---
_id: '7016'
abstract:
- lang: eng
text: Organisms cope with change by employing transcriptional regulators. However,
when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. We ask whether the intrinsic instability
of gene duplication and amplification provides a generic alternative to canonical
gene regulation. By real-time monitoring of gene copy number mutations in E. coli,
we show that gene duplications and amplifications enable adaptation to fluctuating
environments by rapidly generating copy number, and hence expression level, polymorphism.
This ‘amplification-mediated gene expression tuning’ occurs on timescales similar
to canonical gene regulation and can deal with rapid environmental changes. Mathematical
modeling shows that amplifications also tune gene expression in stochastic environments
where transcription factor-based schemes are hard to evolve or maintain. The fleeting
nature of gene amplifications gives rise to a generic population-level mechanism
that relies on genetic heterogeneity to rapidly tune expression of any gene, without
leaving any genomic signature.
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016
apa: Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016
chicago: Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of
Population-Level Gene Expression Regulation.’” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.
ieee: I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation.’” Institute of Science and Technology Austria, 2019.
ista: Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.
mla: Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:7016.
short: I. Tomanek, (2019).
contributor:
- contributor_type: project_leader
first_name: Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
date_created: 2019-11-13T09:07:31Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2024-02-21T12:45:25Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7016
file:
- access_level: open_access
checksum: 72441055043eda4cbf1398a422e2c118
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:52:21Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - amplified.
file_id: '7017'
file_name: D8_S35_R2_001.fastq
file_size: 2456192500
relation: main_file
title: Locus1_amplified
- access_level: open_access
checksum: a4ac50bf655d9c751f0305ade5c2ee16
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:52:59Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - ancestral.
file_id: '7018'
file_name: IT028_S11_R2_001.fastq
file_size: 2833452234
relation: main_file
title: Locus1_ancestral
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content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:54:10Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - amplified, after
DOG-selection.
file_id: '7019'
file_name: D8-DOG1_S47_R2_001.fastq
file_size: 2878017264
relation: main_file
title: Locus1_amplified_DOG
- access_level: open_access
checksum: d9550a4c044116075fa83f8f2ea31d6f
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:54:27Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - amplified.
file_id: '7020'
file_name: D4_S71_R2_001.fastq
file_size: 2180826995
relation: main_file
title: Locus2_amplified
- access_level: open_access
checksum: 466ceb302c020ac013007a879fcde69d
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:55:58Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - ancestral.
file_id: '7021'
file_name: IT030_S23_R2_001.fastq
file_size: 2108826444
relation: main_file
title: Locus2_ancestral
- access_level: open_access
checksum: 8aeb1da771713c7baa5a847eff889604
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-21T12:31:01Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - amplified, after
DOG-selection.
file_id: '7092'
file_name: D4-DOG1_S83_R2_001.fastq
file_size: 3144330494
relation: main_file
title: Locus2_amplified_DOG
- access_level: open_access
checksum: bf7d4b053f14af4655fb5574209fdb2d
content_type: application/zip
creator: itomanek
date_created: 2020-01-14T11:22:27Z
date_updated: 2020-07-14T12:47:47Z
description: Compressed genbank file format containing the sequence of the chromosomal
reporter gene cassette.
file_id: '7273'
file_name: galK_dual_reporter_cassette.gb.zip
file_size: 4179
relation: main_file
title: DNA sequence of the chromosomal reporter gene cassette
- access_level: open_access
checksum: 5e91cee2eff6f4a7cde456c6fb07c2ff
content_type: text/plain
creator: dernst
date_created: 2020-01-15T14:15:55Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7335'
file_name: Readme_7016.txt
file_size: 435
relation: main_file
title: Read_me_sequence_data
- access_level: open_access
checksum: 5e6745dcfb9c1b11dd935ac3ee45fe33
content_type: application/zip
creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
description: FACS data associated with Fig. 2c - see read_me_FACS
file_id: '7351'
file_name: FACS_data.xlsx.zip
file_size: 3765861
relation: main_file
title: FACS data
- access_level: open_access
checksum: a85caf092ae4b17668f70af2d93fad00
content_type: text/rtf
creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7352'
file_name: read_me_FACS.rtf
file_size: 4996
relation: main_file
- access_level: open_access
checksum: fd8ba5d75d24e47ddf7e70bfdadb40d4
content_type: text/rtf
creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7353'
file_name: read_me_microfluidics.rtf
file_size: 868
relation: main_file
- access_level: open_access
checksum: 69c5dc5ca5c069a138183c934acc1778
content_type: application/zip
creator: itomanek
date_created: 2020-01-22T15:44:17Z
date_updated: 2020-07-14T12:47:47Z
description: microfluidics time trace data - see read_me_microfluidics
file_id: '7354'
file_name: microfuidics_data.zip
file_size: 8141727
relation: main_file
title: microfluidics data
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
keyword:
- Escherichia coli
- gene amplification
- galactose
- DOG
- experimental evolution
- Illumina sequence data
- FACS data
- microfluidics data
month: '11'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7652'
relation: used_in_publication
status: public
status: public
title: Data for the paper "Gene amplification as a form of population-level gene expression
regulation"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7154'
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
citation:
ama: Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated
shells.” 2019. doi:10.15479/AT:ISTA:7154
apa: Guseinov, R. (2019). Supplementary data for “Programming temporal morphing
of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154
chicago: Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing
of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:7154.
