---
_id: '198'
abstract:
- lang: eng
text: We consider a class of students learning a language from a teacher. The situation
can be interpreted as a group of child learners receiving input from the linguistic
environment. The teacher provides sample sentences. The students try to learn
the grammar from the teacher. In addition to just listening to the teacher, the
students can also communicate with each other. The students hold hypotheses about
the grammar and change them if they receive counter evidence. The process stops
when all students have converged to the correct grammar. We study how the time
to convergence depends on the structure of the classroom by introducing and evaluating
various complexity measures. We find that structured communication between students,
although potentially introducing confusion, can greatly reduce some of the complexity
measures. Our theory can also be interpreted as applying to the scientific process,
where nature is the teacher and the scientists are the students.
article_number: '20180073'
article_processing_charge: No
article_type: original
author:
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with
communication between learners. Journal of the Royal Society Interface.
2018;15(140). doi:10.1098/rsif.2018.0073
apa: Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language
acquisition with communication between learners. Journal of the Royal Society
Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073
chicago: Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. “Language Acquisition with Communication between Learners.” Journal
of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073.
ieee: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition
with communication between learners,” Journal of the Royal Society Interface,
vol. 15, no. 140. The Royal Society, 2018.
ista: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition
with communication between learners. Journal of the Royal Society Interface. 15(140),
20180073.
mla: Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between
Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073,
The Royal Society, 2018, doi:10.1098/rsif.2018.0073.
short: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal
Society Interface 15 (2018).
date_created: 2018-12-11T11:45:09Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-10-18T06:36:00Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rsif.2018.0073
ec_funded: 1
external_id:
isi:
- '000428576200023'
pmid:
- '29593089'
file:
- access_level: open_access
checksum: 444e1a9d98eb0e780671be82b13025f3
content_type: application/pdf
creator: dernst
date_created: 2019-02-12T07:54:37Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5955'
file_name: 2018_RS_IbsenJensen.pdf
file_size: 219837
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '140'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
publication_status: published
publisher: The Royal Society
publist_id: '7715'
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://dx.doi.org/10.6084/m9.figshare.c.4028971
record:
- id: '9814'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Language acquisition with communication between learners
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '199'
abstract:
- lang: eng
text: Sex-biased genes are central to the study of sexual selection, sexual antagonism,
and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome
in the common frog Rana temporaria based on five developmental stages and three
adult tissues from both sexes, obtained from a population with karyotypically
homomorphic but genetically differentiated sex chromosomes. This allows the study
of sex-biased gene expression throughout development, and its effect on the rate
of gene evolution while accounting for pleiotropic expression, which is known
to negatively correlate with the evolutionary rate. Overall, sex-biased genes
had little overlap among developmental stages and adult tissues. Late developmental
stages and gonad tissues had the highest numbers of stage-or tissue-specific genes.
We find that pleiotropic gene expression is a better predictor than sex bias for
the evolutionary rate of genes, though it often interacts with sex bias. Although
genetically differentiated, the sex chromosomes were not enriched in sex-biased
genes, possibly due to a very recent arrest of XY recombination. These results
extend our understanding of the developmental dynamics, tissue specificity, and
genomic localization of sex-biased genes.
article_number: '294'
article_processing_charge: No
author:
- first_name: Wen
full_name: Ma, Wen
last_name: Ma
- first_name: Paris
full_name: Veltsos, Paris
last_name: Veltsos
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Nicolas
full_name: Rodrigues, Nicolas
last_name: Rodrigues
- first_name: Roberto
full_name: Sermier, Roberto
last_name: Sermier
- first_name: Daniel
full_name: Jeffries, Daniel
last_name: Jeffries
- first_name: Nicolas
full_name: Perrin, Nicolas
last_name: Perrin
citation:
ama: Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased
gene expression in a common frog population with differentiated, yet homomorphic,
sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294
apa: Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D.,
& Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression
in a common frog population with differentiated, yet homomorphic, sex chromosomes.
Genes. MDPI AG. https://doi.org/10.3390/genes9060294
chicago: Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier,
Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased
Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic,
Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294.
ieee: W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression
in a common frog population with differentiated, yet homomorphic, sex chromosomes,”
Genes, vol. 9, no. 6. MDPI AG, 2018.
ista: Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018.
Tissue specificity and dynamics of sex biased gene expression in a common frog
population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6),
294.
mla: Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression
in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.”
Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.
short: W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N.
Perrin, Genes 9 (2018).
date_created: 2018-12-11T11:45:09Z
date_published: 2018-06-12T00:00:00Z
date_updated: 2023-09-19T10:15:31Z
day: '12'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes9060294
external_id:
isi:
- '000436494200026'
file:
- access_level: open_access
checksum: 423069beb1cd3cdd25bf3f464b38f1d7
content_type: application/pdf
creator: dernst
date_created: 2019-02-01T07:52:28Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5905'
file_name: 2018_Genes_Ma.pdf
file_size: 3985796
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Genes
publication_status: published
publisher: MDPI AG
publist_id: '7714'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tissue specificity and dynamics of sex biased gene expression in a common frog
population with differentiated, yet homomorphic, sex chromosomes
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '2'
abstract:
- lang: eng
text: Indirect reciprocity explores how humans act when their reputation is at stake,
and which social norms they use to assess the actions of others. A crucial question
in indirect reciprocity is which social norms can maintain stable cooperation
in a society. Past research has highlighted eight such norms, called “leading-eight”
strategies. This past research, however, is based on the assumption that all relevant
information about other population members is publicly available and that everyone
agrees on who is good or bad. Instead, here we explore the reputation dynamics
when information is private and noisy. We show that under these conditions, most
leading-eight strategies fail to evolve. Those leading-eight strategies that do
evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism
for cooperation based on shared moral systems and individual reputations. It assumes
that members of a community routinely observe and assess each other and that they
use this information to decide who is good or bad, and who deserves cooperation.
When information is transmitted publicly, such that all community members agree
on each other’s reputation, previous research has highlighted eight crucial moral
systems. These “leading-eight” strategies can maintain cooperation and resist
invasion by defectors. However, in real populations individuals often hold their
own private views of others. Once two individuals disagree about their opinion
of some third party, they may also see its subsequent actions in a different light.
Their opinions may further diverge over time. Herein, we explore indirect reciprocity
when information transmission is private and noisy. We find that in the presence
of perception errors, most leading-eight strategies cease to be stable. Even if
a leading-eight strategy evolves, cooperation rates may drop considerably when
errors are common. Our research highlights the role of reliable information and
synchronized reputations to maintain stable moral systems.
article_processing_charge: No
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with
private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246.
doi:10.1073/pnas.1810565115
apa: Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018).
Indirect reciprocity with private, noisy, and incomplete information. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115
chicago: Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and
Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.”
PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115.
ieee: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity
with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48.
National Academy of Sciences, pp. 12241–12246, 2018.
ista: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity
with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.
mla: Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete
Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018,
pp. 12241–46, doi:10.1073/pnas.1810565115.
short: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018)
12241–12246.
date_created: 2018-12-11T11:44:05Z
date_published: 2018-11-27T00:00:00Z
date_updated: 2025-07-14T09:10:09Z
day: '27'
department:
- _id: KrCh
doi: 10.1073/pnas.1810565115
ec_funded: 1
external_id:
isi:
- '000451351000063'
pmid:
- '30429320'
intvolume: ' 115'
isi: 1
issue: '48'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30429320
month: '11'
oa: 1
oa_version: Submitted Version
page: 12241-12246
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/no-cooperation-without-open-communication/
record:
- id: '10293'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Indirect reciprocity with private, noisy, and incomplete information
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '20'
abstract:
- lang: eng
text: 'Background: Norepinephrine (NE) signaling has a key role in white adipose
tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under
certain conditions, conversion of white into brite (brown-in-white) adipocytes.
However, acute effects of NE stimulation have not been described at the transcriptional
network level. Results: We used RNA-seq to uncover a broad transcriptional response.
The inference of protein-protein and protein-DNA interaction networks allowed
us to identify a set of immediate-early genes (IEGs) with high betweenness, validating
our approach and suggesting a hierarchical control of transcriptional regulation.
In addition, we identified a transcriptional regulatory network with IEGs as master
regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover,
a functional enrichment analysis and gene clustering into functional modules suggest
a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether,
our network biology approach explores for the first time the immediate-early systems
level response of human adipocytes to acute sympathetic activation, thereby providing
a first network basis of early cell fate programs and crosstalks between metabolic
and transcriptional networks required for proper WAT function.'
acknowledgement: This work was funded by the German Centre for Diabetes Research (DZD)
and the Austrian Science Fund (FWF, P25729-B19).
article_processing_charge: No
article_type: original
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an
immediate-early regulatory network response in primary human white adipocytes.
BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0
apa: Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes. BMC Genomics.
BioMed Central. https://doi.org/10.1186/s12864-018-5173-0
chicago: Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.”
BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.
ieee: J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes,” BMC Genomics,
vol. 19, no. 1. BioMed Central, 2018.
ista: Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S,
Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network
response in primary human white adipocytes. BMC Genomics. 19(1).
mla: Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early
Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics,
vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, BMC Genomics 19 (2018).
date_created: 2018-12-11T11:44:12Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1186/s12864-018-5173-0
external_id:
isi:
- '000450976700002'
file:
- access_level: open_access
checksum: a56516e734dab589dc7f3e1915973b4d
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:52:57Z
date_updated: 2020-07-14T12:45:23Z
file_id: '5712'
file_name: 2018_BMCGenomics_Higareda.pdf
file_size: 4629784
relation: main_file
file_date_updated: 2020-07-14T12:45:23Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
issn:
- 1471-2164
publication_status: published
publisher: BioMed Central
publist_id: '8035'
quality_controlled: '1'
related_material:
record:
- id: '9807'
relation: research_data
status: public
- id: '9808'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Norepinephrine triggers an immediate-early regulatory network response in primary
human white adipocytes
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '200'
abstract:
- lang: eng
text: This thesis is concerned with the inference of current population structure
based on geo-referenced genetic data. The underlying idea is that population structure
affects its spatial genetic structure. Therefore, genotype information can be
utilized to estimate important demographic parameters such as migration rates.
These indirect estimates of population structure have become very attractive,
as genotype data is now widely available. However, there also has been much concern
about these approaches. Importantly, genetic structure can be influenced by many
complex patterns, which often cannot be disentangled. Moreover, many methods merely
fit heuristic patterns of genetic structure, and do not build upon population
genetics theory. Here, I describe two novel inference methods that address these
shortcomings. In Chapter 2, I introduce an inference scheme based on a new type
of signal, identity by descent (IBD) blocks. Recently, it has become feasible
to detect such long blocks of genome shared between pairs of samples. These blocks
are direct traces of recent coalescence events. As such, they contain ample signal
for inferring recent demography. I examine sharing of IBD blocks in two-dimensional
populations with local migration. Using a diffusion approximation, I derive formulas
for an isolation by distance pattern of long IBD blocks and show that sharing
of long IBD blocks approaches rapid exponential decay for growing sample distance.
I describe an inference scheme based on these results. It can robustly estimate
the dispersal rate and population density, which is demonstrated on simulated
data. I also show an application to estimate mean migration and the rate of recent
population growth within Eastern Europe. Chapter 3 is about a novel method to
estimate barriers to gene flow in a two dimensional population. This inference
scheme utilizes geographically localized allele frequency fluctuations - a classical
isolation by distance signal. The strength of these local fluctuations increases
on average next to a barrier, and there is less correlation across it. I again
use a framework of diffusion of ancestral lineages to model this effect, and provide
an efficient numerical implementation to fit the results to geo-referenced biallelic
SNP data. This inference scheme is able to robustly estimate strong barriers to
gene flow, as tests on simulated data confirm.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
citation:
ama: Ringbauer H. Inferring recent demography from spatial genetic structure. 2018.
doi:10.15479/AT:ISTA:th_963
apa: Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963
chicago: Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.
ieee: H. Ringbauer, “Inferring recent demography from spatial genetic structure,”
Institute of Science and Technology Austria, 2018.
ista: Ringbauer H. 2018. Inferring recent demography from spatial genetic structure.
Institute of Science and Technology Austria.
mla: Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.
short: H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure,
Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:45:10Z
date_published: 2018-02-21T00:00:00Z
date_updated: 2025-05-28T11:57:06Z
day: '21'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:th_963
file:
- access_level: open_access
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creator: system
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content_type: application/zip
creator: dernst
date_created: 2019-04-05T09:30:12Z
date_updated: 2020-07-14T12:45:23Z
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file_size: 113365
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language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: '146'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7713'
pubrep_id: '963'
related_material:
record:
- id: '563'
relation: part_of_dissertation
status: public
- id: '1074'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Inferring recent demography from spatial genetic structure
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '201'
abstract:
- lang: eng
text: 'We describe arrangements of three-dimensional spheres from a geometrical
and topological point of view. Real data (fitting this setup) often consist of
soft spheres which show certain degree of deformation while strongly packing against
each other. In this context, we answer the following questions: If we model a
soft packing of spheres by hard spheres that are allowed to overlap, can we measure
the volume in the overlapped areas? Can we be more specific about the overlap
volume, i.e. quantify how much volume is there covered exactly twice, three times,
or k times? What would be a good optimization criteria that rule the arrangement
of soft spheres while making a good use of the available space? Fixing a particular
criterion, what would be the optimal sphere configuration? The first result of
this thesis are short formulas for the computation of volumes covered by at least
k of the balls. The formulas exploit information contained in the order-k Voronoi
diagrams and its closely related Level-k complex. The used complexes lead to a
natural generalization into poset diagrams, a theoretical formalism that contains
the order-k and degree-k diagrams as special cases. In parallel, we define different
criteria to determine what could be considered an optimal arrangement from a geometrical
point of view. Fixing a criterion, we find optimal soft packing configurations
in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools
from computational topology on real physical data, to show the potentials of higher-order
diagrams in the description of melting crystals. The results of the experiments
leaves us with an open window to apply the theories developed in this thesis in
real applications.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026
apa: Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026
chicago: Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.
