---
_id: '6440'
abstract:
- lang: eng
text: In order to guarantee that each method of a data structure updates the logical
state exactly once, al-most all non-blocking implementations employ Compare-And-Swap
(CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods
competing among themselves to update the same variable, the tail or the head,
respectively, leading to high contention and poor scalability. Recent non-blocking
queue implementations try to alleviate high contentionby increasing the number
of contention points, all the while using CAS-based synchronization. Furthermore,
obtaining a wait-free implementation with competition is achieved by additional
synchronization which leads to further degradation of performance.In this paper
we formalize the notion of competitiveness of a synchronizing statement which
can beused as a measure for the scalability of concurrent implementations. We
present a new queue implementation, the Speculative Pairing (SP) queue, which,
as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead
of CAS. We prove that the SP queue is linearizable and lock-free.We also show
that replacing CAS with FAI leads to wait-freedom for dequeue methods without
an adverse effect on performance. In fact, our experiments suggest that the SP
queue can perform and scale better than the state-of-the-art queue implementations.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: Henzinger TA, Payer H, Sezgin A. Replacing Competition with Cooperation
to Achieve Scalable Lock-Free FIFO Queues . IST Austria; 2013. doi:10.15479/AT:IST-2013-124-v1-1
apa: Henzinger, T. A., Payer, H., & Sezgin, A. (2013). Replacing competition
with cooperation to achieve scalable lock-free FIFO queues . IST Austria.
https://doi.org/10.15479/AT:IST-2013-124-v1-1
chicago: Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. Replacing Competition
with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria,
2013. https://doi.org/10.15479/AT:IST-2013-124-v1-1.
ieee: T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation
to achieve scalable lock-free FIFO queues . IST Austria, 2013.
ista: Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation
to achieve scalable lock-free FIFO queues , IST Austria, 23p.
mla: Henzinger, Thomas A., et al. Replacing Competition with Cooperation to Achieve
Scalable Lock-Free FIFO Queues . IST Austria, 2013, doi:10.15479/AT:IST-2013-124-v1-1.
short: T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation
to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013.
date_created: 2019-05-13T14:13:27Z
date_published: 2013-06-13T00:00:00Z
date_updated: 2020-07-14T23:06:19Z
day: '13'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2013-124-v1-1
file:
- access_level: open_access
checksum: a219ba4eada6cd62befed52262ee15d4
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T14:11:39Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6441'
file_name: 2013_TechRep_Henzinger.pdf
file_size: 549684
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '23'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '124'
status: public
title: 'Replacing competition with cooperation to achieve scalable lock-free FIFO
queues '
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '6768'
abstract:
- lang: eng
text: The paper presents an algorithm that applies a stack filter simulating the
Mean Curvature Motion equation via a finite difference scheme.
article_type: original
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Mondelli M. A finite difference scheme for the stack filter simulating the
MCM. Image Processing On Line. 2013;3:68-111. doi:10.5201/ipol.2013.53
apa: Mondelli, M. (2013). A finite difference scheme for the stack filter simulating
the MCM. Image Processing On Line. Image Processing On Line. https://doi.org/10.5201/ipol.2013.53
chicago: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating
the MCM.” Image Processing On Line. Image Processing On Line, 2013. https://doi.org/10.5201/ipol.2013.53.
ieee: M. Mondelli, “A finite difference scheme for the stack filter simulating the
MCM,” Image Processing On Line, vol. 3. Image Processing On Line, pp. 68–111,
2013.
ista: Mondelli M. 2013. A finite difference scheme for the stack filter simulating
the MCM. Image Processing On Line. 3, 68–111.
mla: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating
the MCM.” Image Processing On Line, vol. 3, Image Processing On Line, 2013,
pp. 68–111, doi:10.5201/ipol.2013.53.
short: M. Mondelli, Image Processing On Line 3 (2013) 68–111.
date_created: 2019-08-05T12:30:38Z
date_published: 2013-07-11T00:00:00Z
date_updated: 2021-01-12T08:08:56Z
day: '11'
ddc:
- '510'
doi: 10.5201/ipol.2013.53
extern: '1'
file:
- access_level: open_access
checksum: 83b7d429bc248c6c461229d3504fb139
content_type: application/pdf
creator: dernst
date_created: 2019-08-05T12:33:40Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6769'
file_name: 2013_IPOL_Mondelli.pdf
file_size: 4306158
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 68-111
publication: Image Processing On Line
publication_identifier:
issn:
- 2105-1232
publication_status: published
publisher: Image Processing On Line
quality_controlled: '1'
status: public
title: A finite difference scheme for the stack filter simulating the MCM
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2013'
...