ieee: R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated
shells.’” Institute of Science and Technology Austria, 2019.
ista: Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of
self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.
mla: Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing
of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019,
doi:10.15479/AT:ISTA:7154.
short: R. Guseinov, (2019).
contributor:
- first_name: Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Connor
last_name: McMahan
- first_name: Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Chiara
last_name: Daraio
- first_name: Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
date_created: 2019-12-09T07:52:46Z
date_published: 2019-12-06T00:00:00Z
date_updated: 2024-02-21T12:45:03Z
day: '06'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.15479/AT:ISTA:7154
ec_funded: 1
file:
- access_level: open_access
checksum: 155133e6e188e85b3c0676a5e70b9341
content_type: application/x-zip-compressed
creator: dernst
date_created: 2019-12-09T07:52:17Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7155'
file_name: temporal_morphing_supp_data.zip
file_size: 65307107
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8433'
relation: used_in_publication
status: deleted
- id: '7262'
relation: used_in_publication
status: public
status: public
title: Supplementary data for "Programming temporal morphing of self-actuated shells"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6060'
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019.
doi:10.15479/AT:ISTA:6060
apa: Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al.,
2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060
chicago: Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et
Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.
ieee: B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). .” Institute of Science and Technology Austria, 2019.
ista: Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.
mla: Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et
Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.
short: B. Vicoso, (2019).
date_created: 2019-02-28T10:55:15Z
date_published: 2019-02-28T00:00:00Z
date_updated: 2024-02-21T12:45:42Z
day: '28'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:6060
file:
- access_level: open_access
checksum: a338a622d728af0e3199cb07e6dd64d3
content_type: application/zip
creator: bvicoso
date_created: 2019-02-28T10:54:27Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6061'
file_name: SupData.zip
file_size: 36646050
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6418'
relation: research_paper
status: public
status: public
title: 'Supplementary data for "Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). '
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6074'
abstract:
- lang: eng
text: "This dataset contains the supplementary data for the research paper \"Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary
Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary
Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary
Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential
gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro
(ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene
Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro
(GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro
samples were split into upregulated and downregulated genes (up/down) and the
analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary
Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults
for the differential gene expression analysis for samples from adult mice before
(HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively).
Each sheet shows the results for a different comparison. Sheets 1-3 show results
for comparisons between timepoints for wild type (WT) samples only and sheets
4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results
for comparisons between genotypes at each time point and sheet 10 contains the
results for the analysis of differential expression trajectories between wild
type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults
for k-means clustering of genes by expression. Sheet 1 shows clustering of just
the genes with significantly different expression trajectories between genotypes.
Sheet 2 shows clustering of all genes that are significantly differentially expressed
in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary
Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis and EWCE analysis for enrichment of cell type specific genes for each
cluster identified by clustering genes with different expression trajectories
(see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults
showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet
1 shows protein protein interaction data generated from these results (combined
with data from the STRING database. Sheet 2 shows the results of the statistical
analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults
for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows
results for differential binding of PolII at the transcription start site (TSS)
between genotypes and sheets 2+3 show the corresponding GO enrichment analysis
for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with
increased binding of PolII at the TSS."
article_processing_charge: No
author:
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.” 2019. doi:10.15479/AT:ISTA:6074
apa: Dotter, C., & Novarino, G. (2019). Supplementary data for the research
paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental
gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074
chicago: Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research
Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6074.
ieee: C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.’” Institute of Science and Technology Austria, 2019.
ista: Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.
mla: Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research
Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:6074.
short: C. Dotter, G. Novarino, (2019).
date_created: 2019-03-07T13:32:35Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2024-02-21T13:41:01Z
day: '09'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:6074
file:
- access_level: open_access
checksum: bc1b285edca9e98a2c63d153c79bb75b
content_type: application/zip
creator: dernst
date_created: 2019-03-07T13:37:19Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6084'
file_name: Setd5_paper.zip
file_size: 33202743
relation: supplementary_material
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '3'
relation: research_paper
status: public
status: public
title: Supplementary data for the research paper "Haploinsufficiency of the intellectual
disability gene SETD5 disturbs developmental gene expression and cognition"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6062'
abstract:
- lang: eng
text: Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section
with Python 3.7).
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
citation:
ama: Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive
Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062
apa: Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal
Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6062
chicago: Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal
Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6062.
ieee: M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive
Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.
ista: Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal
Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:6062.
mla: Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal
Cognitive Map Is Attracted to Goals.” Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6062.
short: M. Nardin, (2019).
date_created: 2019-03-04T14:20:58Z
date_published: 2019-03-29T00:00:00Z
date_updated: 2024-02-21T12:46:04Z
day: '29'
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6062
file:
- access_level: open_access
checksum: 48e7b9a02939b763417733239522a236
content_type: application/zip
creator: mnardin
date_created: 2019-03-05T09:29:37Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6068'
file_name: Online_data.zip
file_size: 37002186
relation: main_file
title: Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals"
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6194'
relation: research_paper
status: public
status: public
title: Supplementary Code and Data for the paper "The Entorhinal Cognitive Map is
Attracted to Goals"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6089'
abstract:
- lang: eng
text: Pleiotropy is the well-established idea that a single mutation affects multiple
phenotypes. If a mutation has opposite effects on fitness when expressed in different
contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce
the efficacy of selection by limiting the fixation of beneficial mutations through
adaptation, and the removal of deleterious mutations through purifying selection.