ieee: M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology
Austria, 2018.
ista: Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and
Technology Austria.
mla: Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science
and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.
short: M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology
Austria, 2018.
date_created: 2018-12-11T11:45:10Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2023-09-07T12:25:32Z
day: '11'
ddc:
- '514'
- '516'
degree_awarded: PhD
department:
- _id: HeEd
doi: 10.15479/AT:ISTA:th_1026
file:
- access_level: closed
checksum: dd699303623e96d1478a6ae07210dd05
content_type: application/zip
creator: kschuh
date_created: 2019-02-05T07:43:31Z
date_updated: 2020-07-14T12:45:24Z
file_id: '5918'
file_name: IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip
file_size: 11827713
relation: source_file
- access_level: open_access
checksum: ba163849a190d2b41d66fef0e4983294
content_type: application/pdf
creator: kschuh
date_created: 2019-02-05T07:43:45Z
date_updated: 2020-07-14T12:45:24Z
file_id: '5919'
file_name: IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf
file_size: 4783846
relation: main_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '171'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7712'
pubrep_id: '1026'
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Multiple covers with balls
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '2015'
abstract:
- lang: eng
text: We consider the problem of learning a Bayesian network or directed acyclic
graph model from observational data. A number of constraint‐based, score‐based
and hybrid algorithms have been developed for this purpose. Statistical consistency
guarantees of these algorithms rely on the faithfulness assumption, which has
been shown to be restrictive especially for graphs with cycles in the skeleton.
We here propose the sparsest permutation (SP) algorithm, showing that learning
Bayesian networks is possible under strictly weaker assumptions than faithfulness.
This comes at a computational price, thereby indicating a statistical‐computational
trade‐off for causal inference algorithms. In the Gaussian noiseless setting,
we prove that the SP algorithm boils down to finding the permutation of the variables
with the sparsest Cholesky decomposition of the inverse covariance matrix, which
is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation
study showing that in line with the proven stronger consistency guarantees, and
the SP algorithm compares favourably to standard causal inference algorithms in
terms of accuracy for a given sample size.
article_number: e183
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Garvesh
full_name: Raskutti, Garvesh
last_name: Raskutti
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations.
STAT. 2018;7(1). doi:10.1002/sta4.183
apa: Raskutti, G., & Uhler, C. (2018). Learning directed acyclic graphs based
on sparsest permutations. STAT. Wiley. https://doi.org/10.1002/sta4.183
chicago: Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs
Based on Sparsest Permutations.” STAT. Wiley, 2018. https://doi.org/10.1002/sta4.183.
ieee: G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest
permutations,” STAT, vol. 7, no. 1. Wiley, 2018.
ista: Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest
permutations. STAT. 7(1), e183.
mla: Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based
on Sparsest Permutations.” STAT, vol. 7, no. 1, e183, Wiley, 2018, doi:10.1002/sta4.183.
short: G. Raskutti, C. Uhler, STAT 7 (2018).
date_created: 2018-12-11T11:55:13Z
date_published: 2018-04-17T00:00:00Z
date_updated: 2021-01-12T06:54:44Z
day: '17'
doi: 10.1002/sta4.183
extern: '1'
external_id:
arxiv:
- '1307.0366'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.0366
month: '04'
oa: 1
oa_version: Preprint
publication: STAT
publication_status: published
publisher: Wiley
publist_id: '5061'
quality_controlled: '1'
status: public
title: Learning directed acyclic graphs based on sparsest permutations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2018'
...
---
_id: '203'
abstract:
- lang: eng
text: Asymmetric auxin distribution is instrumental for the differential growth
that causes organ bending on tropic stimuli and curvatures during plant development.
Local differences in auxin concentrations are achieved mainly by polarized cellular
distribution of PIN auxin transporters, but whether other mechanisms involving
auxin homeostasis are also relevant for the formation of auxin gradients is not
clear. Here we show that auxin methylation is required for asymmetric auxin distribution
across the hypocotyl, particularly during its response to gravity. We found that
loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1)
prematurely unfold the apical hook, and that their hypocotyls are impaired in
gravitropic reorientation. This defect is linked to an auxin-dependent increase
in PIN gene expression, leading to an increased polar auxin transport and lack
of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation
in the iamt1 mutant could be restored with either endodermis-specific expression
of IAMT1 or partial inhibition of polar auxin transport, which also results in
normal PIN gene expression levels. We propose that IAA methylation is necessary
in gravity-sensing cells to restrict polar auxin transport within the range of
auxin levels that allow for differential responses.
article_processing_charge: No
author:
- first_name: Mohamad
full_name: Abbas, Mohamad
id: 47E8FC1C-F248-11E8-B48F-1D18A9856A87
last_name: Abbas
- first_name: García J
full_name: Hernández, García J
last_name: Hernández
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Sophia L
full_name: Samodelov, Sophia L
last_name: Samodelov
- first_name: Martina
full_name: Kolb, Martina
last_name: Kolb
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ulrich Z
full_name: Hammes, Ulrich Z
last_name: Hammes
- first_name: Matias D
full_name: Zurbriggen, Matias D
last_name: Zurbriggen
- first_name: Miguel
full_name: Blázquez, Miguel
last_name: Blázquez
- first_name: David
full_name: Alabadí, David
last_name: Alabadí
citation:
ama: Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for
differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115
apa: Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml,
J., … Alabadí, D. (2018). Auxin methylation is required for differential growth
in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115
chicago: Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov,
Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez,
and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.”
PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.
ieee: M. Abbas et al., “Auxin methylation is required for differential growth
in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences,
pp. 6864–6869, 2018.
ista: Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ,
Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for
differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.
mla: Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth
in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences,
2018, pp. 6864–69, doi:10.1073/pnas.1806565115.
short: M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml,
U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.
date_created: 2018-12-11T11:45:11Z
date_published: 2018-06-26T00:00:00Z
date_updated: 2025-05-07T11:12:32Z
day: '26'
department:
- _id: JiFr
doi: 10.1073/pnas.1806565115
ec_funded: 1
external_id:
isi:
- '000436245000096'
intvolume: ' 115'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.nottingham.ac.uk/52388/
month: '06'
oa: 1
oa_version: None
page: 6864-6869
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7710'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin methylation is required for differential growth in Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '13374'
abstract:
- lang: eng
text: Confining molecules to volumes only slightly larger than the molecules themselves
can profoundly alter their properties. Molecular switches—entities that can be
toggled between two or more forms upon exposure to an external stimulus—often
require conformational freedom to isomerize. Therefore, placing these switches
in confined spaces can render them non-operational. To preserve the switchability
of these species under confinement, we work with a water-soluble coordination
cage that is flexible enough to adapt its shape to the conformation of the encapsulated
guest. We show that owing to its flexibility, the cage is not only capable of
accommodating—and solubilizing in water—several light-responsive spiropyran-based
molecular switches, but, more importantly, it also provides an environment suitable
for the efficient, reversible photoisomerization of the bound guests. Our findings
pave the way towards studying various molecular switching processes in confined
environments.
article_number: '641'
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Daria
full_name: Galaktionova, Daria
last_name: Galaktionova
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Liat
full_name: Avram, Liat
last_name: Avram
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran
in the cavity of a flexible coordination cage. Nature Communications. 2018;9.
doi:10.1038/s41467-017-02715-6
apa: Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner,
Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity
of a flexible coordination cage. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-02715-6
chicago: Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael
Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of
Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications.
Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6.
ieee: D. Samanta et al., “Reversible chromism of spiropyran in the cavity
of a flexible coordination cage,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L,
Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible
coordination cage. Nature Communications. 9, 641.
mla: Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of
a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer
Nature, 2018, doi:10.1038/s41467-017-02715-6.
short: D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L.
Avram, P. Král, R. Klajn, Nature Communications 9 (2018).
date_created: 2023-08-01T09:39:32Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-08-07T10:54:05Z
day: '13'
doi: 10.1038/s41467-017-02715-6
extern: '1'
external_id:
pmid:
- '29440687'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-02715-6
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-018-03701-2
scopus_import: '1'
status: public
title: Reversible chromism of spiropyran in the cavity of a flexible coordination
cage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '13375'
abstract:
- lang: eng
text: 'Dissipative self-assembly leads to structures and materials that exist away
from equilibrium by continuously exchanging energy and materials with the external
environment. Although this mode of self-assembly is ubiquitous in nature, where
it gives rise to functions such as signal processing, motility, self-healing,
self-replication, and ultimately life, examples of dissipative self-assembly processes
in man-made systems are few and far between. Herein, recent progress in developing
diverse synthetic dissipative self-assembly systems is discussed. The systems
reported thus far can be categorized into three classes, in which: i) the fuel
chemically modifies the building blocks, thus triggering their self-assembly,
ii) the fuel acts as a template interacting with the building blocks noncovalently,
and iii) transient states are induced by the addition of two mutually exclusive
stimuli. These early studies give rise to materials that would be difficult to
obtain otherwise, including hydrogels with programmable lifetimes, vesicular nanoreactors,
and membranes exhibiting transient conductivity.'
article_number: '1706750'
article_processing_charge: No
article_type: original
author:
- first_name: Soumen
full_name: De, Soumen
last_name: De
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: De S, Klajn R. Dissipative self-assembly driven by the consumption of chemical
fuels. Advanced Materials. 2018;30(41). doi:10.1002/adma.201706750
apa: De, S., & Klajn, R. (2018). Dissipative self-assembly driven by the consumption
of chemical fuels. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201706750
chicago: De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption
of Chemical Fuels.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201706750.
ieee: S. De and R. Klajn, “Dissipative self-assembly driven by the consumption of
chemical fuels,” Advanced Materials, vol. 30, no. 41. Wiley, 2018.
ista: De S, Klajn R. 2018. Dissipative self-assembly driven by the consumption of
chemical fuels. Advanced Materials. 30(41), 1706750.
mla: De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption
of Chemical Fuels.” Advanced Materials, vol. 30, no. 41, 1706750, Wiley,
2018, doi:10.1002/adma.201706750.
short: S. De, R. Klajn, Advanced Materials 30 (2018).
date_created: 2023-08-01T09:39:46Z
date_published: 2018-10-11T00:00:00Z
date_updated: 2023-08-07T10:56:26Z
day: '11'
doi: 10.1002/adma.201706750
extern: '1'
external_id:
pmid:
- '29520846'
intvolume: ' 30'
issue: '41'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- General Materials Science
language:
- iso: eng
month: '10'
oa_version: None
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dissipative self-assembly driven by the consumption of chemical fuels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2018'
...
---
_id: '13376'
abstract:
- lang: eng
text: Efficient molecular switching in confined spaces is critical for the successful
development of artificial molecular machines. However, molecular switching events
often entail large structural changes and therefore require conformational freedom,
which is typically limited under confinement conditions. Here, we investigated
the behavior of azobenzene—the key building block of light-controlled molecular
machines—in a confined environment that is flexible and can adapt its shape to
that of the bound guest. To this end, we encapsulated several structurally diverse
azobenzenes within the cavity of a flexible, water-soluble coordination cage,
and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy
and a combination of NMR methods, we showed that each of the encapsulated azobenzenes
exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest
inclusion complex could be efficiently photoisomerized in a reversible fashion.
In contrast, successful switching in inclusion complexes incorporating two azobenzene
guests was dependent on the availability of free cages in the system, and it involved
reversible trafficking of azobenzene between the cages. In the absence of extra
cages, photoswitching was either suppressed or it involved expulsion of azobenzene
from the cage and consequently its precipitation from the solution. This finding
was utilized to develop an information storage medium in which messages could
be written and erased in a reversible fashion using light.
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Zonglin
full_name: Chu, Zonglin
last_name: Chu
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible
photoswitching of encapsulated azobenzenes in water. Proceedings of the National
Academy of Sciences. 2018;115(38):9379-9384. doi:10.1073/pnas.1712787115
apa: Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., &
Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water.
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.1712787115
chicago: Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J.
W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes
in Water.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1712787115.
ieee: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn,
“Reversible photoswitching of encapsulated azobenzenes in water,” Proceedings
of the National Academy of Sciences, vol. 115, no. 38. Proceedings of the
National Academy of Sciences, pp. 9379–9384, 2018.
ista: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible
photoswitching of encapsulated azobenzenes in water. Proceedings of the National
Academy of Sciences. 115(38), 9379–9384.
mla: Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes
in Water.” Proceedings of the National Academy of Sciences, vol. 115, no.