---
_id: '10384'
abstract:
- lang: eng
text: 'Recent studies aimed at investigating artificial analogs of bacterial colonies
have shown that low-density suspensions of self-propelled particles confined in
two dimensions can assemble into finite aggregates that merge and split, but have
a typical size that remains constant (living clusters). In this Letter, we address
the problem of the formation of living clusters and crystals of active particles
in three dimensions. We study two systems: self-propelled particles interacting
via a generic attractive potential and colloids that can move toward each other
as a result of active agents (e.g., by molecular motors). In both cases, fluidlike
“living” clusters form. We explain this general feature in terms of the balance
between active forces and regression to thermodynamic equilibrium. This balance
can be quantified in terms of a dimensionless number that allows us to collapse
the observed clustering behavior onto a universal curve. We also discuss how active
motion affects the kinetics of crystal formation.'
acknowledgement: This work was supported by the ERC Advanced Grant 227758, the National
Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3
of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge
T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support
from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941
ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support
from the Alexander von Humboldt Foundation.
article_number: '245702'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: B. M.
full_name: Mognetti, B. M.
last_name: Mognetti
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: S.
full_name: Angioletti-Uberti, S.
last_name: Angioletti-Uberti
- first_name: A.
full_name: Cacciuto, A.
last_name: Cacciuto
- first_name: C.
full_name: Valeriani, C.
last_name: Valeriani
- first_name: D.
full_name: Frenkel, D.
last_name: Frenkel
citation:
ama: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel
D. Living clusters and crystals from low-density suspensions of active colloids.
Physical Review Letters. 2013;111(24). doi:10.1103/physrevlett.111.245702
apa: Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani,
C., & Frenkel, D. (2013). Living clusters and crystals from low-density suspensions
of active colloids. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.111.245702
chicago: Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of
Active Colloids.” Physical Review Letters. American Physical Society, 2013.
https://doi.org/10.1103/physrevlett.111.245702.
ieee: B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
and D. Frenkel, “Living clusters and crystals from low-density suspensions of
active colloids,” Physical Review Letters, vol. 111, no. 24. American Physical
Society, 2013.
ista: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel
D. 2013. Living clusters and crystals from low-density suspensions of active colloids.
Physical Review Letters. 111(24), 245702.
mla: Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions
of Active Colloids.” Physical Review Letters, vol. 111, no. 24, 245702,
American Physical Society, 2013, doi:10.1103/physrevlett.111.245702.
short: B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
D. Frenkel, Physical Review Letters 111 (2013).
date_created: 2021-11-29T13:29:31Z
date_published: 2013-12-11T00:00:00Z
date_updated: 2021-11-29T14:05:19Z
day: '11'
doi: 10.1103/physrevlett.111.245702
extern: '1'
external_id:
arxiv:
- '1311.4681'
pmid:
- '24483677'
intvolume: ' 111'
issue: '24'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.4681
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Living clusters and crystals from low-density suspensions of active colloids
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2013'
...
---
_id: '10396'
abstract:
- lang: eng
text: Stimfit is a free cross-platform software package for viewing and analyzing
electrophysiological data. It supports most standard file types for cellular neurophysiology
and other biomedical formats. Its analysis algorithms have been used and validated
in several experimental laboratories. Its embedded Python scripting interface
makes Stimfit highly extensible and customizable.
article_number: '000010151520134181'
article_processing_charge: No
article_type: original
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: C.
full_name: Schmidt-Hieber, C.
last_name: Schmidt-Hieber
- first_name: S. J.
full_name: Guzman, S. J.
last_name: Guzman
citation:
ama: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181'
apa: 'Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013).
Stimfit: A fast visualization and analysis environment for cellular neurophysiology.
Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter.
https://doi.org/10.1515/bmt-2013-4181'
chicago: 'Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit:
A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical
Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.'
ieee: 'A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A
fast visualization and analysis environment for cellular neurophysiology,” Biomedical
Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter,
2013.'
ista: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.'
mla: 'Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment
for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik,
vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.'
short: A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering
/ Biomedizinische Technik 58 (2013).
conference:
end_date: 2013-09-21
location: Graz, Austria
name: 'BMT: Biomedizinische Technik '
start_date: 2013-09-19
date_created: 2021-12-01T14:35:35Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-12-02T12:51:12Z
day: '01'
ddc:
- '005'
- '610'
department:
- _id: PeJo
doi: 10.1515/bmt-2013-4181
external_id:
pmid:
- '24042795'
file:
- access_level: open_access
checksum: cdfc5339b530a25d6079f7223f0b1f16
content_type: application/pdf
creator: schloegl
date_created: 2021-12-01T14:38:08Z
date_updated: 2021-12-01T14:38:08Z
file_id: '10397'
file_name: Schloegl_Abstract-BMT2013.pdf
file_size: 149825
relation: main_file
success: 1
file_date_updated: 2021-12-01T14:38:08Z
has_accepted_license: '1'
intvolume: ' 58'
issue: SI-1-Track-G
keyword:
- biomedical engineering
- data analysis
- free software
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Biomedical Engineering / Biomedizinische Technik
publication_identifier:
eissn:
- 1862-278X
issn:
- 0013-5585
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
status: public
title: 'Stimfit: A fast visualization and analysis environment for cellular neurophysiology'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2013'
...
---
_id: '10749'
abstract:
- lang: eng
text: Fluxoid quantization provides a direct means to study phase coherence. In
cuprate superconductors, there have been observations which suggest that phase
coherent superconducting fluctuations may persist at temperatures significantly
above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate
superconducting samples to directly probe phase coherence over a wide range of
temperatures. We present cantilever torque susceptometry measurements of micron
and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique
allowed observation of transitions between different fluxoid states of a single
ring, and the discrete vortex states of micron size disks. The dependence of magnetic
susceptibility on diameter and wall thickness of the ring was investigated. Measurements
were made at different values of the in-plane magnetic field, and over a wide
range of temperatures.
acknowledgement: This work was supported by the Center for Emergent Superconductivity,
an Energy Frontier Research Center funded by the US DOE, Office of Science.
