'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs (Vol.
57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark:
Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ESA.2016.28'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant
Treewidth Graphs,” Vol. 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016. https://doi.org/10.4230/LIPIcs.ESA.2016.28.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs,”
presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016,
vol. 57.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs. ESA:
European Symposium on Algorithms, LIPIcs, vol. 57, 28.'
mla: Chatterjee, Krishnendu, et al. Optimal Reachability and a Space Time Tradeoff
for Distance Queries in Constant Treewidth Graphs. Vol. 57, 28, Schloss Dagstuhl-
Leibniz-Zentrum fur Informatik, 2016, doi:10.4230/LIPIcs.ESA.2016.28.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2018-12-11T11:49:59Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T12:01:58Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ESA.2016.28
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:31Z
date_updated: 2018-12-12T10:14:31Z
file_id: '5084'
file_name: IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf
file_size: 579225
relation: main_file
file_date_updated: 2018-12-12T10:14:31Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik
publist_id: '6312'
pubrep_id: '777'
quality_controlled: '1'
related_material:
record:
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Optimal reachability and a space time tradeoff for distance queries in constant
treewidth graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '10746'
abstract:
- lang: eng
text: Vortex states in superconducting (SC) structures, their dynamics and ways
to manipulate them are topics of great interest. We report a new method of magnetic
force microscopy (MFM) that allows the study of vortex states in mesoscopic SC
samples. For the case of a SC ring, which is biased to a half-integer flux quantum,
the flux modulation through the ring caused by the motion of the magnetic tip
drives the ring between two consecutive fluxoid states. The corresponding current
switching in the ring produces strong position-dependent forces on the cantilever.
In the regime where the frequency of the thermally activated jumps between fluxoid
states is close to the frequency of the cantilever, large changes in the cantilever
frequency and dissipation are observed. This effect may be understood as a stochastic
resonance (SR) process. These changes in the cantilever’s mechanical properties
are used to “image” the barrier energies between fluxoid states. Additionally,
SR imaging of the barrier energies are used to study the effect of the locally
applied magnetic field from the MFM tip on the barrier heights. We report the
results of measurements for Al rings. Further, the same imaging technique can
be applied to more sophisticated SC structures such as arrays of Josephson junctions.
alternative_title:
- Bulletin of the American Physical Society
article_number: E25.00007
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Tyler
full_name: Naibert, Tyler
last_name: Naibert
- first_name: Victor
full_name: Chua, Victor
last_name: Chua
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: 'Polshyn H, Naibert T, Chua V, Budakian R. Study of vortex states and dynamics
in mesoscopic superconducting samples with MFM. In: APS March Meeting 2016.
Vol 61. American Physical Society; 2016.'
apa: 'Polshyn, H., Naibert, T., Chua, V., & Budakian, R. (2016). Study of vortex
states and dynamics in mesoscopic superconducting samples with MFM. In APS
March Meeting 2016 (Vol. 61). Baltimore, MD, United States: American Physical
Society.'
chicago: Polshyn, Hryhoriy, Tyler Naibert, Victor Chua, and Raffi Budakian. “Study
of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.”
In APS March Meeting 2016, Vol. 61. American Physical Society, 2016.
ieee: H. Polshyn, T. Naibert, V. Chua, and R. Budakian, “Study of vortex states
and dynamics in mesoscopic superconducting samples with MFM,” in APS March
Meeting 2016, Baltimore, MD, United States, 2016, vol. 61, no. 2.
ista: 'Polshyn H, Naibert T, Chua V, Budakian R. 2016. Study of vortex states and
dynamics in mesoscopic superconducting samples with MFM. APS March Meeting 2016.
APS: American Physical Society, Bulletin of the American Physical Society, vol.
61, E25.00007.'
mla: Polshyn, Hryhoriy, et al. “Study of Vortex States and Dynamics in Mesoscopic
Superconducting Samples with MFM.” APS March Meeting 2016, vol. 61, no.
2, E25.00007, American Physical Society, 2016.
short: H. Polshyn, T. Naibert, V. Chua, R. Budakian, in:, APS March Meeting 2016,
American Physical Society, 2016.
conference:
end_date: 2016-03-18
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2016-03-14
date_created: 2022-02-08T09:55:09Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-02-08T10:44:06Z
day: '01'
extern: '1'
intvolume: ' 61'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR16/Session/E25.7
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2016
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Study of vortex states and dynamics in mesoscopic superconducting samples with
MFM
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 61
year: '2016'
...