Although this has been widely discussed, in particular in the context of a putative
“gender load,” it has yet to be systematically quantified. In this work, we empirically
estimate to which extent different pleiotropic regimes impede the efficacy of
selection in Drosophila melanogaster. We use whole-genome polymorphism data from
a single African population and divergence data from D. simulans to estimate the
fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction
of selection (DoS). After controlling for confounding covariates, we find that
the different pleiotropic regimes have a relatively small, but significant, effect
on selection efficacy. Specifically, our results suggest that pleiotropic sexual
antagonism may restrict the efficacy of selection, but that this conflict can
be resolved by limiting the expression of genes to the sex where they are beneficial.
Intermediate levels of pleiotropy across tissues and life stages can also lead
to maladaptation in D. melanogaster, due to inefficient purifying selection combined
with low frequency of mutations that confer a selective advantage. Thus, our study
highlights the need to consider the efficacy of selection in the context of antagonistic
pleiotropy, and of genetic conflict in general.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection
in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515.
doi:10.1093/molbev/msy246
apa: Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates
the efficacy of selection in drosophila melanogaster. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246
chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy
Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular
Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.
ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy
of selection in drosophila melanogaster,” Molecular biology and evolution,
vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.
ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy
of selection in drosophila melanogaster. Molecular biology and evolution. 36(3),
500–515.
mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection
in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36,
no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.
short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36
(2019) 500–515.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2024-02-21T13:59:17Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/molbev/msy246
external_id:
isi:
- '000462585100006'
pmid:
- '30590559'
intvolume: ' 36'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30590559
month: '03'
oa: 1
oa_version: Submitted Version
page: 500-515
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular biology and evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '5757'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2019'
...
---
_id: '6179'
abstract:
- lang: eng
text: "In the first part of this thesis we consider large random matrices with arbitrary
expectation and a general slowly decaying correlation among its entries. We prove
universality of the local eigenvalue statistics and optimal local laws for the
resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic
control of a multivariate cumulant expansion.\r\nIn the second part we consider
Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue
distribution the local eigenvalue statistics are uni- versal and form a Pearcey
process. Since the density of states typically exhibits only square root or cubic
root cusp singularities, our work complements previous results on the bulk and
edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta
universality conjecture for the last remaining universality type. Our analysis
holds not only for exact cusps, but approximate cusps as well, where an ex- tended
Pearcey process emerges. As a main technical ingredient we prove an optimal local
law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow-
nian motion to the cusp regime.\r\nIn the third and final part we explore the
entrywise linear statistics of Wigner ma- trices and identify the fluctuations
for a large class of test functions with little regularity. This enables us to
study the rectangular Young diagram obtained from the interlacing eigenvalues
of the random matrix and its minor, and we find that, despite having the same
limit, the fluctuations differ from those of the algebraic Young tableaux equipped
with the Plancharel measure."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: 'Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix
theory. 2019. doi:10.15479/AT:ISTA:th6179'
apa: 'Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in
random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179'
chicago: 'Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179.'
ieee: 'D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix
theory,” Institute of Science and Technology Austria, 2019.'
ista: 'Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random
matrix theory. Institute of Science and Technology Austria.'
mla: 'Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.'
short: 'D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix
Theory, Institute of Science and Technology Austria, 2019.'
date_created: 2019-03-28T08:58:59Z
date_published: 2019-03-18T00:00:00Z
date_updated: 2024-02-22T14:34:33Z
day: '18'
ddc:
- '515'
- '519'
degree_awarded: PhD
department:
- _id: LaEr
doi: 10.15479/AT:ISTA:th6179
ec_funded: 1
file:
- access_level: closed
checksum: 6926f66f28079a81c4937e3764be00fc
content_type: application/x-gzip
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6180'
file_name: 2019_Schroeder_Thesis.tar.gz
file_size: 7104482
relation: source_file
- access_level: open_access
checksum: 7d0ebb8d1207e89768cdd497a5bf80fb
content_type: application/pdf
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6181'
file_name: 2019_Schroeder_Thesis.pdf
file_size: 4228794
relation: main_file
file_date_updated: 2020-07-14T12:47:21Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '375'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1144'
relation: part_of_dissertation
status: public
- id: '6186'
relation: part_of_dissertation
status: public
- id: '6185'
relation: part_of_dissertation
status: public
- id: '6182'
relation: part_of_dissertation
status: public
- id: '1012'
relation: part_of_dissertation
status: public
- id: '6184'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: 'From Dyson to Pearcey: Universal statistics in random matrix theory'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6482'
abstract:
- lang: eng
text: 'Computer vision systems for automatic image categorization have become accurate
and reliable enough that they can run continuously for days or even years as components
of real-world commercial applications. A major open problem in this context, however,
is quality control. Good classification performance can only be expected if systems
run under the specific conditions, in particular data distributions, that they
were trained for. Surprisingly, none of the currently used deep network architectures
have a built-in functionality that could detect if a network operates on data
from a distribution it was not trained for, such that potentially a warning to
the human users could be triggered. In this work, we describe KS(conf), a procedure
for detecting such outside of specifications (out-of-specs) operation, based on
statistical testing of the network outputs. We show by extensive experiments using
the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that
KS(conf) reliably detects out-of-specs situations. It furthermore has a number
of properties that make it a promising candidate for practical deployment: it
is easy to implement, adds almost no overhead to the system, works with all networks,
including pretrained ones, and requires no a priori knowledge of how the data
distribution could change. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Rémy
full_name: Sun, Rémy
last_name: Sun
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside
of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18'
apa: 'Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet
operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at
the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature.
https://doi.org/10.1007/978-3-030-12939-2_18'
chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a
ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature,
2019. https://doi.org/10.1007/978-3-030-12939-2_18.'
ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates
outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition,
Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.'
ista: 'Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates
outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS,
vol. 11269, 244–259.'
mla: 'Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet
Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019,
pp. 244–59, doi:10.1007/978-3-030-12939-2_18.'
short: R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.
conference:
end_date: 2018-10-12
location: Stuttgart, Germany
name: 'GCPR: Conference on Pattern Recognition'
start_date: 2018-10-09
date_created: 2019-05-24T09:48:36Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2024-02-22T14:57:29Z
day: '14'
department:
- _id: ChLa
doi: 10.1007/978-3-030-12939-2_18
ec_funded: 1
external_id:
arxiv:
- '1804.04171'
intvolume: ' 11269'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04171
month: '02'
oa: 1
oa_version: Preprint
page: 244-259
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030129385'
- '9783030129392'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '6944'
relation: later_version
status: public
scopus_import: '1'
status: public
title: 'KS(conf): A light-weight test if a ConvNet operates outside of Its specifications'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11269
year: '2019'
...
---
_id: '6642'
abstract:
- lang: eng
text: We present a thermodynamically based approach to the design of models for
viscoelastic fluids with stress diffusion effect. In particular, we show how to
add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus,
FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that
the resulting models with the added stress diffusion term are thermodynamically
consistent in the sense that they obey the first and the second law of thermodynamics.
We point out the potential applications of the provided thermodynamical background
in the study of flows of fluids described by the proposed models.
article_number: '020002'
article_processing_charge: No
author:
- first_name: Mark
full_name: Dostalík, Mark
last_name: Dostalík
- first_name: Vít
full_name: Pruša, Vít
last_name: Pruša
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
citation:
ama: 'Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic
rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing;
2019. doi:10.1063/1.5109493'
apa: 'Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of
some classical viscoelastic rate-type models. In AIP Conference Proceedings
(Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493'
chicago: Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of
Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings,
Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493.
ieee: M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical
viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech
Republic, 2019, vol. 2107.
ista: Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical
viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference
on Novel Trends in Rheology vol. 2107, 020002.
mla: Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic
Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing,
2019, doi:10.1063/1.5109493.
short: M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing,
2019.
conference:
end_date: 2019-07-31
location: Zlin, Czech Republic
name: 8th International Conference on Novel Trends in Rheology
start_date: 2019-07-30
date_created: 2019-07-15T10:07:09Z
date_published: 2019-05-21T00:00:00Z
date_updated: 2024-02-28T13:01:28Z
day: '21'
department:
- _id: ChWo
doi: 10.1063/1.5109493
external_id:
arxiv:
- '1902.07983'
isi:
- '000479303100002'
intvolume: ' 2107'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07983
month: '05'
oa: 1
oa_version: Preprint
publication: AIP Conference Proceedings
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: On diffusive variants of some classical viscoelastic rate-type models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2107
year: '2019'
...
---
_id: '7226'
article_number: '123504'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Vojkan
full_name: Jaksic, Vojkan
last_name: Jaksic
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Jaksic V, Seiringer R. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
2019;60(12). doi:10.1063/1.5138135'
apa: 'Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical
Physics. AIP Publishing. https://doi.org/10.1063/1.5138135'
chicago: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135.'
ieee: 'V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics,
vol. 60, no. 12. AIP Publishing, 2019.'
ista: 'Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
60(12), 123504.'
mla: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.'
short: V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).
date_created: 2020-01-05T23:00:46Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2024-02-28T13:01:45Z
day: '01'
ddc:
- '500'
department:
- _id: RoSe
doi: 10.1063/1.5138135
external_id:
isi:
- '000505529800002'
file:
- access_level: open_access
checksum: bbd12ad1999a9ad7ba4d3c6f2e579c22
content_type: application/pdf
creator: dernst
date_created: 2020-01-07T14:59:13Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7244'
file_name: 2019_JournalMathPhysics_Jaksic.pdf
file_size: 1025015
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Introduction to the Special Collection: International Congress on Mathematical
Physics (ICMP) 2018'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2019'
...
---
_id: '7190'
abstract:
- lang: eng
text: We investigate the ground-state energy of a one-dimensional Fermi gas with
two bosonic impurities. We consider spinless fermions with no fermion-fermion
interactions. The fermion-impurity and impurity-impurity interactions are modeled
with Dirac delta functions. First, we study the case where impurity and fermion
have equal masses, and the impurity-impurity two-body interaction is identical
to the fermion-impurity interaction, such that the system is solvable with the
Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity
subsystem is below the energy of the bound state that exists without the Fermi
gas. We interpret this as a manifestation of attractive boson-boson interactions
induced by the fermionic medium, and refer to the impurity-impurity subsystem
as an in-medium bound state. For repulsive interactions, we find no in-medium
bound states. Second, we construct an effective model to describe these interactions,
and compare its predictions to the exact solution. We use this effective model
to study nonintegrable systems with unequal masses and/or potentials. We discuss
parameter regimes for which impurity-impurity attraction induced by the Fermi
gas can lead to the formation of in-medium bound states made of bosons that repel
each other in the absence of the Fermi gas.
article_number: '033177'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Huber, D.
last_name: Huber
- first_name: H.-W.
full_name: Hammer, H.-W.