38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:10.1073/pnas.1712787115.
short: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn,
Proceedings of the National Academy of Sciences 115 (2018) 9379–9384.
date_created: 2023-08-01T09:40:00Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-08-07T10:58:11Z
day: '01'
doi: 10.1073/pnas.1712787115
extern: '1'
external_id:
pmid:
- '29717041'
intvolume: ' 115'
issue: '38'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1712787115
month: '05'
oa: 1
oa_version: Published Version
page: 9379-9384
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible photoswitching of encapsulated azobenzenes in water
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '13377'
abstract:
- lang: eng
text: Confining organic molecules to the surfaces of inorganic nanoparticles can
induce intermolecular interactions between them, which can affect the composition
of the mixed self-assembled monolayers obtained by co-adsorption from solution
of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic
sulfobetaine) that can interact with each other electrostatically were coadsorbed
onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these
two molecules that is largely independent of the molar ratio in solution. Changing
the solution molar ratio of the two ligands by a factor of 5 000 affects the on-nanoparticle
ratio of these ligands by only threefold. This behavior is reminiscent of the
formation of insoluble inorganic salts (such as AgCl), which similarly compensate
positive and negative charges upon crystallizing. Our results pave the way towards
developing well-defined hybrid organic–inorganic nanostructures.
article_processing_charge: No
article_type: original
author:
- first_name: Zonglin
full_name: Chu, Zonglin
last_name: Chu
- first_name: Yanxiao
full_name: Han, Yanxiao
last_name: Han
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: 'Chu Z, Han Y, Král P, Klajn R. “Precipitation on nanoparticles”: Attractive
intermolecular interactions stabilize specific ligand ratios on the surfaces of
nanoparticles. Angewandte Chemie International Edition. 2018;57(24):7023-7027.
doi:10.1002/anie.201800673'
apa: 'Chu, Z., Han, Y., Král, P., & Klajn, R. (2018). “Precipitation on nanoparticles”:
Attractive intermolecular interactions stabilize specific ligand ratios on the
surfaces of nanoparticles. Angewandte Chemie International Edition. Wiley.
https://doi.org/10.1002/anie.201800673'
chicago: 'Chu, Zonglin, Yanxiao Han, Petr Král, and Rafal Klajn. “‘Precipitation
on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand
Ratios on the Surfaces of Nanoparticles.” Angewandte Chemie International Edition.
Wiley, 2018. https://doi.org/10.1002/anie.201800673.'
ieee: 'Z. Chu, Y. Han, P. Král, and R. Klajn, “‘Precipitation on nanoparticles’:
Attractive intermolecular interactions stabilize specific ligand ratios on the
surfaces of nanoparticles,” Angewandte Chemie International Edition, vol.
57, no. 24. Wiley, pp. 7023–7027, 2018.'
ista: 'Chu Z, Han Y, Král P, Klajn R. 2018. “Precipitation on nanoparticles”: Attractive
intermolecular interactions stabilize specific ligand ratios on the surfaces of
nanoparticles. Angewandte Chemie International Edition. 57(24), 7023–7027.'
mla: 'Chu, Zonglin, et al. “‘Precipitation on Nanoparticles’: Attractive Intermolecular
Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.”
Angewandte Chemie International Edition, vol. 57, no. 24, Wiley, 2018,
pp. 7023–27, doi:10.1002/anie.201800673.'
short: Z. Chu, Y. Han, P. Král, R. Klajn, Angewandte Chemie International Edition
57 (2018) 7023–7027.
date_created: 2023-08-01T09:40:16Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2023-08-07T11:14:28Z
day: '11'
doi: 10.1002/anie.201800673
extern: '1'
external_id:
pmid:
- '29673022'
intvolume: ' 57'
issue: '24'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/anie.201800673
month: '06'
oa: 1
oa_version: Published Version
page: 7023-7027
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: '“Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize
specific ligand ratios on the surfaces of nanoparticles'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2018'
...
---
_id: '13379'
article_number: '1700827'
article_processing_charge: No
article_type: letter_note
author:
- first_name: David
full_name: Bléger, David
last_name: Bléger
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Bléger D, Klajn R. Integrating macromolecules with molecular switches. Macromolecular
Rapid Communications. 2018;39(1). doi:10.1002/marc.201700827
apa: Bléger, D., & Klajn, R. (2018). Integrating macromolecules with molecular
switches. Macromolecular Rapid Communications. Wiley. https://doi.org/10.1002/marc.201700827
chicago: Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular
Switches.” Macromolecular Rapid Communications. Wiley, 2018. https://doi.org/10.1002/marc.201700827.
ieee: D. Bléger and R. Klajn, “Integrating macromolecules with molecular switches,”
Macromolecular Rapid Communications, vol. 39, no. 1. Wiley, 2018.
ista: Bléger D, Klajn R. 2018. Integrating macromolecules with molecular switches.
Macromolecular Rapid Communications. 39(1), 1700827.
mla: Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular
Switches.” Macromolecular Rapid Communications, vol. 39, no. 1, 1700827,
Wiley, 2018, doi:10.1002/marc.201700827.
short: D. Bléger, R. Klajn, Macromolecular Rapid Communications 39 (2018).
date_created: 2023-08-01T09:40:48Z
date_published: 2018-01-08T00:00:00Z
date_updated: 2023-08-07T11:16:49Z
day: '08'
doi: 10.1002/marc.201700827
extern: '1'
external_id:
pmid:
- '29314396'
intvolume: ' 39'
issue: '1'
keyword:
- Materials Chemistry
- Polymers and Plastics
- Organic Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/marc.201700827
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Macromolecular Rapid Communications
publication_identifier:
eissn:
- 1521-3927
issn:
- 1022-1336
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Integrating macromolecules with molecular switches
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2018'
...
---
_id: '134'
abstract:
- lang: eng
text: "The current state of the art in real-time two-dimensional water wave simulation
requires developers to choose between efficient Fourier-based methods, which lack
interactions with moving obstacles, and finite-difference or finite element methods,
which handle environmental interactions but are significantly more expensive.
This paper attempts to bridge this long-standing gap between complexity and performance,
by proposing a new wave simulation method that can faithfully simulate wave interactions
with moving obstacles in real time while simultaneously preserving minute details
and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating
2D water waves directly compute the change in height of the water surface, a strategy
which imposes limitations based on the CFL condition (fast moving waves require
small time steps) and Nyquist's limit (small wave details require closely-spaced
simulation variables). This paper proposes a novel wavelet transformation that
discretizes the liquid motion in terms of amplitude-like functions that vary over
space, frequency, and direction, effectively generalizing Fourier-based methods
to handle local interactions. Because these new variables change much more slowly
over space than the original water height function, our change of variables drastically
reduces the limitations of the CFL condition and Nyquist limit, allowing us to
simulate highly detailed water waves at very large visual resolutions. Our discretization
is amenable to fast summation and easy to parallelize. We also present basic extensions
like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue
that our discretization provides a convenient set of variables for artistic manipulation,
which we illustrate with a novel wave-painting interface."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- SIGGRAPH
article_number: '94'
article_processing_charge: No
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Matthias
full_name: Mueller Fischer, Matthias
last_name: Mueller Fischer
- first_name: Nuttapong
full_name: Chentanez, Nuttapong
last_name: Chentanez
- first_name: Miles
full_name: Macklin, Miles
last_name: Macklin
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336
apa: Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M.,
& Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/3197517.3201336
chicago: Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez,
Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions
on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.
ieee: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and
C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol.
