---
_id: '10815'
abstract:
- lang: eng
text: In the last several decades, developmental biology has clarified the molecular
mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated
that the “tool-kit genes” essential for regulating developmental processes are
not only highly conserved among species, but are also used as systems at various
times and places in an organism to control distinct developmental events. Therefore,
mutations in many of these tool-kit genes may cause congenital diseases involving
morphological abnormalities. This link between genes and abnormal morphological
phenotypes underscores the importance of understanding how cells behave and contribute
to morphogenesis as a result of gene function. Recent improvements in live imaging
and in quantitative analyses of cellular dynamics will advance our understanding
of the cellular pathogenesis of congenital diseases associated with aberrant morphologies.
In these studies, it is critical to select an appropriate model organism for the
particular phenomenon of interest.
acknowledgement: The authors thank all the members of the Division of Morphogenesis,
National Institute for Basic Biology, for their contributions to the research, their
encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical
reading of the manuscript. We also thank the Model Animal Research and Spectrography
and Bioimaging Facilities, NIBB Core Research Facilities, for technical support.
M.H. was supported by a research fellowship from the Japan Society for the Promotion
of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid
for Scientific Research on Innovative Areas from the Ministry of Education, Culture,
Sports, Science, and Technology (MEXT), Japan, to N.U.
article_processing_charge: No
article_type: original
author:
- first_name: Masakazu
full_name: Hashimoto, Masakazu
last_name: Hashimoto
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Naoto
full_name: Ueno, Naoto
last_name: Ueno
citation:
ama: Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development
underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039
apa: Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms
of development underlying congenital diseases. Congenital Anomalies. Wiley.
https://doi.org/10.1111/cga.12039
chicago: Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular
Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies.
Wiley, 2014. https://doi.org/10.1111/cga.12039.
ieee: M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of
development underlying congenital diseases,” Congenital Anomalies, vol.
54, no. 1. Wiley, pp. 1–7, 2014.
ista: Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of
development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.
mla: Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development
Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1,
Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039.
short: M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.
date_created: 2022-03-04T08:17:25Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2022-03-04T08:26:05Z
day: '01'
department:
- _id: CaHe
doi: 10.1111/cga.12039
external_id:
pmid:
- '24666178'
intvolume: ' 54'
issue: '1'
keyword:
- Developmental Biology
- Embryology
- General Medicine
- Pediatrics
- Perinatology
- and Child Health
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/cga.12039
month: '02'
oa: 1
oa_version: None
page: 1-7
pmid: 1
publication: Congenital Anomalies
publication_identifier:
issn:
- 0914-3505
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular and cellular mechanisms of development underlying congenital diseases
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2014'
...
---
_id: '9458'
abstract:
- lang: eng
text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.
Their genomes are typically depleted of CG dinucleotides because of imperfect
repair of deaminated methylcytosines. Here, we extensively survey diverse species
lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless
frequently present and catalyzed by a different DNA methyltransferase family,
Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years
ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered
methylation occurs at unprecedented densities and directly disfavors nucleosomes,
contributing to nucleosome positioning between clusters. Dense methylation is
enabled by a regime of genomic sequence evolution that enriches CG dinucleotides
and drives the highest CG frequencies known. Species with linker methylation have
small, transcriptionally active nuclei that approach the physical limits of chromatin
compaction. These features constitute a previously unappreciated genome architecture,
in which dense methylation influences nucleosome positions, likely facilitating
nuclear processes under extreme spatial constraints.
article_processing_charge: No
article_type: original
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome
positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029
chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation
Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2014.01.029.
ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6.
Elsevier, pp. 1286–1297, 2014.
ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to
nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.
mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes
to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6,
Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.
short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
date_created: 2021-06-04T12:00:16Z
date_published: 2014-03-13T00:00:00Z
date_updated: 2021-12-14T08:22:36Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cell.2014.01.029
extern: '1'
external_id:
pmid:
- '24630728'
intvolume: ' 156'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.01.029
month: '03'
oa: 1
oa_version: Published Version
page: 1286-1297
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: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse
eukaryotes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 156
year: '2014'
...
---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
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: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9519'
abstract:
- lang: eng
text: Transposons are selfish genetic sequences that can increase their copy number
and inflict substantial damage on their hosts. To combat these genomic parasites,
plants have evolved multiple pathways to identify and silence transposons by methylating
their DNA. Plants have also evolved mechanisms to limit the collateral damage
from the antitransposon machinery. In this review, we examine recent developments
that have elucidated many of the molecular workings of these pathways. We also
highlight the evidence that the methylation and demethylation pathways interact,
indicating that plants have a highly sophisticated, integrated system of transposon
defense that has an important role in the regulation of gene expression.
article_processing_charge: No
article_type: review
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant
genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014
chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic
immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326,
2014.
ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 19(5), 320–326.
mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014,
pp. 320–26, doi:10.1016/j.tplants.2014.01.014.
short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
date_created: 2021-06-07T14:38:09Z
date_published: 2014-05-04T00:00:00Z
date_updated: 2021-12-14T08:24:48Z
day: '04'
department:
- _id: DaZi
doi: 10.1016/j.tplants.2014.01.014
extern: '1'
external_id:
pmid:
- '24618094 '
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 320-326
pmid: 1
publication: Trends in Plant Science
publication_identifier:
eissn:
- 1878-4372
issn:
- 1360-1385
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation as a system of plant genomic immunity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 19
year: '2014'
...
---
_id: '9594'
abstract:
- lang: eng
text: Let d≥3 be a fixed integer. We give an asympotic formula for the expected
number of spanning trees in a uniformly random d-regular graph with n vertices.
(The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain
the asymptotic distribution of the number of spanning trees in a uniformly random
cubic graph, and conjecture that the corresponding result holds for arbitrary
(fixed) d. Numerical evidence is presented which supports our conjecture.
article_number: P1.45
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: David
full_name: Wind, David
last_name: Wind
citation:
ama: Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular
graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752
apa: Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning
trees in random regular graphs. The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752
chicago: Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number
of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752.
ieee: C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in
random regular graphs,” The Electronic Journal of Combinatorics, vol. 21,
no. 1. The Electronic Journal of Combinatorics, 2014.
ista: Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random
regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.
mla: Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular
Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45,
The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752.
short: C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics
21 (2014).
date_created: 2021-06-23T06:29:35Z
date_published: 2014-02-28T00:00:00Z
date_updated: 2023-02-23T14:02:12Z
day: '28'
doi: 10.37236/3752
extern: '1'
external_id:
arxiv:
- '1309.6710'
intvolume: ' 21'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.37236/3752
month: '02'
oa: 1
oa_version: Published Version
publication: The Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: The Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the number of spanning trees in random regular graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 21
year: '2014'
...
---
_id: '96'
abstract:
- lang: eng
text: Multielectron spin qubits are demonstrated, and performance examined by comparing
coherent exchange oscillations in coupled single-electron and multielectron quantum
dots, measured in the same device. Fast (>1 GHz) exchange oscillations with
a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for
the single-electron case, the latter consistent with experiments in the literature.
A model of dephasing that includes voltage and hyperfine noise is developed that
is in good agreement with both single- and multielectron data, though in both
cases additional exchange-independent dephasing is needed to obtain quantitative
agreement across a broad parameter range.
acknowledgement: The research is supported by the Intelligence Advanced Research Projects
Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the
DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish
National Research Foundation.
article_number: '026801'
arxiv: 1
author:
- 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: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Micah
full_name: Hanson, Micah
last_name: Hanson
- first_name: Arthur
full_name: Gossard, Arthur
last_name: Gossard
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations
and screening in multielectron spin qubits. APS Physics, Physical Review Letters.
2014;112(2). doi:10.1103/PhysRevLett.112.026801
apa: Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., & Marcus, C.
(2014). Coherent operations and screening in multielectron spin qubits. APS
Physics, Physical Review Letters. American Physiological Society. https://doi.org/10.1103/PhysRevLett.112.026801
chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard,
and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.”
APS Physics, Physical Review Letters. American Physiological Society, 2014.
https://doi.org/10.1103/PhysRevLett.112.026801.
ieee: A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent
operations and screening in multielectron spin qubits,” APS Physics, Physical
Review Letters, vol. 112, no. 2. American Physiological Society, 2014.
ista: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent
operations and screening in multielectron spin qubits. APS Physics, Physical Review
Letters. 112(2), 026801.
mla: Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron
Spin Qubits.” APS Physics, Physical Review Letters, vol. 112, no. 2, 026801,
American Physiological Society, 2014, doi:10.1103/PhysRevLett.112.026801.