alternative_title:
- Bulletin of the American Physical Society
article_number: N36.00001
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: Raffi
full_name: Budakian, Raffi
last_name: Budakian
- first_name: Genda
full_name: Gu, Genda
last_name: Gu
citation:
ama: 'Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. In: APS March Meeting 2013. Vol 58. American Physical Society;
2013.'
apa: 'Polshyn, H., Budakian, R., & Gu, G. (2013). Cantilever micro-susceptometry
of mesoscopic Bi2212 samples. In APS March Meeting 2013 (Vol. 58). Baltimore,
MD, United States: American Physical Society.'
chicago: Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry
of Mesoscopic Bi2212 Samples.” In APS March Meeting 2013, Vol. 58. American
Physical Society, 2013.
ieee: H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic
Bi2212 samples,” in APS March Meeting 2013, Baltimore, MD, United States,
2013, vol. 58, no. 1.
ista: 'Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin
of the American Physical Society, vol. 58, N36.00001.'
mla: Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212
Samples.” APS March Meeting 2013, vol. 58, no. 1, N36.00001, American Physical
Society, 2013.
short: H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical
Society, 2013.
conference:
end_date: 2013-03-22
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2013-03-18
date_created: 2022-02-08T10:34:29Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2022-02-08T10:48:06Z
day: '01'
extern: '1'
intvolume: ' 58'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR13/Event/186873
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2013
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Cantilever micro-susceptometry of mesoscopic Bi2212 samples
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2013'
...
---
_id: '9459'
abstract:
- lang: eng
text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation
of transposable elements, but the reason for this is unknown. How DDM1 interacts
with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM),
which is thought to mediate plant asymmetric methylation through DRM enzymes,
is also unclear. Here, we show that most asymmetric methylation is facilitated
by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find
that heterochromatic sequences preferentially require DDM1 for DNA methylation
and that this preference depends on linker histone H1. RdDM is instead inhibited
by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together,
DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress
transposition and regulate the methylation and expression of genes. Our results
indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin
to allow stable silencing of transposable elements in cooperation with the RdDM
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Ka
full_name: Thao, Ka
last_name: Thao
- first_name: Stacey L.
full_name: Harmer, Stacey L.
last_name: Harmer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1
allows DNA methyltransferases to access H1-containing heterochromatin. Cell.
2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033
apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L.,
Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.02.033
chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor
Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis
Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing
Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.
ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin,” Cell,
vol. 153, no. 1. Elsevier, pp. 193–205, 2013.
ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer
SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases
to access H1-containing heterochromatin. Cell. 153(1), 193–205.
mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA
Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol.
153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033.
short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K.
Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.
date_created: 2021-06-04T12:23:28Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-12-14T08:25:35Z
day: '28'
department:
- _id: DaZi
doi: 10.1016/j.cell.2013.02.033
extern: '1'
external_id:
pmid:
- '23540698'
intvolume: ' 153'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.02.033
month: '03'
oa: 1
oa_version: Published Version
page: 193-205
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to
access H1-containing heterochromatin
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 153
year: '2013'
...
---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: Pamela C
full_name: Ronald, Pamela C
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...
---
_id: '9520'
abstract:
- lang: eng
text: Plants undergo alternation of generation in which reproductive cells develop
in the plant body ("sporophytic generation") and then differentiate into a multicellular
gamete-forming "gametophytic generation." Different populations of helper cells
assist in this transgenerational journey, with somatic tissues supporting early
development and single nurse cells supporting gametogenesis. New data reveal a
two-way relationship between early reproductive cells and their helpers involving
complex epigenetic and signaling networks determining cell number and fate. Later,
the egg cell plays a central role in specifying accessory cells, whereas in both
gametophytes, companion cells contribute non-cell-autonomously to the epigenetic
landscape of the gamete genomes.
article_processing_charge: No
article_type: review
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Hugh
full_name: Dickinson, Hugh
last_name: Dickinson
citation:
ama: 'Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ
cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014'
apa: 'Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across
generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2013.01.014'
chicago: 'Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across
Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier,
2013. https://doi.org/10.1016/j.devcel.2013.01.014.'
ieee: 'X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations:
Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3.
Elsevier, pp. 215–225, 2013.'
ista: 'Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations:
Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.'
mla: 'Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk
in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25,
doi:10.1016/j.devcel.2013.01.014.'
short: X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.
date_created: 2021-06-08T06:14:50Z
date_published: 2013-02-11T00:00:00Z
date_updated: 2023-05-08T11:00:59Z
day: '11'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.devcel.2013.01.014
extern: '1'
external_id:
pmid:
- '23410937'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2013.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 215-225
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A conversation across generations: Soma-germ cell crosstalk in plants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '9663'
abstract:
- lang: eng
text: 'Molecular dynamics simulations of small Cu nanoparticles using three different
interatomic potentials at rising temperature indicate that small nanoparticles
can undergo solid-solid structural transitions through a direct geometrical conversion
route. The direct geometrical conversion can happen for cuboctahedral nanoparticles,
which turn into an icosahedra shape: one diagonal of the square faces contracts,
and the faces are folded along the diagonal to give rise to two equilateral triangles.