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities
in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177
apa: Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states
of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research.
American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177
chicago: Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of
Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research.
American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.
ieee: D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas,” Physical Review Research, vol.
1, no. 3. American Physical Society, 2019.
ista: Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.
mla: Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional
Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical
Society, 2019, doi:10.1103/physrevresearch.1.033177.
short: D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).
date_created: 2019-12-17T13:03:41Z
date_published: 2019-12-16T00:00:00Z
date_updated: 2024-02-28T13:11:40Z
day: '16'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.1.033177
ec_funded: 1
external_id:
arxiv:
- '1908.02483'
file:
- access_level: open_access
checksum: 382eb67e62a77052a23887332d363f96
content_type: application/pdf
creator: dernst
date_created: 2019-12-18T07:13:14Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7193'
file_name: 2019_PhysRevResearch_Huber.pdf
file_size: 1370022
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '3'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: In-medium bound states of two bosonic impurities in a one-dimensional Fermi
gas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2019'
...
---
_id: '6575'
abstract:
- lang: eng
text: Motivated by recent experimental observations of coherent many-body revivals
in a constrained Rydbergatom chain, we construct a weak quasilocal deformation
of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect.
Our analysis suggests the existence of an underlying nonintegrableHamiltonian
which supports an emergent SU(2)-spin dynamics within a small subspace of the
many-bodyHilbert space. We show that such perfect dynamics necessitates the existence
of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore,
using these insights, we construct a toymodel that hosts exact quantum many-body
scars, providing an intuitive explanation of their origin. Ourresults offer specific
routes to enhancing coherent many-body revivals and provide a step towardestablishing
the stability of quantum many-body scars in the thermodynamic limit.
article_number: '220603'
article_processing_charge: No
article_type: original
author:
- first_name: Soonwon
full_name: Choi, Soonwon
last_name: Choi
- first_name: Christopher J.
full_name: Turner, Christopher J.
last_name: Turner
- first_name: Hannes
full_name: Pichler, Hannes
last_name: Pichler
- first_name: Wen Wei
full_name: Ho, Wen Wei
last_name: Ho
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail D.
full_name: Lukin, Mikhail D.
last_name: Lukin
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
citation:
ama: Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum
many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603
apa: Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z.,
… Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body
scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603
chicago: Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios
Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin.
“Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review
Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603.
ieee: S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body
scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society,
2019.
ista: Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin
MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars.
Physical Review Letters. 122(22), 220603.
mla: Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body
Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical
Society, 2019, doi:10.1103/PhysRevLett.122.220603.
short: S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn,
M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019).
date_created: 2019-06-23T21:59:13Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2024-02-28T13:12:22Z
day: '07'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.122.220603
external_id:
arxiv:
- '1812.05561'
isi:
- '000470885800005'
intvolume: ' 122'
isi: 1
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.05561
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergent SU(2) dynamics and perfect quantum many-body scars
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2019'
...
---
_id: '6092'
abstract:
- lang: eng
text: In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization
of a magnetic material results in mechanical rotation and vice versa. At the microscopic
level, this effect governs the transfer between electron spin and orbital angular
momentum, and lattice degrees of freedom, understanding which is key for molecular
magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now,
the timescales of electron-to-lattice angular momentum transfer remain unclear,
since modeling this process on a microscopic level requires the addition of an
infinite amount of quantum angular momenta. We show that this problem can be solved
by reformulating it in terms of the recently discovered angulon quasiparticles,
which results in a rotationally invariant quantum many-body theory. In particular,
we demonstrate that nonperturbative effects take place even if the electron-phonon
coupling is weak and give rise to angular momentum transfer on femtosecond timescales.
article_number: '064428'
article_processing_charge: No
author:
- first_name: Johann H
full_name: Mentink, Johann H
last_name: Mentink
- first_name: Mikhail
full_name: Katsnelson, Mikhail
last_name: Katsnelson
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de
Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428
apa: Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body
dynamics of the Einstein-de Haas effect. Physical Review B. American Physical
Society. https://doi.org/10.1103/PhysRevB.99.064428
chicago: Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body
Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical
Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428.
ieee: J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics
of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American
Physical Society, 2019.
ista: Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of
the Einstein-de Haas effect. Physical Review B. 99(6), 064428.
mla: Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas
Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society,
2019, doi:10.1103/PhysRevB.99.064428.