short: A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics,
Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:36Z
date_published: 2014-01-14T00:00:00Z
date_updated: 2021-01-12T08:22:14Z
day: '14'
doi: 10.1103/PhysRevLett.112.026801
extern: '1'
external_id:
arxiv:
- '1306.2720'
intvolume: ' 112'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.2720
month: '01'
oa: 1
oa_version: Preprint
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physiological Society
publist_id: '7958'
quality_controlled: '1'
status: public
title: Coherent operations and screening in multielectron spin qubits
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '9655'
abstract:
- lang: eng
text: Correlative microscopy incorporates the specificity of fluorescent protein
labeling into high-resolution electron micrographs. Several approaches exist for
correlative microscopy, most of which have used the green fluorescent protein
(GFP) as the label for light microscopy. Here we use chemical tagging and synthetic
fluorophores instead, in order to achieve protein-specific labeling, and to perform
multicolor imaging. We show that synthetic fluorophores preserve their post-embedding
fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is
of such quality that the specimen can be prepared with identical protocols for
scanning electron microscopy (SEM) and transmission electron microscopy (TEM);
this is particularly valuable when singular or otherwise difficult samples are
examined. We show that synthetic fluorophores give bright, well-resolved signals
in super-resolution light microscopy, enabling us to superimpose light microscopic
images with a precision of up to 25 nm in the x–y plane on electron micrographs.
To exemplify the preservation quality of our new method we visualize the molecular
arrangement of cadherins in adherens junctions of mouse epithelial cells.
article_processing_charge: No
article_type: original
author:
- first_name: Mario
full_name: Perkovic, Mario
last_name: Perkovic
- first_name: Michael
full_name: Kunz, Michael
last_name: Kunz
- first_name: Ulrike
full_name: Endesfelder, Ulrike
last_name: Endesfelder
- first_name: Stefanie
full_name: Bunse, Stefanie
last_name: Bunse
- first_name: Christoph
full_name: Wigge, Christoph
last_name: Wigge
- first_name: Zhou
full_name: Yu, Zhou
last_name: Yu
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Margot P.
full_name: Scheffer, Margot P.
last_name: Scheffer
- first_name: Anja
full_name: Seybert, Anja
last_name: Seybert
- first_name: Sebastian
full_name: Malkusch, Sebastian
last_name: Malkusch
- first_name: Erin M.
full_name: Schuman, Erin M.
last_name: Schuman
- first_name: Mike
full_name: Heilemann, Mike
last_name: Heilemann
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
citation:
ama: Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy
with chemical tags. Journal of Structural Biology. 2014;186(2):205-213.
doi:10.1016/j.jsb.2014.03.018
apa: Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis,
A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal
of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018
chicago: Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph
Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron
Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier,
2014. https://doi.org/10.1016/j.jsb.2014.03.018.
ieee: M. Perkovic et al., “Correlative light- and electron microscopy with
chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier,
pp. 205–213, 2014.
ista: Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer
MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative
light- and electron microscopy with chemical tags. Journal of Structural Biology.
186(2), 205–213.
mla: Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical
Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014,
pp. 205–13, doi:10.1016/j.jsb.2014.03.018.
short: M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau,
M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis,
Journal of Structural Biology 186 (2014) 205–213.
date_created: 2021-07-14T09:05:42Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-07-22T08:26:32Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2014.03.018
extern: '1'
external_id:
pmid:
- '24698954'
file:
- access_level: open_access
checksum: a322991b43cdc5935c99db88d285aa3a
content_type: application/pdf
creator: asandaue
date_created: 2021-07-22T08:06:34Z
date_updated: 2021-07-22T08:06:34Z
file_id: '9701'
file_name: 2014_JournalOfStructuralBiology_Perkovic.pdf
file_size: 3454628
relation: main_file
success: 1
file_date_updated: 2021-07-22T08:06:34Z
has_accepted_license: '1'
intvolume: ' 186'
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 205-213
pmid: 1
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Correlative light- and electron microscopy with chemical tags
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 186
year: '2014'
...
---
_id: '9662'
abstract:
- lang: eng
text: Fractionation of isotopes among distinct molecules or phases is a quantum
effect which is often exploited to obtain insights on reaction mechanisms, biochemical,
geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios
in atomistic simulations is challenging, because one needs to perform a thermodynamic
integration with respect to the isotope mass, along with time-consuming path integral
calculations. By re-formulating the problem as a particle exchange in the ring
polymer partition function, we derive new estimators giving direct access to the
differential partitioning of isotopes, which can simplify the calculations by
avoiding thermodynamic integration. We demonstrate the efficiency of these estimators
by applying them to investigate the isotope fractionation ratios in the gas-phase
Zundel cation, and in a few simple hydrocarbons.
article_number: '244112'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293
apa: Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope
fractionation ratios. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4904293
chicago: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators
for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP
Publishing, 2014. https://doi.org/10.1063/1.4904293.
ieee: B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation
ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing,
2014.
ista: Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 141(24), 244112.
mla: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for
Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141,
no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).
date_created: 2021-07-15T09:22:49Z
date_published: 2014-12-28T00:00:00Z
date_updated: 2021-08-09T12:32:24Z
day: '28'
doi: 10.1063/1.4904293
extern: '1'
external_id:
arxiv:
- '1412.1308'
pmid:
- '25554138'
intvolume: ' 141'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.1308
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: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct path integral estimators for isotope fractionation ratios
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 141
year: '2014'
...