The transition is a kinetic process that cannot be fully explained through an
energetic point of view. It has low activation energy and fast reaction time in
the simulations. The transition mechanism is via the transmission of shear waves
initiated from the particle surface and does not involve dislocation activity.'
article_number: '164314'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H. W.
full_name: Ngan, Alfonso H. W.
last_name: Ngan
citation:
ama: Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper
nanoparticles through direct geometrical conversion. The Journal of Chemical
Physics. 2013;138(16). doi:10.1063/1.4802025
apa: Cheng, B., & Ngan, A. H. W. (2013). Thermally induced solid-solid structural
transition of copper nanoparticles through direct geometrical conversion. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4802025
chicago: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid
Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.”
The Journal of Chemical Physics. AIP Publishing, 2013. https://doi.org/10.1063/1.4802025.
ieee: B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion,” The Journal
of Chemical Physics, vol. 138, no. 16. AIP Publishing, 2013.
ista: Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion. The Journal of
Chemical Physics. 138(16), 164314.
mla: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural
Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The
Journal of Chemical Physics, vol. 138, no. 16, 164314, AIP Publishing, 2013,
doi:10.1063/1.4802025.
short: B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).
date_created: 2021-07-15T09:27:58Z
date_published: 2013-04-28T00:00:00Z
date_updated: 2021-08-09T12:35:34Z
day: '28'
doi: 10.1063/1.4802025
extern: '1'
external_id:
pmid:
- '23635145'
intvolume: ' 138'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pubmed.ncbi.nlm.nih.gov/23635145/
month: '04'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermally induced solid-solid structural transition of copper nanoparticles
through direct geometrical conversion
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 138
year: '2013'
...
---
_id: '970'
abstract:
- lang: eng
text: 'Recently a new high-mobility Dirac material, trilayer graphene, was realized
experimentally. The band structure of ABA-stacked trilayer graphene consists of
a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties
of ABA-stacked trilayer graphene biased by a perpendicular electric field. We
find that the combination of the bias and trigonal warping gives rise to a set
of new Dirac points: In each valley, seven species of Dirac fermions with small
masses of order of a few meV emerge. The positions and masses of the emergent
Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless
at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity
at the neutrality point is expected to show nonmonotonic behavior, becoming of
the order of a few e2/h when some Dirac masses vanish. Further, we analyze the
evolution of the Landau level spectrum as a function of bias. The emergence of
new Dirac points in the band structure translates into new threefold-degenerate
groups of Landau levels. This leads to an anomalous quantum Hall effect, in which
some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies
of all Landau levels get lifted, and in this regime all quantum Hall plateaus
are spaced by e2/h. Finally, we show that the pattern of Landau level crossings
is very sensitive to certain band structure parameters, and can therefore provide
a useful tool for determining their precise values.'
acknowledgement: We thank Pablo Jarillo-Herrero, Leonardo Campos, and Thiti Taychatanapat
for attracting our attention to the problem of biased trilayer graphene, and for
many helpful discussions.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Abanin D. New Dirac points and multiple Landau level crossings in
biased trilayer graphene. Physical Review B - Condensed Matter and Materials
Physics. 2013;87(11). doi:10.1103/PhysRevB.87.115422
apa: Serbyn, M., & Abanin, D. (2013). New Dirac points and multiple Landau level
crossings in biased trilayer graphene. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.115422
chicago: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau
Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.115422.
ieee: M. Serbyn and D. Abanin, “New Dirac points and multiple Landau level crossings
in biased trilayer graphene,” Physical Review B - Condensed Matter and Materials
Physics, vol. 87, no. 11. American Physical Society, 2013.
ista: Serbyn M, Abanin D. 2013. New Dirac points and multiple Landau level crossings
in biased trilayer graphene. Physical Review B - Condensed Matter and Materials
Physics. 87(11).
mla: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level
Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 11, American Physical Society, 2013, doi:10.1103/PhysRevB.87.115422.
short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials
Physics 87 (2013).
date_created: 2018-12-11T11:49:28Z
date_published: 2013-03-18T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '18'
doi: 10.1103/PhysRevB.87.115422
extern: 1
intvolume: ' 87'
issue: '11'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1212.6251
month: '03'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6428'
quality_controlled: 0
status: public
title: New Dirac points and multiple Landau level crossings in biased trilayer graphene
type: journal_article
volume: 87
year: '2013'
...
---
_id: '971'
abstract:
- lang: eng
text: We study the stability of the normal state in a mesoscopic NSN junction biased
by a constant voltage V with respect to the formation of the superconducting order.
Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature
dependence of the instability line, V inst(T), where nucleation of superconductivity
takes place. For sufficiently low biases, a stationary symmetric superconducting
state emerges below the instability line. For higher biases, the normal phase
is destroyed by the formation of a nonstationary bimodal state with two superconducting
nuclei localized near the opposite terminals. The low-temperature and large-voltage
behavior of the instability line is highly sensitive to the details of the inelastic
relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T)
in NSN junctions may be used as an effective tool to access the parameters of
the inelastic relaxation in the normal state.
acknowledgement: We are grateful to M. V. Feigel'man, A. Kamenev, T. M. Klapwijk,
J. P. Pekola, V. V. Ryazanov, J. C. W. Song, and D. Y. Vodolazov for discussions.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail
full_name: Skvortsov, Mikhail A
last_name: Skvortsov
citation:
ama: Serbyn M, Skvortsov M. Onset of superconductivity in a voltage-biased normal-superconducting-normal
microbridge. Physical Review B - Condensed Matter and Materials Physics.