37, no. 4. ACM, 2018.
ista: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.
mla: Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics,
vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.
short: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C.
Wojtan, ACM Transactions on Graphics 37 (2018).
date_created: 2018-12-11T11:44:48Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2024-02-28T13:58:51Z
day: '30'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3197517.3201336
ec_funded: 1
external_id:
isi:
- '000448185000055'
file:
- access_level: open_access
checksum: db75ebabe2ec432bf41389e614d6ef62
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:59:23Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5744'
file_name: 2018_ACM_Jeschke.pdf
file_size: 22185016
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '7789'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/
scopus_import: '1'
status: public
title: Water surface wavelets
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2018'
...
---
_id: '13473'
abstract:
- lang: eng
text: Stripped-envelope stars form in binary systems after losing mass through Roche-lobe
overflow. They bear astrophysical significance as sources of UV and ionizing radiation
in older stellar populations and, if sufficiently massive, as stripped supernova
progenitors. Binary evolutionary models predict that they are common, but only
a handful of subdwarfs with B-type companions are known. The question is whether
a large population of such systems has evaded detection as a result of biases,
or whether the model predictions are wrong. We reanalyze the well-studied post-interaction
binary φ Persei. Recently, new data have improved the orbital solution of the
system, which contains an ~1.2M⊙ stripped-envelope star and a rapidly rotating
~9.6M⊙ Be star. We compare with an extensive grid of evolutionary models using
a Bayesian approach and constrain the initial masses of the progenitor to 7.2
± 0.4M⊙ for the stripped star and 3.8 ± 0.4M⊙ for the Be star. The system must
have evolved through near-conservative mass transfer. These findings are consistent
with earlier studies. The age we obtain, 57 ± 9 Myr, is in excellent agreement
with the age of the α Persei cluster. We note that neither star was initially
massive enough to produce a core-collapse supernova, but mass exchange pushed
the Be star above the mass threshold. We find that the subdwarf is overluminous
for its mass by almost an order of magnitude, compared to the expectations for
a helium core burning star. We can only reconcile this if the subdwarf resides
in a late phase of helium shell burning, which lasts only 2–3% of the total lifetime
as a subdwarf. Assuming continuous star formation implies that up to ~50 less
evolved, dimmer subdwarfs exist for each system similar to φ Persei, but have
evaded detection so far. Our findings can be interpreted as a strong indication
that a substantial population of stripped-envelope stars indeed exists, but has
so far evaded detection because of observational biases and lack of large-scale
systematic searches.
article_number: A30
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: A.
full_name: Schootemeijer, A.
last_name: Schootemeijer
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: S. E.
full_name: de Mink, S. E.
last_name: de Mink
- first_name: D.
full_name: Gies, D.
last_name: Gies
- first_name: E.
full_name: Zapartas, E.
last_name: Zapartas
citation:
ama: Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. Clues about the
scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be
binary system φ Persei. Astronomy & Astrophysics. 2018;615. doi:10.1051/0004-6361/201731194
apa: Schootemeijer, A., Götberg, Y. L. L., de Mink, S. E., Gies, D., & Zapartas,
E. (2018). Clues about the scarcity of stripped-envelope stars from the evolutionary
state of the sdO+Be binary system φ Persei. Astronomy & Astrophysics.
EDP Sciences. https://doi.org/10.1051/0004-6361/201731194
chicago: Schootemeijer, A., Ylva Louise Linsdotter Götberg, S. E. de Mink, D. Gies,
and E. Zapartas. “Clues about the Scarcity of Stripped-Envelope Stars from the
Evolutionary State of the SdO+Be Binary System φ Persei.” Astronomy & Astrophysics.
EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201731194.
ieee: A. Schootemeijer, Y. L. L. Götberg, S. E. de Mink, D. Gies, and E. Zapartas,
“Clues about the scarcity of stripped-envelope stars from the evolutionary state
of the sdO+Be binary system φ Persei,” Astronomy & Astrophysics, vol.
615. EDP Sciences, 2018.
ista: Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. 2018. Clues
about the scarcity of stripped-envelope stars from the evolutionary state of the
sdO+Be binary system φ Persei. Astronomy & Astrophysics. 615, A30.
mla: Schootemeijer, A., et al. “Clues about the Scarcity of Stripped-Envelope Stars
from the Evolutionary State of the SdO+Be Binary System φ Persei.” Astronomy
& Astrophysics, vol. 615, A30, EDP Sciences, 2018, doi:10.1051/0004-6361/201731194.
short: A. Schootemeijer, Y.L.L. Götberg, S.E. de Mink, D. Gies, E. Zapartas, Astronomy
& Astrophysics 615 (2018).
date_created: 2023-08-03T10:14:37Z
date_published: 2018-07-06T00:00:00Z
date_updated: 2023-08-09T12:22:52Z
day: '06'
doi: 10.1051/0004-6361/201731194
extern: '1'
external_id:
arxiv:
- '1803.02379'
intvolume: ' 615'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201731194
month: '07'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clues about the scarcity of stripped-envelope stars from the evolutionary state
of the sdO+Be binary system φ Persei
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 615
year: '2018'
...