---
_id: '9686'
abstract:
- lang: eng
text: It is well known that ultrasonic vibration can soften metals, and this phenomenon
has been widely exploited in industrial applications concerning metal forming
and bonding. Recent experiments show that the simultaneous application of oscillatory
stresses from audible to ultrasonic frequency ranges can lead to not only softening
but also significant dislocation annihilation and subgrain formation in metal
samples from the nano- to macro-size range. These findings indicate that the existing
understanding of ultrasound softening – that the vibrations either impose additional
stress waves to augment the quasi-static applied load, or cause heating of the
metal, whereas the metal’s intrinsic deformation resistance or mechanism remains
unaltered – is far from complete. To understand the softening and the associated
enhanced subgrain formation and dislocation annihilation, a new simulator based
on the dynamics of dislocation-density functions is employed. This new simulator
considers the flux, production and annihilation, as well as the Taylor and elastic
interactions between dislocation densities. Softening during vibrations as well
as enhanced cell formation is predicted. The simulations reveal the main mechanism
for subcell formation under oscillatory loadings to be the enhanced elimination
of statistically stored dislocations (SSDs) by the oscillatory stress, leaving
behind geometrically necessary dislocations with low Schmid factors which then
form the subgrain walls. The oscillatory stress helps the depletion of the SSDs,
because the chance for them to meet up and annihilate is increased with reversals
of dislocation motions. This is the first simulation effort to successfully predict
the cell formation phenomenon under vibratory loadings.
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: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 2014;95(16-18):1845-1865.
doi:10.1080/14786435.2014.897008
apa: Cheng, B., Leung, H. S., & Ngan, A. H. W. (2014). Strength of metals under
vibrations – dislocation-density-function dynamics simulations. Philosophical
Magazine. Taylor & Francis. https://doi.org/10.1080/14786435.2014.897008
chicago: Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under
Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical
Magazine. Taylor & Francis, 2014. https://doi.org/10.1080/14786435.2014.897008.
ieee: B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations
– dislocation-density-function dynamics simulations,” Philosophical Magazine,
vol. 95, no. 16–18. Taylor & Francis, pp. 1845–1865, 2014.
ista: Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865.
mla: Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function
Dynamics Simulations.” Philosophical Magazine, vol. 95, no. 16–18, Taylor
& Francis, 2014, pp. 1845–65, doi:10.1080/14786435.2014.897008.
short: B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865.
date_created: 2021-07-19T09:27:15Z
date_published: 2014-06-23T00:00:00Z
date_updated: 2023-02-23T14:04:59Z
day: '23'
doi: 10.1080/14786435.2014.897008
extern: '1'
intvolume: ' 95'
issue: 16-18
language:
- iso: eng
month: '06'
oa_version: None
page: 1845-1865
publication: Philosophical Magazine
publication_identifier:
eissn:
- 1478-6443
issn:
- 1478-6435
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strength of metals under vibrations – dislocation-density-function dynamics
simulations
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 95
year: '2014'
...
---
_id: '97'
abstract:
- lang: eng
text: The distribution of Coulomb blockade peak heights as a function of magnetic
field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit
coupling in this hole-gas system leads to antilocalization of Coulomb blockade
peaks, consistent with theory. In particular, the peak height distribution has
its maximum away from zero at zero magnetic field, with an average that decreases
with increasing field. Magnetoconductance in the open-wire regime places a bound
on the spin-orbit length (lso < 20 nm), consistent with values extracted in the
Coulomb blockade regime (lso < 25 nm).
acknowledgement: Research supported by the Danish National Research Foundation, the
Office of Science at the U.S. Department of Energy, the National Science Foundation
(PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST
Program.
article_number: '216806'
arxiv: 1
author:
- 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: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Thorvald
full_name: Larsen, Thorvald
last_name: Larsen
- first_name: Mattias
full_name: Fitzpatrick, Mattias
last_name: Fitzpatrick
- first_name: Jun
full_name: Yao, Jun
last_name: Yao
- first_name: Hao
full_name: Yan, Hao
last_name: Yan
- first_name: Charles
full_name: Lieber, Charles
last_name: Lieber
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade
in a Ge/Si nanowire. APS Physics, Physical Review Letters. 2014;112(21).
doi:10.1103/PhysRevLett.112.216806
apa: Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan,
H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire.
APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.216806
chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick,
Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb
Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters. American
Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.216806.
ieee: A. P. Higginbotham et al., “Antilocalization of coulomb blockade in
a Ge/Si nanowire,” APS Physics, Physical Review Letters, vol. 112, no.
21. American Physical Society, 2014.
ista: Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber
C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS
Physics, Physical Review Letters. 112(21), 216806.
mla: Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a
Ge/Si Nanowire.” APS Physics, Physical Review Letters, vol. 112, no. 21,
216806, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.216806.
short: A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan,
C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:36Z
date_published: 2014-05-29T00:00:00Z
date_updated: 2021-01-12T08:22:19Z
day: '29'
doi: 10.1103/PhysRevLett.112.216806
extern: '1'
external_id:
arxiv:
- '1401.2948'
intvolume: ' 112'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.2948
month: '05'
oa: 1
oa_version: None
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7957'
quality_controlled: '1'
status: public
title: Antilocalization of coulomb blockade in a Ge/Si nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '9722'
article_processing_charge: No
author:
- first_name: Anna
full_name: Lovrics, Anna
last_name: Lovrics
- first_name: Yu
full_name: Gao, Yu
last_name: Gao
- first_name: Bianka
full_name: Juhász, Bianka
last_name: Juhász
- first_name: István
full_name: Bock, István
last_name: Bock
- first_name: Helen M.
full_name: Byrne, Helen M.
last_name: Byrne
- first_name: András
full_name: Dinnyés, András
last_name: Dinnyés
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
citation:
ama: Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression
states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &
Kovács, K. (2014). Transition probability between TF expression states when Dbx2
inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András
Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.
ieee: A. Lovrics et al., “Transition probability between TF expression states
when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition
probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library
of Science, 10.1371/journal.pone.0111430.s006.
mla: Lovrics, Anna, et al. Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács,
(2014).
date_created: 2021-07-26T14:35:00Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2023-02-23T10:24:07Z
day: '14'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430.s006
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2004'
relation: used_in_publication
status: public
status: public
title: Transition probability between TF expression states when Dbx2 inhibits Nkx2.2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9739'
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: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Novak, Martin
last_name: Novak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time
scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed
proofs for “The time scale of evolutionary innovation.” Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003818.s001
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak.
“Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library
of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for
‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for
“The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.
mla: Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary
Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).
date_created: 2021-07-28T08:13:57Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T10:25:37Z
day: '11'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818.s001
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2039'
relation: used_in_publication
status: public
status: public
title: Detailed proofs for “The time scale of evolutionary innovation”
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9740'
abstract:
- lang: eng
text: The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens.
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:10.5061/dryad.vm0vc'
apa: 'Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2014). Data from:
Anti-pathogen protection versus survival costs mediated by an ectosymbiont in
an ant host. Dryad. https://doi.org/10.5061/dryad.vm0vc'
chicago: 'Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data
from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont
in an Ant Host.” Dryad, 2014. https://doi.org/10.5061/dryad.vm0vc.'
ieee: 'M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host.”
Dryad, 2014.'
ista: 'Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad,
10.5061/dryad.vm0vc.'
mla: 'Konrad, Matthias, et al. Data from: Anti-Pathogen Protection versus Survival
Costs Mediated by an Ectosymbiont in an Ant Host. Dryad, 2014, doi:10.5061/dryad.vm0vc.'
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).
date_created: 2021-07-28T08:38:40Z
date_published: 2014-11-13T00:00:00Z
date_updated: 2023-02-23T10:23:32Z
day: '13'
department:
- _id: SyCr
doi: 10.5061/dryad.vm0vc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.vm0vc
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1993'
relation: used_in_publication
status: public
status: public
title: 'Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9741'
abstract:
- lang: eng
text: In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: 'Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. 2014.
doi:10.5061/dryad.85dn7'
apa: 'Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history
and epistatic interactions impact dynamics of adaptation to novel environmental
stresses. Dryad. https://doi.org/10.5061/dryad.85dn7'
chicago: 'Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History
and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental
Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.'
ieee: 'M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and
epistatic interactions impact dynamics of adaptation to novel environmental stresses.”