short: J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2024-02-28T13:11:54Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.99.064428
external_id:
arxiv:
- '1802.01638'
isi:
- '000459223400004'
intvolume: ' 99'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.01638
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum many-body dynamics of the Einstein-de Haas effect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '6090'
abstract:
- lang: eng
text: Cells need to reliably sense external ligand concentrations to achieve various
biological functions such as chemotaxis or signaling. The molecular recognition
of ligands by surface receptors is degenerate in many systems, leading to crosstalk
between ligand-receptor pairs. Crosstalk is often thought of as a deviation from
optimal specific recognition, as the binding of noncognate ligands can interfere
with the detection of the receptor's cognate ligand, possibly leading to a false
triggering of a downstream signaling pathway. Here we quantify the optimal precision
of sensing the concentrations of multiple ligands by a collection of promiscuous
receptors. We demonstrate that crosstalk can improve precision in concentration
sensing and discrimination tasks. To achieve superior precision, the additional
information about ligand concentrations contained in short binding events of the
noncognate ligand should be exploited. We present a proofreading scheme to realize
an approximate estimation of multiple ligand concentrations that reaches a precision
close to the derived optimal bounds. Our results help rationalize the observed
ubiquity of receptor crosstalk in molecular sensing.
article_number: '022423'
article_processing_charge: No
author:
- first_name: Martín
full_name: Carballo-Pacheco, Martín
last_name: Carballo-Pacheco
- first_name: Jonathan
full_name: Desponds, Jonathan
last_name: Desponds
- first_name: Tatyana
full_name: Gavrilchenko, Tatyana
last_name: Gavrilchenko
- first_name: Andreas
full_name: Mayer, Andreas
last_name: Mayer
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Gautam
full_name: Reddy, Gautam
last_name: Reddy
- first_name: Ilya
full_name: Nemenman, Ilya
last_name: Nemenman
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves
concentration sensing of multiple ligands. Physical Review E. 2019;99(2).
doi:10.1103/PhysRevE.99.022423
apa: Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R.,
Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing
of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423
chicago: Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas
Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor
Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review
E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.
ieee: M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration
sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American
Physical Society, 2019.
ista: Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G,
Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of
multiple ligands. Physical Review E. 99(2), 022423.
mla: Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration
Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423,
American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.
short: M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G.
Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-26T00:00:00Z
date_updated: 2024-02-28T13:12:06Z
day: '26'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.99.022423
external_id:
isi:
- '000459916500007'
intvolume: ' 99'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/448118v1.abstract
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Receptor crosstalk improves concentration sensing of multiple ligands
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '6786'
abstract:
- lang: eng
text: Dipolar coupling plays a fundamental role in the interaction between electrically
or magnetically polarized species such as magnetic atoms and dipolar molecules
in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike
interactions found in many atomic, molecular, and condensed-matter systems, this
interaction is long-ranged and highly anisotropic, as it changes from repulsive
to attractive depending on the relative positions and orientation of the dipoles.
Because of this unique property, many exotic, symmetry-breaking collective states
have been recently predicted for cold dipolar gases, but only a few have been
experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates.
Here, we report on the first observation of attractive dipolar coupling between
excitonic dipoles using a new design of stacked semiconductor bilayers. We show
that the presence of a dipolar exciton fluid in one bilayer modifies the spatial
distribution and increases the binding energy of excitonic dipoles in a vertically
remote layer. The binding energy changes are explained using a many-body polaron
model describing the deformation of the exciton cloud due to its interaction with
a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud
density indicates the important role of dipolar correlations, which is unique
to dense, strongly interacting dipolar solid-state systems. Our concept provides
a route for the realization of dipolar lattices with strong anisotropic interactions
in semiconductor systems, which open the way for the observation of theoretically
predicted new and exotic collective phases, as well as for engineering and sensing
their collective excitations.
article_number: '021026'
article_processing_charge: No
article_type: original
author:
- first_name: Colin
full_name: Hubert, Colin
last_name: Hubert
- first_name: Yifat
full_name: Baruchi, Yifat
last_name: Baruchi
- first_name: Yotam
full_name: Mazuz-Harpaz, Yotam
last_name: Mazuz-Harpaz
- first_name: Kobi
full_name: Cohen, Kobi
last_name: Cohen
- first_name: Klaus
full_name: Biermann, Klaus
last_name: Biermann
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Ken
full_name: West, Ken
last_name: West
- first_name: Loren
full_name: Pfeiffer, Loren
last_name: Pfeiffer
- first_name: Ronen
full_name: Rapaport, Ronen
last_name: Rapaport
- first_name: Paulo
full_name: Santos, Paulo
last_name: Santos
citation:
ama: Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between
stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026
apa: Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko,
M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids.
Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026
chicago: Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann,
Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos.
“Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review
X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026.
ieee: C. Hubert et al., “Attractive dipolar coupling between stacked exciton
fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019.
ista: Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West
K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between
stacked exciton fluids. Physical Review X. 9(2), 021026.
mla: Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton
Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society,
2019, doi:10.1103/PhysRevX.9.021026.
short: C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko,
K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).
date_created: 2019-08-11T21:59:20Z
date_published: 2019-05-08T00:00:00Z
date_updated: 2024-02-28T13:12:48Z
day: '08'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevX.9.021026
external_id:
arxiv:
- '1807.11238'
isi:
- '000467402900001'
file:
- access_level: open_access
checksum: 065ff82ee4a1d2c3773ce4b76ff4213c
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T12:14:18Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6802'
file_name: 2019_PhysReviewX_Hubert.pdf
file_size: 1193550
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attractive dipolar coupling between stacked exciton fluids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2019'
...