2013;87(2). doi:10.1103/PhysRevB.87.020501
apa: Serbyn, M., & Skvortsov, M. (2013). Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.020501
chicago: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a
Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2013.
https://doi.org/10.1103/PhysRevB.87.020501.
ieee: M. Serbyn and M. Skvortsov, “Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge,” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 2. American Physical Society, 2013.
ista: Serbyn M, Skvortsov M. 2013. Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge. Physical Review B - Condensed Matter
and Materials Physics. 87(2).
mla: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased
Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.87.020501.
short: M. Serbyn, M. Skvortsov, Physical Review B - Condensed Matter and Materials
Physics 87 (2013).
date_created: 2018-12-11T11:49:28Z
date_published: 2013-01-02T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '02'
doi: 10.1103/PhysRevB.87.020501
extern: 1
intvolume: ' 87'
issue: '2'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1208.6004
month: '01'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6429'
quality_controlled: 0
status: public
title: Onset of superconductivity in a voltage-biased normal-superconducting-normal
microbridge
type: journal_article
volume: 87
year: '2013'
...
---
_id: '972'
abstract:
- lang: eng
text: In topological crystalline insulators (TCIs), topology and crystal symmetry
intertwine to create surface states with distinct characteristics. The breaking
of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac
fermions. Here, we report high-resolution scanning tunneling microscopy studies
of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected
by crystal symmetry with massive Dirac fermions consistent with crystal symmetry
breaking. In addition, we show two distinct regimes of the Fermi surface topology
separated by a Van-Hove singularity at the Lifshitz transition point. Our work
paves the way for engineering the Dirac band gap and realizing interaction-driven
topological quantum phenomena in TCIs.
arxiv: 1
author:
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Chetan
full_name: Dhital, Chetan
last_name: Dhital
- first_name: Madhab
full_name: Neupane, Madhab
last_name: Neupane
- first_name: Suyang
full_name: Xu, Suyang
last_name: Xu
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Md
full_name: Hasan, Md
last_name: Hasan
- first_name: Stephen
full_name: Wilson, Stephen
last_name: Wilson
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Okada Y, Serbyn M, Lin H, et al. Observation of dirac node formation and mass
acquisition in a topological crystalline insulator. Science. 2013;341(6153):1496-1499.
doi:10.1126/science.1239451
apa: Okada, Y., Serbyn, M., Lin, H., Walkup, D., Zhou, W., Dhital, C., … Madhavan,
V. (2013). Observation of dirac node formation and mass acquisition in a topological
crystalline insulator. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1239451
chicago: Okada, Yoshinori, Maksym Serbyn, Hsin Lin, Daniel Walkup, Wenwen Zhou,
Chetan Dhital, Madhab Neupane, et al. “Observation of Dirac Node Formation and
Mass Acquisition in a Topological Crystalline Insulator.” Science. American
Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239451.
ieee: Y. Okada et al., “Observation of dirac node formation and mass acquisition
in a topological crystalline insulator,” Science, vol. 341, no. 6153. American
Association for the Advancement of Science, pp. 1496–1499, 2013.
ista: Okada Y, Serbyn M, Lin H, Walkup D, Zhou W, Dhital C, Neupane M, Xu S, Wang
Y, Sankar R, Chou F, Bansil A, Hasan M, Wilson S, Fu L, Madhavan V. 2013. Observation
of dirac node formation and mass acquisition in a topological crystalline insulator.
Science. 341(6153), 1496–1499.
mla: Okada, Yoshinori, et al. “Observation of Dirac Node Formation and Mass Acquisition
in a Topological Crystalline Insulator.” Science, vol. 341, no. 6153, American
Association for the Advancement of Science, 2013, pp. 1496–99, doi:10.1126/science.1239451.
short: Y. Okada, M. Serbyn, H. Lin, D. Walkup, W. Zhou, C. Dhital, M. Neupane, S.
Xu, Y. Wang, R. Sankar, F. Chou, A. Bansil, M. Hasan, S. Wilson, L. Fu, V. Madhavan,
Science 341 (2013) 1496–1499.
date_created: 2018-12-11T11:49:29Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '01'
doi: 10.1126/science.1239451
extern: '1'
external_id:
arxiv:
- '1305.2823'
intvolume: ' 341'
issue: '6153'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1305.2823
month: '01'
oa: 1
oa_version: Preprint
page: 1496 - 1499
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6430'
quality_controlled: '1'
status: public
title: Observation of dirac node formation and mass acquisition in a topological crystalline
insulator
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 341
year: '2013'
...
---
_id: '973'
abstract:
- lang: eng
text: We construct a complete set of local integrals of motion that characterize
the many-body localized (MBL) phase. Our approach relies on the assumption that
local perturbations act locally on the eigenstates in the MBL phase, which is
supported by numerical simulations of the random-field XXZ spin chain. We describe
the structure of the eigenstates in the MBL phase and discuss the implications
of local conservation laws for its nonequilibrium quantum dynamics. We argue that
the many-body localization can be used to protect coherence in the system by suppressing
relaxation between eigenstates with different local integrals of motion.