Dryad, 2014.'
ista: 'Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses, Dryad,
10.5061/dryad.85dn7.'
mla: 'Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions
Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014,
doi:10.5061/dryad.85dn7.'
short: M. Lagator, N. Colegrave, P. Neve, (2014).
date_created: 2021-07-28T08:48:06Z
date_published: 2014-08-21T00:00:00Z
date_updated: 2023-02-23T10:25:31Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.85dn7
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.85dn7
month: '08'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2036'
relation: used_in_publication
status: public
status: public
title: 'Data from: Selection history and epistatic interactions impact dynamics of
adaptation to novel environmental stresses'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9747'
abstract:
- lang: eng
text: Understanding the effects of sex and migration on adaptation to novel environments
remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas
reinhardtii, we investigated how sex and migration affected rates of evolutionary
rescue in a sink environment, and subsequent changes in fitness following evolutionary
rescue. We show that sex and migration affect both the rate of evolutionary rescue
and subsequent adaptation. However, their combined effects change as the populations
adapt to a sink habitat. Both sex and migration independently increased rates
of evolutionary rescue, but the effect of sex on subsequent fitness improvements,
following initial rescue, changed with migration, as sex was beneficial in the
absence of migration but constraining adaptation when combined with migration.
These results suggest that sex and migration are beneficial during the initial
stages of adaptation, but can become detrimental as the population adapts to its
environment.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Andrew
full_name: Morgan, Andrew
last_name: Morgan
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
citation:
ama: 'Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration
in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1'
apa: 'Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from:
Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1'
chicago: 'Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from:
Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.'
ieee: 'M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex
and migration in adaptation to sink environments.” Dryad, 2014.'
ista: 'Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and
migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.'
mla: 'Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation
to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.'
short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).
date_created: 2021-07-28T15:32:55Z
date_published: 2014-04-17T00:00:00Z
date_updated: 2023-02-23T10:27:31Z
day: '17'
department:
- _id: CaGu
doi: 10.5061/dryad.s42n1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s42n1
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2083'
relation: used_in_publication
status: public
status: public
title: 'Data from: Role of sex and migration in adaptation to sink environments'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9752'
abstract:
- lang: eng
text: Redundancies and correlations in the responses of sensory neurons may seem
to waste neural resources, but they can also carry cues about structured stimuli
and may help the brain to correct for response errors. To investigate the effect
of stimulus structure on redundancy in retina, we measured simultaneous responses
from populations of retinal ganglion cells presented with natural and artificial
stimuli that varied greatly in correlation structure; these stimuli and recordings
are publicly available online. Responding to spatio-temporally structured stimuli
such as natural movies, pairs of ganglion cells were modestly more correlated
than in response to white noise checkerboards, but they were much less correlated
than predicted by a non-adapting functional model of retinal response. Meanwhile,
responding to stimuli with purely spatial correlations, pairs of ganglion cells
showed increased correlations consistent with a static, non-adapting receptive
field and nonlinearity. We found that in response to spatio-temporally correlated
stimuli, ganglion cells had faster temporal kernels and tended to have stronger
surrounds. These properties of individual cells, along with gain changes that
opposed changes in effective contrast at the ganglion cell input, largely explained
the pattern of pairwise correlations across stimuli where receptive field measurements
were possible.
article_processing_charge: No
author:
- first_name: Kristina
full_name: Simmons, Kristina
last_name: Simmons
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Heather
full_name: Yee, Heather
last_name: Yee
- first_name: Stephanie
full_name: Palmer, Stephanie
last_name: Palmer
- first_name: Philip
full_name: Nelson, Philip
last_name: Nelson
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
citation:
ama: 'Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus
correlations by the retina. 2014. doi:10.5061/dryad.246qg'
apa: 'Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., …
Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations
by the retina. Dryad. https://doi.org/10.5061/dryad.246qg'
chicago: 'Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather
Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation
of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/10.5061/dryad.246qg.'
ieee: 'K. Simmons et al., “Data from: Transformation of stimulus correlations
by the retina.” Dryad, 2014.'
ista: 'Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian
V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad,
10.5061/dryad.246qg.'
mla: 'Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations
by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.'
short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson,
V. Balasubramanian, (2014).
date_created: 2021-07-30T08:13:52Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-02-23T10:35:57Z
day: '07'
department:
- _id: GaTk
doi: 10.5061/dryad.246qg
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.246qg
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2277'
relation: used_in_publication
status: public
status: public
title: 'Data from: Transformation of stimulus correlations by the retina'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9753'
abstract:
- lang: eng
text: 'Background: The brood of ants and other social insects is highly susceptible
to pathogens, particularly those that penetrate the soft larval and pupal cuticle.