---
_id: '7013'
abstract:
- lang: eng
text: Chains of superconducting circuit devices provide a natural platform for studies
of synthetic bosonic quantum matter. Motivated by the recent experimental progress
in realizing disordered and interacting chains of superconducting transmon devices,
we study the bosonic many-body localization phase transition using the methods
of exact diagonalization as well as matrix product state dynamics. We estimate
the location of transition separating the ergodic and the many-body localized
phases as a function of the disorder strength and the many-body on-site interaction
strength. The main difference between the bosonic model realized by superconducting
circuits and similar fermionic model is that the effect of the on-site interaction
is stronger due to the possibility of multiple excitations occupying the same
site. The phase transition is found to be robust upon including longer-range hopping
and interaction terms present in the experiments. Furthermore, we calculate experimentally
relevant local observables and show that their temporal fluctuations can be used
to distinguish between the dynamics of Anderson insulator, many-body localization,
and delocalized phases. While we consider unitary dynamics, neglecting the effects
of dissipation, decoherence, and measurement back action, the timescales on which
the dynamics is unitary are sufficient for observation of characteristic dynamics
in the many-body localized phase. Moreover, the experimentally available disorder
strength and interactions allow for tuning the many-body localization phase transition,
thus making the arrays of superconducting circuit devices a promising platform
for exploring localization physics and phase transition.
article_number: '134504'
article_processing_charge: No
article_type: original
author:
- first_name: Tuure
full_name: Orell, Tuure
last_name: Orell
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Matti
full_name: Silveri, Matti
last_name: Silveri
citation:
ama: Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization
phase transition with superconducting circuits. Physical Review B. 2019;100(13).
doi:10.1103/physrevb.100.134504
apa: Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the
many-body localization phase transition with superconducting circuits. Physical
Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504
chicago: Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing
the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical
Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504.
ieee: T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body
localization phase transition with superconducting circuits,” Physical Review
B, vol. 100, no. 13. American Physical Society, 2019.
ista: Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization
phase transition with superconducting circuits. Physical Review B. 100(13), 134504.
mla: Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with
Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504,
American Physical Society, 2019, doi:10.1103/physrevb.100.134504.
short: T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).
date_created: 2019-11-13T08:25:48Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2024-02-28T13:13:13Z
day: '01'
department:
- _id: MaSe
doi: 10.1103/physrevb.100.134504
external_id:
arxiv:
- '1907.04043'
isi:
- '000489036500004'
intvolume: ' 100'
isi: 1
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.04043
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probing the many-body localization phase transition with superconducting circuits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7200'
abstract:
- lang: eng
text: Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting
films found an emergent inhomogeneity at the scale of tens of nanometers. This
inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity
measured in transport above the superconducting critical temperature Tc. This
behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper
pairs that display a quasiconfinement (i.e., a slowing down of their diffusive
dynamics) on length scales shorter than the inhomogeneity identified by tunneling
experiments. Here, we assume this anomalous diffusive behavior of fluctuating
Cooper pairs and calculate the effect of these fluctuations on the electron density
of states above Tc. We find that the density of states is substantially suppressed
up to temperatures well above Tc. This behavior, which is closely reminiscent
of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper
pairs in the absence of stable preformed pairs, setting the stage for an intermediate
behavior between the two common paradigms in the superconducting-insulator transition,
namely, the localization of Cooper pairs (the so-called bosonic scenario) and
the breaking of Cooper pairs into unpaired electrons due to strong disorder (the
so-called fermionic scenario).
article_number: '174518'
article_processing_charge: No
article_type: original
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marco
full_name: Grilli, Marco
last_name: Grilli
- first_name: Brigitte
full_name: Leridon, Brigitte
last_name: Leridon
- first_name: Sergio
full_name: Caprara, Sergio
last_name: Caprara
citation:
ama: Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of
fluctuating Cooper pairs on the density of states of superconducting NbN thin
films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518
apa: Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous
diffusion of fluctuating Cooper pairs on the density of states of superconducting
NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518
chicago: Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect
of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of
Superconducting NbN Thin Films.” Physical Review B. American Physical Society,
2019. https://doi.org/10.1103/PhysRevB.100.174518.
ieee: P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion
of fluctuating Cooper pairs on the density of states of superconducting NbN thin
films,” Physical Review B, vol. 100, no. 17. American Physical Society,
2019.
ista: Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion
of fluctuating Cooper pairs on the density of states of superconducting NbN thin
films. Physical Review B. 100(17), 174518.
mla: Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper
Pairs on the Density of States of Superconducting NbN Thin Films.” Physical
Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.
short: P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).
date_created: 2019-12-22T23:00:41Z
date_published: 2019-11-25T00:00:00Z
date_updated: 2024-02-28T13:14:08Z
day: '25'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.100.174518
external_id:
arxiv:
- '1907.13579'
isi:
- '000498845700006'
intvolume: ' 100'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.13579
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effect of anomalous diffusion of fluctuating Cooper pairs on the density of
states of superconducting NbN thin films
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '6779'
abstract:
- lang: eng
text: "Recent studies suggest that unstable recurrent solutions of the Navier-Stokes
equation provide new insights\r\ninto dynamics of turbulent flows. In this study,
we compute an extensive network of dynamical connections\r\nbetween such solutions
in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion
symmetric subspace. In particular, we find numerous isolated heteroclinic connections
between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic
orbits—as well as continua of connections forming\r\nhigher-dimensional connecting
manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide
strong evidence that the associated homoclinic tangle forms the chaotic repeller
that underpins transient\r\nturbulence in the symmetric subspace."
article_number: '013112'
article_processing_charge: No
article_type: original
author:
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Ravi Kumar
full_name: Pallantla, Ravi Kumar
last_name: Pallantla
- first_name: Michael F.
full_name: Schatz, Michael F.
last_name: Schatz
- first_name: Roman O.
full_name: Grigoriev, Roman O.
last_name: Grigoriev
citation:
ama: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic
connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1).
doi:10.1103/physreve.100.013112
apa: Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic
and homoclinic connections in a Kolmogorov-like flow. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.100.013112
chicago: Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O.
Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.”
Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.
ieee: B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic
and homoclinic connections in a Kolmogorov-like flow,” Physical Review E,
vol. 100, no. 1. American Physical Society, 2019.
ista: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic
connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.
mla: Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like
Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society,
2019, doi:10.1103/physreve.100.013112.
short: B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100
(2019).
date_created: 2019-08-09T09:40:41Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2024-02-28T13:13:00Z
day: '25'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/physreve.100.013112
ec_funded: 1
external_id:
arxiv:
- '1907.05860'
isi:
- '000477911800012'
intvolume: ' 100'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.05860
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heteroclinic and homoclinic connections in a Kolmogorov-like flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7015'
abstract:
- lang: eng
text: We modify the "floating crystal" trial state for the classical homogeneous
electron gas (also known as jellium), in order to suppress the boundary charge
fluctuations that are known to lead to a macroscopic increase of the energy. The
argument is to melt a thin layer of the crystal close to the boundary and consequently
replace it by an incompressible fluid. With the aid of this trial state we show
that three different definitions of the ground-state energy of jellium coincide.
In the first point of view the electrons are placed in a neutralizing uniform
background. In the second definition there is no background but the electrons
are submitted to the constraint that their density is constant, as is appropriate
in density functional theory. Finally, in the third system each electron interacts
with a periodic image of itself; that is, periodic boundary conditions are imposed
on the interaction potential.
article_number: '035127'
article_processing_charge: No
article_type: original
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Elliott H.
full_name: Lieb, Elliott H.
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge
fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127
apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal
with no boundary charge fluctuations. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.100.035127
chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner
Crystal with No Boundary Charge Fluctuations.” Physical Review B. American
Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127.
ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary
charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical
Society, 2019.
ista: Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary
charge fluctuations. Physical Review B. 100(3), 035127.
mla: Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.”
Physical Review B, vol. 100, no. 3, 035127, American Physical Society,
2019, doi:10.1103/physrevb.100.035127.
short: M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).
date_created: 2019-11-13T08:41:48Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2024-02-28T13:13:23Z
day: '25'
department:
- _id: RoSe
doi: 10.1103/physrevb.100.035127
ec_funded: 1
external_id:
arxiv:
- '1905.09138'
isi:
- '000477888200001'
intvolume: ' 100'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.09138
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal with no boundary charge fluctuations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7145'
abstract:
- lang: eng
text: End-to-end correlated bound states are investigated in superconductor-semiconductor
hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently
identified from each wire end, and a cross-correlation function is computed that
counts end-to-end coincidences, averaging over thousands of subgap features. Strong
correlations in a short, 300-nm device are reduced by a factor of 4 in a long,
900-nm device. In addition, subgap conductance distributions are investigated,
and correlations between the left and right distributions are identified based
on their mutual information.
article_number: '205412'
article_processing_charge: No
article_type: original
author:
- first_name: G. L. R.
full_name: Anselmetti, G. L. R.
last_name: Anselmetti
- first_name: E. A.
full_name: Martinez, E. A.
last_name: Martinez
- first_name: G. C.
full_name: Ménard, G. C.
last_name: Ménard
- first_name: D.
full_name: Puglia, D.
last_name: Puglia
- first_name: F. K.
full_name: Malinowski, F. K.
last_name: Malinowski
- first_name: J. S.
full_name: Lee, J. S.
last_name: Lee
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: M.
full_name: Pendharkar, M.
last_name: Pendharkar
- first_name: C. J.
full_name: Palmstrøm, C. J.
last_name: Palmstrøm
- first_name: C. M.
full_name: Marcus, C. M.
last_name: Marcus
- first_name: L.
full_name: Casparis, L.
last_name: Casparis
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412
apa: Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski,
F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. American Physical Society.
https://doi.org/10.1103/physrevb.100.205412
chicago: Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski,
J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.”
Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412.
ieee: G. L. R. Anselmetti et al., “End-to-end correlated subgap states in
hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical
Society, 2019.
ista: Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi
S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end
correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.
mla: Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid
Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical
Society, 2019, doi:10.1103/physrevb.100.205412.
short: G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski,
J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P.
Higginbotham, Physical Review B 100 (2019).
date_created: 2019-12-04T16:02:25Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2024-02-28T13:13:51Z
day: '15'
department:
- _id: AnHi
doi: 10.1103/physrevb.100.205412
external_id:
arxiv:
- '1908.05549'
isi:
- '000495967500006'
intvolume: ' 100'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.05549
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: End-to-end correlated subgap states in hybrid nanowires
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...