acknowledgement: We thank J. Moore for useful discussions. Research at Perimeter Institute
is supported by the Government of Canada through Industry Canada and by the Province
of Ontario through the Ministry of Economic Development & Innovation. Z. P. was
supported by DOE Grant No. DE-SC0002140. M. S. was supported by the National Science
Foundation under Grant No. DMR-1104498. The simulations presented in this article
were performed on computational resources supported by the High Performance Computing
Center (PICSciE) at Princeton University.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Local conservation laws and the structure of the
many body localized states. Physical Review Letters. 2013;111(12). doi:10.1103/PhysRevLett.111.127201
apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Local conservation laws and
the structure of the many body localized states. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.111.127201
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Local Conservation Laws
and the Structure of the Many Body Localized States.” Physical Review Letters.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.111.127201.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Local conservation laws and the structure
of the many body localized states,” Physical Review Letters, vol. 111,
no. 12. American Physical Society, 2013.
ista: Serbyn M, Papić Z, Abanin D. 2013. Local conservation laws and the structure
of the many body localized states. Physical Review Letters. 111(12).
mla: Serbyn, Maksym, et al. “Local Conservation Laws and the Structure of the Many
Body Localized States.” Physical Review Letters, vol. 111, no. 12, American
Physical Society, 2013, doi:10.1103/PhysRevLett.111.127201.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 111 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-09-17T00:00:00Z
date_updated: 2021-01-12T08:22:21Z
day: '17'
doi: 10.1103/PhysRevLett.111.127201
extern: 1
intvolume: ' 111'
issue: '12'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1305.5554
month: '09'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6424'
quality_controlled: 0
status: public
title: Local conservation laws and the structure of the many body localized states
type: journal_article
volume: 111
year: '2013'
...
---
_id: '974'
abstract:
- lang: eng
text: We propose a possible realization of the overscreened Kondo impurity problem
by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid
with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid
behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid
fixed point in the overscreened Kondo problem. Using a large-N expansion together
with an expansion in the dynamical exponent of the gauge field, we find that the
coupling to the gauge field leads to weak but observable changes in the physical
properties of the system at the overscreened Kondo fixed point. We discuss the
extrapolation of this result to a physical case and argue that the realization
of overscreened Kondo physics could lead to observations of effects due to gauge
fields.
arxiv: 1
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Todadri
full_name: Senthil, Todadri
last_name: Senthil
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Serbyn M, Senthil T, Lee P. Overscreened Kondo fixed point in S=1 spin liquid.
Physical Review B - Condensed Matter and Materials Physics. 2013;88(2).
doi:10.1103/PhysRevB.88.024419
apa: Serbyn, M., Senthil, T., & Lee, P. (2013). Overscreened Kondo fixed point
in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.88.024419
chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Overscreened Kondo Fixed
Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.024419.
ieee: M. Serbyn, T. Senthil, and P. Lee, “Overscreened Kondo fixed point in S=1
spin liquid,” Physical Review B - Condensed Matter and Materials Physics,
vol. 88, no. 2. American Physical Society, 2013.
ista: Serbyn M, Senthil T, Lee P. 2013. Overscreened Kondo fixed point in S=1 spin
liquid. Physical Review B - Condensed Matter and Materials Physics. 88(2).
mla: Serbyn, Maksym, et al. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.”
Physical Review B - Condensed Matter and Materials Physics, vol. 88, no.
2, American Physical Society, 2013, doi:10.1103/PhysRevB.88.024419.
short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials
Physics 88 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-07-19T00:00:00Z
date_updated: 2021-01-12T08:22:21Z
day: '19'
doi: 10.1103/PhysRevB.88.024419
extern: '1'
external_id:
arxiv:
- '1212.5179'
intvolume: ' 88'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1212.5179
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6425'
quality_controlled: '1'
status: public
title: Overscreened Kondo fixed point in S=1 spin liquid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2013'
...
---
_id: '975'
abstract:
- lang: eng
text: Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic
in time, growth of the entanglement entropy for initial product states in a putative
many-body localized phase. We show that this surprising phenomenon results from
the dephasing due to exponentially small interaction-induced corrections to the
eigenenergies of different states. For weak interactions, we find that the entanglement
entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the
single-particle localization length. The saturated value of the entanglement entropy
at long times is determined by the participation ratios of the initial state over
the eigenstates of the subsystem. Our work shows that the logarithmic entanglement
growth is a universal phenomenon characteristic of the many-body localized phase
in any number of spatial dimensions, and reveals a broad hierarchy of dephasing
time scales present in such a phase.
acknowledgement: We would like to thank E. Altman and J. Moore for useful comments
on the manuscript. This research was supported in part by Perimeter Institute for
Theoretical Physics. Research at Perimeter Institute is supported by the Government
of Canada through Industry Canada and by the Province of Ontario through the Ministry
of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140.
The simulations presented in this article were performed on computational resources
supported by the High Performance Computing Center (PICSciE) at Princeton University.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Universal slow growth of entanglement in interacting
strongly disordered systems. Physical Review Letters. 2013;110(26). doi:10.1103/PhysRevLett.110.260601
apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Universal slow growth of entanglement
in interacting strongly disordered systems. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.110.260601
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Universal Slow Growth
of Entanglement in Interacting Strongly Disordered Systems.” Physical Review
Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.260601.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Universal slow growth of entanglement
in interacting strongly disordered systems,” Physical Review Letters, vol.