We here test whether the presence of a pupal cocoon, which occurs in some ant
species but not in others, affects the sanitary brood care and fungal infection
patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We
use a) a comparative approach analysing four species with either naked or cocooned
pupae and b) a within-species analysis of a single ant species, in which both
pupal types co-exist in the same colony. Results: We found that the presence of
a cocoon did not compromise fungal pathogen detection by the ants and that species
with cocooned pupae increased brood grooming after pathogen exposure. All tested
ant species further removed brood from their nests, which was predominantly expressed
towards larvae and naked pupae treated with the live fungal pathogen. In contrast,
cocooned pupae exposed to live fungus were not removed at higher rates than cocooned
pupae exposed to dead fungus or a sham control. Consistent with this, exposure
to the live fungus caused high numbers of infections and fungal outgrowth in larvae
and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed
the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion:
Our study suggests that the pupal cocoon has a protective effect against fungal
infection, causing an adaptive change in sanitary behaviours by the ants. It further
demonstrates that brood removal - originally described for honeybees as “hygienic
behaviour” – is a widespread sanitary behaviour in ants, which likely has important
implications on disease dynamics in social insect colonies.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons
affect sanitary brood care and limit fungal infections in ant colonies. 2014.
doi:10.5061/dryad.nc0gc'
apa: 'Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2014).
Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies. Dryad. https://doi.org/10.5061/dryad.nc0gc'
chicago: 'Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia
Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal
Infections in Ant Colonies.” Dryad, 2014. https://doi.org/10.5061/dryad.nc0gc.'
ieee: 'S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data
from: Pupal cocoons affect sanitary brood care and limit fungal infections in
ant colonies.” Dryad, 2014.'
ista: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from:
Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,
Dryad, 10.5061/dryad.nc0gc.'
mla: 'Tragust, Simon, et al. Data from: Pupal Cocoons Affect Sanitary Brood Care
and Limit Fungal Infections in Ant Colonies. Dryad, 2014, doi:10.5061/dryad.nc0gc.'
short: S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).
date_created: 2021-07-30T08:24:11Z
date_published: 2014-10-08T00:00:00Z
date_updated: 2023-02-23T10:36:17Z
day: '08'
department:
- _id: SyCr
doi: 10.5061/dryad.nc0gc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.nc0gc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2284'
relation: used_in_publication
status: public
status: public
title: 'Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '977'
abstract:
- lang: eng
text: We propose a method for detecting many-body localization (MBL) in disordered
spin systems. The method involves pulsed coherent spin manipulations that probe
the dephasing of a given spin due to its entanglement with a set of distant spins.
It allows one to distinguish the MBL phase from a noninteracting localized phase
and a delocalized phase. In particular, we show that for a properly chosen pulse
sequence the MBL phase exhibits a characteristic power-law decay reflecting its
slow growth of entanglement. We find that this power-law decay is robust with
respect to thermal and disorder averaging, provide numerical simulations supporting
our results, and discuss possible experimental realizations in solid-state and
cold-atom systems.
acknowledgement: |-
We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.
M. S., M. K., and S. G. contributed equally to this work.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Michael
full_name: Knap, Michael J
last_name: Knap
- first_name: Sarang
full_name: Gopalakrishnan, Sarang
last_name: Gopalakrishnan
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Norman
full_name: Yao, Norman Y
last_name: Yao
- first_name: Chris
full_name: Laumann, Chris R
last_name: Laumann
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
- first_name: Mikhail
full_name: Lukin, Mikhail D
last_name: Lukin
- first_name: Eugene
full_name: Demler, Eugene A
last_name: Demler
citation:
ama: Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body
localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204
apa: Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C.,
… Demler, E. (2014). Interferometric probes of many-body localization. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204
chicago: Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman
Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric
Probes of Many-Body Localization.” Physical Review Letters. American Physical
Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204.
ieee: M. Serbyn et al., “Interferometric probes of many-body localization,”
Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014.
ista: Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin
M, Demler E. 2014. Interferometric probes of many-body localization. Physical
Review Letters. 113(14).
mla: Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.”
Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014,
doi:10.1103/PhysRevLett.113.147204.
short: M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin,
M. Lukin, E. Demler, Physical Review Letters 113 (2014).
date_created: 2018-12-11T11:49:30Z
date_published: 2014-10-03T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '03'
doi: 10.1103/PhysRevLett.113.147204
extern: 1
intvolume: ' 113'
issue: '14'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.0693
month: '10'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6421'
quality_controlled: 0
status: public
title: Interferometric probes of many-body localization
type: journal_article
volume: 113
year: '2014'
...