---
_id: '13474'
abstract:
- lang: eng
text: Recent surveys of the Magellanic Clouds have revealed a subtype of Wolf–Rayet
(WR) star with peculiar properties. WN3/O3 spectra exhibit both WR-like emission
and O3 V-like absorption – but at lower luminosity than O3 V or WN stars. We examine
the projected spatial distribution of WN3/O3 stars in the Large Magellanic Cloud
as compared to O-type stars. Surprisingly, WN3/O3 stars are among the most isolated
of all classes of massive stars; they have a distribution similar to red supergiants
dominated by initial masses of 10–15 M⊙, and are far more dispersed than classical
WR stars or luminous blue variables. Their lack of association with clusters of
O-type stars suggests strongly that WN3/O3 stars are not the descendants of single
massive stars (30 M⊙ or above). Instead, they are likely products of interacting
binaries at lower initial mass (10–18 M⊙). Comparison with binary models suggests
a probable origin with primaries in this mass range that were stripped of their
H envelopes through non-conservative mass transfer by a low-mass secondary. We
show that model spectra and positions on the Hertzsprung–Russell diagram for binary-stripped
stars are consistent with WN3/O3 stars. Monitoring radial velocities with high-resolution
spectra can test for low-mass companions or runaway velocities. With lower initial
mass and environments that avoid very massive stars, the WN3/O3 stars fit expectations
for progenitors of Type Ib and possibly Type Ibn supernovae.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nathan
full_name: Smith, Nathan
last_name: Smith
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: Selma E
full_name: de Mink, Selma E
last_name: de Mink
citation:
ama: Smith N, Götberg YLL, de Mink SE. Extreme isolation of WN3/O3 stars and implications
for their evolutionary origin as the elusive stripped binaries. Monthly Notices
of the Royal Astronomical Society. 2018;475(1):772-782. doi:10.1093/mnras/stx3181
apa: Smith, N., Götberg, Y. L. L., & de Mink, S. E. (2018). Extreme isolation
of WN3/O3 stars and implications for their evolutionary origin as the elusive
stripped binaries. Monthly Notices of the Royal Astronomical Society. Oxford
University Press. https://doi.org/10.1093/mnras/stx3181
chicago: Smith, Nathan, Ylva Louise Linsdotter Götberg, and Selma E de Mink. “Extreme
Isolation of WN3/O3 Stars and Implications for Their Evolutionary Origin as the
Elusive Stripped Binaries.” Monthly Notices of the Royal Astronomical Society.
Oxford University Press, 2018. https://doi.org/10.1093/mnras/stx3181.
ieee: N. Smith, Y. L. L. Götberg, and S. E. de Mink, “Extreme isolation of WN3/O3
stars and implications for their evolutionary origin as the elusive stripped binaries,”
Monthly Notices of the Royal Astronomical Society, vol. 475, no. 1. Oxford
University Press, pp. 772–782, 2018.
ista: Smith N, Götberg YLL, de Mink SE. 2018. Extreme isolation of WN3/O3 stars
and implications for their evolutionary origin as the elusive stripped binaries.
Monthly Notices of the Royal Astronomical Society. 475(1), 772–782.
mla: Smith, Nathan, et al. “Extreme Isolation of WN3/O3 Stars and Implications for
Their Evolutionary Origin as the Elusive Stripped Binaries.” Monthly Notices
of the Royal Astronomical Society, vol. 475, no. 1, Oxford University Press,
2018, pp. 772–82, doi:10.1093/mnras/stx3181.
short: N. Smith, Y.L.L. Götberg, S.E. de Mink, Monthly Notices of the Royal Astronomical
Society 475 (2018) 772–782.
date_created: 2023-08-03T10:14:47Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-08-09T12:17:34Z
day: '01'
doi: 10.1093/mnras/stx3181
extern: '1'
external_id:
arxiv:
- '1704.03516'
intvolume: ' 475'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/mnras/stx3181
month: '03'
oa: 1
oa_version: Published Version
page: 772-782
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extreme isolation of WN3/O3 stars and implications for their evolutionary origin
as the elusive stripped binaries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 475
year: '2018'
...
---
_id: '13475'
abstract:
- lang: eng
text: Stars stripped of their hydrogen-rich envelope through interaction with a
binary companion are generally not considered when accounting for ionizing radiation
from stellar populations, despite the expectation that stripped stars emit hard
ionizing radiation, form frequently, and live 10–100 times longer than single
massive stars. We compute the first grid of evolutionary and spectral models specially
made for stars stripped in binaries for a range of progenitor masses (2–20 M⊙)
and metallicities ranging from solar to values representative for pop II stars.
For stripped stars with masses in the range 0.3–7 M⊙, we find consistently high
effective temperatures (20 000–100 000 K, increasing with mass), small radii (0.2–1
R⊙), and high bolometric luminosities, comparable to that of their progenitor
before stripping. The spectra show a continuous sequence that naturally bridges
subdwarf-type stars at the low-mass end and Wolf-Rayet-like spectra at the high-mass
end. For intermediate masses we find hybrid spectral classes showing a mixture
of absorption and emission lines. These appear for stars with mass-loss rates
of 10−8−10−6 M⊙ yr−1, which have semi-transparent atmospheres. At low metallicity,
substantial hydrogen-rich layers are left at the surface and we predict spectra
that resemble O-type stars instead. We obtain spectra undistinguishable from subdwarfs
for stripped stars with masses up to 1.7 M⊙, which questions whether the widely
adopted canonical value of 0.47 M⊙ is uniformly valid. Only a handful of stripped
stars of intermediate mass have currently been identified observationally. Increasing
this sample will provide necessary tests for the physics of interaction, internal
mixing, and stellar winds. We use our model spectra to investigate the feasibility
to detect stripped stars next to an optically bright companion and recommend systematic
searches for their UV excess and possible emission lines, most notably HeII λ4686
in the optical and HeII λ1640 in the UV. Our models are publicly available for
further investigations or inclusion in spectral synthesis simulations.
article_number: A78
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: S. E.
full_name: de Mink, S. E.
last_name: de Mink
- first_name: J. H.
full_name: Groh, J. H.
last_name: Groh
- first_name: T.
full_name: Kupfer, T.
last_name: Kupfer
- first_name: P. A.
full_name: Crowther, P. A.
last_name: Crowther
- first_name: E.
full_name: Zapartas, E.
last_name: Zapartas
- first_name: M.
full_name: Renzo, M.
last_name: Renzo
citation:
ama: 'Götberg YLL, de Mink SE, Groh JH, et al. Spectral models for binary products:
Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars.
Astronomy & Astrophysics. 2018;615. doi:10.1051/0004-6361/201732274'
apa: 'Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Kupfer, T., Crowther, P. A.,
Zapartas, E., & Renzo, M. (2018). Spectral models for binary products: Unifying
subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy
& Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732274'
chicago: 'Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, T. Kupfer,
P. A. Crowther, E. Zapartas, and M. Renzo. “Spectral Models for Binary Products:
Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.”
Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201732274.'
ieee: 'Y. L. L. Götberg et al., “Spectral models for binary products: Unifying
subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars,” Astronomy
& Astrophysics, vol. 615. EDP Sciences, 2018.'
ista: 'Götberg YLL, de Mink SE, Groh JH, Kupfer T, Crowther PA, Zapartas E, Renzo
M. 2018. Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet
stars as a sequence of stripped-envelope stars. Astronomy & Astrophysics.
615, A78.'
mla: 'Götberg, Ylva Louise Linsdotter, et al. “Spectral Models for Binary Products:
Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.”