110, no. 26. American Physical Society, 2013.
ista: Serbyn M, Papić Z, Abanin D. 2013. Universal slow growth of entanglement in
interacting strongly disordered systems. Physical Review Letters. 110(26).
mla: Serbyn, Maksym, et al. “Universal Slow Growth of Entanglement in Interacting
Strongly Disordered Systems.” Physical Review Letters, vol. 110, no. 26,
American Physical Society, 2013, doi:10.1103/PhysRevLett.110.260601.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 110 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-06-28T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '28'
doi: 10.1103/PhysRevLett.110.260601
extern: 1
intvolume: ' 110'
issue: '26'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.4605
month: '06'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6426'
quality_controlled: 0
status: public
title: Universal slow growth of entanglement in interacting strongly disordered systems
type: journal_article
volume: 110
year: '2013'
...
---
_id: '9751'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence
for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding
to the attack of an obligately lytic phage by committing suicide in order to prevent
parasite transmission to nearby relatives. We found that bacterial suicide provides
large benefits to survivors at marginal costs to committers. The cost of suicide
was low because infected cells are moribund, rapidly dying upon phage infection,
such that no more opportunity for reproduction remains. As a consequence of its
marginal cost, host suicide was selectively favoured even when relatedness between
committers and survivors approached zero. Altogether, our findings demonstrate
that low-cost suicide can evolve with ease, represents an effective host-defence
strategy, and seems to be widespread among microbes. Moreover, low-cost suicide
might also occur in higher organisms as exemplified by infected social insect
workers leaving the colony to die in isolation.
article_processing_charge: No
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness
is low: evidence from bacteria committing suicide upon phage infection. 2013.
doi:10.5061/dryad.b1q2n'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Data from: Altruism
can evolve when relatedness is low: evidence from bacteria committing suicide
upon phage infection. Dryad. https://doi.org/10.5061/dryad.b1q2n'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism
Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide
upon Phage Infection.” Dryad, 2013. https://doi.org/10.5061/dryad.b1q2n.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection.” Dryad, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection, Dryad, 10.5061/dryad.b1q2n.'
mla: 'Refardt, Dominik, et al. Data from: Altruism Can Evolve When Relatedness
Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection. Dryad,
2013, doi:10.5061/dryad.b1q2n.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, (2013).
date_created: 2021-07-30T08:08:09Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2023-10-18T06:43:22Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.b1q2n
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.b1q2n
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2853'
relation: used_in_publication
status: public
status: public
title: 'Data from: Altruism can evolve when relatedness is low: evidence from bacteria
committing suicide upon phage infection'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '9754'
abstract:
- lang: eng
text: Short-read sequencing technologies have in principle made it feasible to draw
detailed inferences about the recent history of any organism. In practice, however,
this remains challenging due to the difficulty of genome assembly in most organisms
and the lack of statistical methods powerful enough to discriminate among recent,
non-equilibrium histories. We address both the assembly and inference challenges.
We develop a bioinformatic pipeline for generating outgroup-rooted alignments
of orthologous sequence blocks from de novo low-coverage short-read data for a
small number of genomes, and show how such sequence blocks can be used to fit
explicit models of population divergence and admixture in a likelihood framework.
To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding
insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa,
was restricted during Pleistocene ice ages to a longitudinal series of southern
refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled
from a single genome from each of three major glacial refugia reveals support
for an unexpected history dominated by recent admixture. Despite the fact that
80% of the genome is affected by admixture during the last glacial cycle, we are
able to infer the deeper divergence history of these populations. These inferences
are robust to variation in block length, mutation model, and the sampling location
of individual genomes within refugia. This combination of de novo assembly and
numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
citation:
ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies. 2013.
doi:10.5061/dryad.r3r60'
apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013).
Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60'
chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey
Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low
Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.'
ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from:
Likelihood-based inference of population history from low coverage de novo genome
assemblies.” Dryad, 2013.'
ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies, Dryad,
10.5061/dryad.r3r60.'
mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population
History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.'
short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).
date_created: 2021-07-30T08:31:22Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2023-02-23T10:31:17Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.r3r60
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.r3r60
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2170'
relation: used_in_publication
status: public
status: public
title: 'Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '976'
abstract:
- lang: eng
text: 'Motivated by a search for experimental probes to access the physics of fractionalized
excitations called spinons in spin liquids, we study the interaction of spinons
with lattice vibrations. We consider the case of algebraic spin liquid, when spinons
have fermionic statistics and a Dirac-like dispersion. We establish the general
procedure for deriving spinon-phonon interactions, which is based on symmetry
considerations. The procedure is illustrated for four different algebraic spin
liquids: π-flux and staggered-flux phases on a square lattice, π-flux phase on
a kagome lattice, and zero-flux phase on a honeycomb lattice. Although the low-energy
description is similar for all these phases, different underlying symmetry groups
lead to a distinct form of spinon-phonon interaction Hamiltonian. The explicit
form of the spinon-phonon interaction is used to estimate the attenuation of ultrasound
in an algebraic spin liquid. The prospects of the sound attenuation as a probe
of spinons are discussed.'
acknowledgement: M. S. is grateful to X.-G. Wen, L. Levitov, M. Metlitski, K. Michaeli,
K.-T. Chen, and A. Potter for many useful discussions. We acknowledge support by
Grant No. NSF DMR 1104498. We acknowledge the hospitality of KITP, where final stages
of this project were completed.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Serbyn M, Lee P. Spinon-phonon interaction in algebraic spin liquids. Physical
Review B - Condensed Matter and Materials Physics. 2013;87(17). doi:10.1103/PhysRevB.87.174424
apa: Serbyn, M., & Lee, P. (2013). Spinon-phonon interaction in algebraic spin
liquids. Physical Review B - Condensed Matter and Materials Physics. American
Physical Society. https://doi.org/10.1103/PhysRevB.87.174424
chicago: Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic
Spin Liquids.” Physical Review B - Condensed Matter and Materials Physics.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.174424.
ieee: M. Serbyn and P. Lee, “Spinon-phonon interaction in algebraic spin liquids,”
Physical Review B - Condensed Matter and Materials Physics, vol. 87, no.