---
_id: '978'
abstract:
- lang: eng
text: The newly discovered topological crystalline insulators feature a complex
band structure involving multiple Dirac cones, and are potentially highly tunable
by external electric field, temperature or strain. Theoretically, it has been
predicted that the various Dirac cones, which are offset in energy and momentum,
might harbour vastly different orbital character. However, their orbital texture,
which is of immense importance in determining a variety of a materialâ €™ s properties
remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical
topological crystalline insulator. By using Fourier-transform scanning tunnelling
spectroscopy we measure the interference patterns produced by the scattering of
surface-state electrons. We discover that the intensity and energy dependences
of the Fourier transforms show distinct characteristics, which can be directly
attributed to orbital effects. Our experiments reveal a complex band topology
involving two Lifshitz transitions and establish the orbital nature of the Dirac
bands, which could provide an alternative pathway towards future quantum applications.
acknowledgement: V.M. gratefully acknowledges funding from the US Department of Energy,
Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support
of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105
for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern
University is supported by the US Department of Energy grant number DE-FG02-07ER46352,
and benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231.
W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009.
W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University
is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C.
acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Chengyi
full_name: Huang, Chengyi
last_name: Huang
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Wei
full_name: Tsai, Wei-Feng
last_name: Tsai
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture
in topological crystalline insulators. Nature Physics. 2014;10(8):572-577.
doi:10.1038/nphys3012
apa: Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2014). Mapping the unconventional orbital texture in topological crystalline
insulators. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3012
chicago: Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital
Texture in Topological Crystalline Insulators.” Nature Physics. Nature
Publishing Group, 2014. https://doi.org/10.1038/nphys3012.
ieee: I. Zeljkovic et al., “Mapping the unconventional orbital texture in
topological crystalline insulators,” Nature Physics, vol. 10, no. 8. Nature
Publishing Group, pp. 572–577, 2014.
ista: Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou
F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional
orbital texture in topological crystalline insulators. Nature Physics. 10(8),
572–577.
mla: Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological
Crystalline Insulators.” Nature Physics, vol. 10, no. 8, Nature Publishing
Group, 2014, pp. 572–77, doi:10.1038/nphys3012.
short: I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn,
F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics
10 (2014) 572–577.
date_created: 2018-12-11T11:49:30Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '01'
doi: 10.1038/nphys3012
extern: 1
intvolume: ' 10'
issue: '8'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.0164
month: '08'
oa: 1
page: 572 - 577
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6423'
quality_controlled: 0
status: public
title: Mapping the unconventional orbital texture in topological crystalline insulators
type: journal_article
volume: 10
year: '2014'
...
---
_id: '979'
abstract:
- lang: eng
text: In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te,
Se), crystal symmetry and electronic topology intertwine to create topological
surface states with many interesting features including Lifshitz transition, Van-Hove
singularity, and fermion mass generation. These surface states are protected by
mirror symmetry with respect to the (110) plane. In this work we present a comprehensive
study of the effects of different mirror-symmetry-breaking perturbations on the
(001) surface band structure. Pristine (001) surface states have four branches
of Dirac fermions at low energy. We show that ferroelectric-type structural distortion
generates a mass and gaps out some or all of these Dirac points, while strain
shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the
surface state gapless, but introduces asymmetry between Dirac points. Finally,
an out-of-plane magnetic field leads to discrete Landau levels. We show that the
Landau level spectrum has an unusual pattern of degeneracy and interesting features
due to the unique underlying band structure. This suggests that Landau level spectroscopy
can detect and distinguish between different mechanisms of symmetry breaking in
topological crystalline insulators.
acknowledgement: We thank V. Madhavan and Y. Okada for related collaborations, and
P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR
1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division
of Materials Sciences and Engineering under award DE-SC0010526.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
citation:
ama: Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline
insulators. Physical Review B - Condensed Matter and Materials Physics.
2014;90(3). doi:10.1103/PhysRevB.90.035402
apa: Serbyn, M., & Fu, L. (2014). Symmetry breaking and Landau quantization
in topological crystalline insulators. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.035402
chicago: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization
in Topological Crystalline Insulators.” Physical Review B - Condensed Matter
and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.035402.
ieee: M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological
crystalline insulators,” Physical Review B - Condensed Matter and Materials
Physics, vol. 90, no. 3. American Physical Society, 2014.
ista: Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological
crystalline insulators. Physical Review B - Condensed Matter and Materials Physics.
90(3).
mla: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in
Topological Crystalline Insulators.” Physical Review B - Condensed Matter and
Materials Physics, vol. 90, no. 3, American Physical Society, 2014, doi:10.1103/PhysRevB.90.035402.
short: M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics
90 (2014).
date_created: 2018-12-11T11:49:31Z
date_published: 2014-07-03T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '03'
doi: 10.1103/PhysRevB.90.035402
extern: 1
intvolume: ' 90'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.8153
month: '07'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6422'
quality_controlled: 0
status: public
title: Symmetry breaking and Landau quantization in topological crystalline insulators
type: journal_article
volume: 90
year: '2014'
...