Astronomy & Astrophysics, vol. 615, A78, EDP Sciences, 2018, doi:10.1051/0004-6361/201732274.'
short: Y.L.L. Götberg, S.E. de Mink, J.H. Groh, T. Kupfer, P.A. Crowther, E. Zapartas,
M. Renzo, Astronomy & Astrophysics 615 (2018).
date_created: 2023-08-03T10:15:00Z
date_published: 2018-07-17T00:00:00Z
date_updated: 2023-08-09T11:22:17Z
day: '17'
doi: 10.1051/0004-6361/201732274
extern: '1'
external_id:
arxiv:
- '1802.03018'
intvolume: ' 615'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201732274
month: '07'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars
as a sequence of stripped-envelope stars'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 615
year: '2018'
...
---
_id: '135'
abstract:
- lang: eng
text: The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by
combining particles with grids. To improve performance, the subsequent narrow
band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid
surface and a traditional grid‐based fluid simulation away from the surface. This
spatially‐limited FLIP simulation significantly reduces the number of particles
and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP
idea even further, by allowing a simulation to transition between a FLIP‐like
fluid simulation and a grid‐based simulation in arbitrary locations, not just
near the surface. This approach leads to even more savings in memory and computation,
because we can concentrate the particles only in areas where they are needed.
More importantly, this new method allows us to seamlessly transition to smooth
implicit surface geometry wherever the particle‐based simulation is unnecessary.
Consequently, our method leads to a practical algorithm for avoiding the noisy
surface artifacts associated with particle‐based liquid simulations, while simultaneously
maintaining the benefits of a FLIP simulation in regions of dynamic motion.
alternative_title:
- Eurographics
article_processing_charge: No
article_type: original
author:
- first_name: Takahiro
full_name: Sato, Takahiro
last_name: Sato
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Takeo
full_name: Igarashi, Takeo
last_name: Igarashi
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
citation:
ama: Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP
for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351
apa: Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended
narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley.
https://doi.org/10.1111/cgf.13351
chicago: Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi
Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics
Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.
ieee: T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow
band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no.
2. Wiley, pp. 169–177, 2018.
ista: Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band
FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.
mla: Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.”
Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.
short: T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum
37 (2018) 169–177.
date_created: 2018-12-11T11:44:49Z
date_published: 2018-05-22T00:00:00Z
date_updated: 2023-09-11T14:00:26Z
day: '22'
ddc:
- '006'
department:
- _id: ChWo
doi: 10.1111/cgf.13351
ec_funded: 1
external_id:
isi:
- '000434085600016'
file:
- access_level: open_access
checksum: 8edb90da8a72395eb5d970580e0925b6
content_type: application/pdf
creator: wojtan
date_created: 2020-10-08T08:38:23Z
date_updated: 2020-10-08T08:38:23Z
file_id: '8627'
file_name: exnbflip.pdf
file_size: 54309947
relation: main_file
success: 1
file_date_updated: 2020-10-08T08:38:23Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 169 - 177
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: Computer Graphics Forum
publication_identifier:
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extended narrow band FLIP for liquid simulations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '136'
abstract:
- lang: eng
text: Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes
equation may provide deep insights into fluid turbulence. In this article, we
present a combined experimental and numerical study exploring the dynamical role
of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent,
electromagnetically driven, shallow fluid layer. Identifying instants when turbulent
evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional
model of the flow. We establish the dynamical relevance of these unstable equilibria
by showing that they are closely visited by the turbulent flow. We also establish
the dynamical relevance of unstable manifolds by verifying that they are shadowed
by turbulent trajectories departing from the neighborhoods of unstable equilibria
over large distances in state space.
article_processing_charge: No
arxiv: 1
author:
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Jeffrey
full_name: Tithof, Jeffrey
last_name: Tithof
- first_name: Roman
full_name: Grigoriev, Roman
last_name: Grigoriev
- first_name: Michael
full_name: Schatz, Michael
last_name: Schatz
citation:
ama: Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant
manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E.
2018;98(2). doi:10.1103/PhysRevE.98.023105
apa: Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria
and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical
Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105
chicago: Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz.
“Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like
Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.
ieee: B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and
invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical
Review E, vol. 98, no. 2. American Physical Society, 2018.
ista: Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant
manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).
mla: Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional
Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical
Society, 2018, doi:10.1103/PhysRevE.98.023105.
short: B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).
date_created: 2018-12-11T11:44:49Z
date_published: 2018-08-13T00:00:00Z
date_updated: 2023-10-10T13:29:10Z
day: '13'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.98.023105
external_id:
arxiv:
- '1808.02088'
isi:
- '000441466800010'
intvolume: ' 98'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.02088
month: '08'
oa: 1
oa_version: Submitted Version
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like
flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '137'
abstract:
- lang: eng
text: Fluorescent sensors are an essential part of the experimental toolbox of the
life sciences, where they are used ubiquitously to visualize intra- and extracellular
signaling. In the brain, optical neurotransmitter sensors can shed light on temporal
and spatial aspects of signal transmission by directly observing, for instance,
neurotransmitter release and spread. Here we report the development and application
of the first optical sensor for the amino acid glycine, which is both an inhibitory
neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs)
involved in synaptic plasticity. Computational design of a glycine-specific binding
protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can
be used with single and two-photon excitation fluorescence microscopy. We took
advantage of this newly developed sensor to test predictions about the uneven
spatial distribution of glycine in extracellular space and to demonstrate that
extracellular glycine levels are controlled by plasticity-inducing stimuli.
article_processing_charge: No
article_type: original
author:
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Andreas
full_name: Wulff, Andreas
last_name: Wulff
- first_name: Vanessa
full_name: Vongsouthi, Vanessa
last_name: Vongsouthi
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Polina
full_name: Gulakova, Polina
last_name: Gulakova
- first_name: Daniel
full_name: Minge, Daniel
last_name: Minge
- first_name: Björn
full_name: Breithausen, Björn
last_name: Breithausen
- first_name: Susanne
full_name: Schoch, Susanne
last_name: Schoch
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
citation:
ama: Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the
computationally designed optical sensor GlyFS. Nature Chemical Biology.
2018;14(9):861-869. doi:10.1038/s41589-018-0108-2
apa: Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V.,
… Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing
Group. https://doi.org/10.1038/s41589-018-0108-2
chicago: Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas
Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal
Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical
Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.
ieee: W. Zhang et al., “Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9.
Nature Publishing Group, pp. 861–869, 2018.
ista: Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero
I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger
C. 2018. Monitoring hippocampal glycine with the computationally designed optical
sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.
mla: Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally
Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9,
Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.
short: W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I.
Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak,
C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.
date_created: 2018-12-11T11:44:49Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-09-13T08:58:05Z
day: '30'
department:
- _id: HaJa
doi: 10.1038/s41589-018-0108-2
external_id:
isi:
- '000442174500013'
pmid:
- '30061718 '
intvolume: ' 14'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30061718
month: '07'
oa: 1
oa_version: Submitted Version
page: 861 - 869
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7786'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring hippocampal glycine with the computationally designed optical sensor
GlyFS
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...