17. American Physical Society, 2013.
ista: Serbyn M, Lee P. 2013. Spinon-phonon interaction in algebraic spin liquids.
Physical Review B - Condensed Matter and Materials Physics. 87(17).
mla: Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin
Liquids.” Physical Review B - Condensed Matter and Materials Physics, vol.
87, no. 17, American Physical Society, 2013, doi:10.1103/PhysRevB.87.174424.
short: M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics
87 (2013).
date_created: 2018-12-11T11:49:30Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '22'
doi: 10.1103/PhysRevB.87.174424
extern: 1
intvolume: ' 87'
issue: '17'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1303.0772
month: '05'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6427'
quality_controlled: 0
status: public
title: Spinon-phonon interaction in algebraic spin liquids
type: journal_article
volume: 87
year: '2013'
...
---
_id: '2443'
abstract:
- lang: eng
text: The mode of action of auxin is based on its non-uniform distribution within
tissues and organs. Despite the wide use of several auxin analogues in research
and agriculture, little is known about the specificity of different auxin-related
transport and signalling processes towards these compounds. Using seedlings of
Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2),
the physiological activity of several auxin analogues was investigated, together
with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis
and to be transported across the plasma membrane. This study shows that the specificity
criteria for different auxin-related processes vary widely. Notably, the special
behaviour of some synthetic auxin analogues suggests that they might be useful
tools in investigations of the molecular mechanism of auxin action. Thus, due
to their differential stimulatory effects on DR5 expression, indole-3-propionic
(IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of
TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin
signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate
between transcriptional and non-transcriptional pathways of auxin signalling.
The results demonstrate that the major determinants for the auxin-like physiological
potential of a particular compound are very complex and involve its chemical and
metabolic stability, its ability to distribute in tissues in a polar manner and
its activity towards auxin signalling machinery.
acknowledgement: The authors thank Dr Christian Luschnig (University of Natural Resources
and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor
Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds
and, last but not least, to Dr David Morris for critical reading of the manuscript.
We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance.
This work was supported by the Grant Agency of the Czech Republic (P305/11/0797
to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project
CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European
Research Council starting independent research grant ERC-2011-StG-20101109-PSDP
(to J.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: 'Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along
the auxin response chain: A study using auxin analogues. New Phytologist.
2013;200(4):1034-1048. doi:10.1111/nph.12437'
apa: 'Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová,
E. (2013). Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437'
chicago: 'Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev,
Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes
along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist.
Wiley, 2013. https://doi.org/10.1111/nph.12437.'
ieee: 'S. Simon et al., “Defining the selectivity of processes along the
auxin response chain: A study using auxin analogues,” New Phytologist,
vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.'
ista: 'Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová
E. 2013. Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. 200(4), 1034–1048.'
mla: 'Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin
Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200,
no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.'
short: S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek,
E. Zažímalová, New Phytologist 200 (2013) 1034–1048.
das_tickbox: '1'
date_created: 2018-12-11T11:57:41Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2026-06-18T07:49:41Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.12437
ec_funded: 1
intvolume: ' 200'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nph.12437
month: '12'
oa: 1
oa_version: Published Version
page: 1034 - 1048
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: New Phytologist
publication_status: published
publisher: Wiley
publist_id: '4460'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Defining the selectivity of processes along the auxin response chain: A study
using auxin analogues'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 200
year: '2013'
...
---
_id: '2444'
abstract:
- lang: eng
text: 'We consider two core algorithmic problems for probabilistic verification:
the maximal end-component decomposition and the almost-sure reachability set computation
for Markov decision processes (MDPs). For MDPs with treewidth k, we present two
improved static algorithms for both the problems that run in time O(n·k 2.38·2k
) and O(m·logn· k), respectively, where n is the number of states and m is the
number of edges, significantly improving the previous known O(n·k·√n· k) bound
for low treewidth. We also present decremental algorithms for both problems for
MDPs with constant treewidth that run in amortized logarithmic time, which is
a huge improvement over the previously known algorithms that require amortized
linear time.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Ła̧Cki, Jakub
last_name: Ła̧Cki
citation:
ama: Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with
low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36
apa: 'Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision
processes with low treewidth. Presented at the CAV: Computer Aided Verification,
St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36'
chicago: Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov
Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer,
2013. https://doi.org/10.1007/978-3-642-39799-8_36.
ieee: K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes
with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.
ista: Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes
with low treewidth. 8044, 543–558.
mla: Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision
Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36.
short: K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
das_tickbox: '1'
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2026-06-18T07:50:03Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_36
ec_funded: 1
external_id:
arxiv:
- '1304.0084'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.0084
month: '07'
oa: 1
oa_version: Preprint
page: 543 - 558
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4459'
quality_controlled: '1'
scopus_import: '1'
series_title: Lecture Notes in Computer Science
status: public
title: Faster algorithms for Markov decision processes with low treewidth
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...