---
_id: '10747'
abstract:
- lang: eng
text: Vortex interactions are key to explaining the behavior of many two dimensional
superconducting systems. We report on the development of a technique to locally
probe vortex interactions in a 2D array of Josephson junctions. Scanning a magnetic
tip attached to an ultra-soft cantilever over the array produces changes in the
frequency of the cantilever along certain lines, forming geometric patterns in
the scans. Different tip-surface separations and external magnetic fields produce
a number of different patterns. These patterns correspond to tip locations in
which two configurations of vortices in the lattice have degenerate energies.
By imaging the locations of these degeneracies, information on the local vortex
interactions may be obtained.
alternative_title:
- Bulletin of the American Physical Society
article_number: H25.00006
article_processing_charge: No
author:
- first_name: Tyler
full_name: Naibert, Tyler
last_name: Naibert
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Brian
full_name: Wolin, Brian
last_name: Wolin
- first_name: Malcolm
full_name: Durkin, Malcolm
last_name: Durkin
- first_name: Rita
full_name: Garrido Menacho, Rita
last_name: Garrido Menacho
- first_name: Ian Mondragon
full_name: Shem, Ian Mondragon
last_name: Shem
- first_name: Victor
full_name: Chua, Victor
last_name: Chua
- first_name: Taylor
full_name: Hughes, Taylor
last_name: Hughes
- first_name: Nadya
full_name: Mason, Nadya
last_name: Mason
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: 'Naibert T, Polshyn H, Wolin B, et al. Stochastic resonance magnetic force
microscopy imaging of Josephson arrays. In: APS March Meeting 2016. Vol
61. American Physical Society; 2016.'
apa: 'Naibert, T., Polshyn, H., Wolin, B., Durkin, M., Garrido Menacho, R., Shem,
I. M., … Budakian, R. (2016). Stochastic resonance magnetic force microscopy imaging
of Josephson arrays. In APS March Meeting 2016 (Vol. 61). Baltimore, MD,
United States: American Physical Society.'
chicago: Naibert, Tyler, Hryhoriy Polshyn, Brian Wolin, Malcolm Durkin, Rita Garrido
Menacho, Ian Mondragon Shem, Victor Chua, Taylor Hughes, Nadya Mason, and Raffi
Budakian. “Stochastic Resonance Magnetic Force Microscopy Imaging of Josephson
Arrays.” In APS March Meeting 2016, Vol. 61. American Physical Society,
2016.
ieee: T. Naibert et al., “Stochastic resonance magnetic force microscopy
imaging of Josephson arrays,” in APS March Meeting 2016, Baltimore, MD,
United States, 2016, vol. 61, no. 2.
ista: 'Naibert T, Polshyn H, Wolin B, Durkin M, Garrido Menacho R, Shem IM, Chua
V, Hughes T, Mason N, Budakian R. 2016. Stochastic resonance magnetic force microscopy
imaging of Josephson arrays. APS March Meeting 2016. APS: American Physical Society,
Bulletin of the American Physical Society, vol. 61, H25.00006.'
mla: Naibert, Tyler, et al. “Stochastic Resonance Magnetic Force Microscopy Imaging
of Josephson Arrays.” APS March Meeting 2016, vol. 61, no. 2, H25.00006,
American Physical Society, 2016.
short: T. Naibert, H. Polshyn, B. Wolin, M. Durkin, R. Garrido Menacho, I.M. Shem,
V. Chua, T. Hughes, N. Mason, R. Budakian, in:, APS March Meeting 2016, American
Physical Society, 2016.
conference:
end_date: 2016-03-18
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2016-03-14
date_created: 2022-02-08T10:10:39Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-02-08T10:43:33Z
day: '01'
extern: '1'
intvolume: ' 61'
issue: '2'
language:
- iso: eng
main_file_link:
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url: https://meetings.aps.org/Meeting/MAR16/Session/H25.6
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2016
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Stochastic resonance magnetic force microscopy imaging of Josephson arrays
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 61
year: '2016'
...