---
_id: '8129'
abstract:
- lang: eng
text: "Cortical circuits exhibit intricate recurrent architectures that are remarkably
similar across different brain areas. Such stereotyped structure suggests the
existence of common computational principles. However, such principles have remained
largely elusive. Inspired by gated-memory networks, namely long short-term memory
networks (LSTMs), we introduce a recurrent neural network in which information
is gated through inhibitory cells that are subtractive (subLSTM). We propose a
natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical
microcircuits. Our empirical evaluation across sequential image classification
and language modelling tasks shows that subLSTM units can achieve similar performance
to LSTM units. These results suggest that cortical circuits can be optimised to
solve complex contextual problems and proposes a novel view on their computational
function.\r\nOverall our work provides a step towards unifying recurrent networks
as used in machine learning with their biological counterparts."
article_processing_charge: No
arxiv: 1
author:
- first_name: Rui Ponte
full_name: Costa, Rui Ponte
last_name: Costa
- first_name: Yannis M.
full_name: Assael, Yannis M.
last_name: Assael
- first_name: Brendan
full_name: Shillingford, Brendan
last_name: Shillingford
- first_name: Nando de
full_name: Freitas, Nando de
last_name: Freitas
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits
as gated-recurrent neural networks. In: Advances in Neural Information Processing
Systems. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.'
apa: 'Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, & Vogels,
T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In Advances
in Neural Information Processing Systems (Vol. 30, pp. 272–283). Long Beach,
CA, United States: Neural Information Processing Systems Foundation.'
chicago: Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas,
and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.”
In Advances in Neural Information Processing Systems, 30:272–83. Neural
Information Processing Systems Foundation, 2017.
ieee: R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels,
“Cortical microcircuits as gated-recurrent neural networks,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017,
vol. 30, pp. 272–283.
ista: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical
microcircuits as gated-recurrent neural networks. Advances in Neural Information
Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.'
mla: Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural
Networks.” Advances in Neural Information Processing Systems, vol. 30,
Neural Information Processing Systems Foundation, 2017, pp. 272–83.
short: R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:,
Advances in Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2017, pp. 272–283.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NIPS: Neural Information Processing System'
start_date: 2017-12-04
date_created: 2020-07-16T19:13:10Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:17:03Z
day: '01'
extern: '1'
external_id:
arxiv:
- '1711.02448'
intvolume: ' 30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.02448
month: '12'
oa: 1
oa_version: Preprint
page: 272-283
publication: Advances in Neural Information Processing Systems
publication_identifier:
issn:
- '10495258'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Cortical microcircuits as gated-recurrent neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2017'
...
---
_id: '817'
abstract:
- lang: eng
text: Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular
complexes to be imaged in three-dimensions in their native environments. Cryo-electron
tomograms are reconstructed from projection images taken at defined tilt-angles.
In order to recover high-resolution information from cryo-electron tomograms,
it is necessary to measure and correct for the contrast transfer function (CTF)
of the microscope. Most commonly, this is performed using protocols that approximate
the sample as a two-dimensional (2D) plane. This approximation accounts for differences
in defocus and therefore CTF across the tilted sample. It does not account for
differences in defocus of objects at different heights within the sample; instead,
a 3D approach is required. Currently available approaches for 3D-CTF correction
are computationally expensive and have not been widely implemented. Here we simulate
the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and
present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF,
that is compatible with standard tomogram reconstruction workflows in IMOD. We
validate the approach on synthetic data and test it using subtomogram averaging
of real data. Consistent with our simulations, we find that 3D-CTF correction
allows high-resolution structures to be obtained with much smaller subtomogram
averaging datasets than are required using 2D-CTF. We also show that using equivalent
dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures.
We present a 3.4. Å resolution structure determined by subtomogram averaging.
author:
- first_name: Beata
full_name: Turoňová, Beata
last_name: Turoňová
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron
tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal
of Structural Biology. 2017;199(3):187-195. doi:10.1016/j.jsb.2017.07.007
apa: Turoňová, B., Schur, F. K., Wan, W., & Briggs, J. (2017). Efficient 3D-CTF
correction for cryo-electron tomography using NovaCTF improves subtomogram averaging
resolution to 3.4Å. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2017.07.007
chicago: Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient
3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram
Averaging Resolution to 3.4Å.” Journal of Structural Biology. Academic
Press, 2017. https://doi.org/10.1016/j.jsb.2017.07.007.
ieee: B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction
for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å,” Journal of Structural Biology, vol. 199, no. 3. Academic Press,
pp. 187–195, 2017.
ista: Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for
cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å. Journal of Structural Biology. 199(3), 187–195.
mla: Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography
Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of
Structural Biology, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:10.1016/j.jsb.2017.07.007.
short: B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology
199 (2017) 187–195.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:17:16Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2017.07.007
extern: '1'
file:
- access_level: open_access
checksum: 7f2d4bbac767f9acc254d1a4114d181a
content_type: application/pdf
creator: kschuh
date_created: 2019-03-22T09:29:44Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6168'
file_name: 2017_Elsevier_Turonova.pdf
file_size: 1310009
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 199'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 187-195
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6832'
quality_controlled: '1'
status: public
title: Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves
subtomogram averaging resolution to 3.4Å
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2017'
...
---
_id: '818'
abstract:
- lang: eng
text: 'Antibiotics have diverse effects on bacteria, including massive changes in
bacterial gene expression. Whereas the gene expression changes under many antibiotics
have been measured, the temporal organization of these responses and their dependence
on the bacterial growth rate are unclear. As described in Chapter 1, we quantified
the temporal gene expression changes in the bacterium Escherichia coli in response
to the sudden exposure to antibiotics using a fluorescent reporter library and
a robotic system. Our data show temporally structured gene expression responses,
with response times for individual genes ranging from tens of minutes to several
hours. We observed that many stress response genes were activated in response
to antibiotics. As certain stress responses cross-protect bacteria from other
stressors, we then asked whether cellular responses to antibiotics have a similar
protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid
stress response protects bacteria from subsequent acid stress. We combined microfluidics
with time-lapse imaging to monitor survival, intracellular pH, and acid stress
response in single cells. This approach revealed that the variable expression
of the acid resistance operon gadBC strongly correlates with single-cell survival
time. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. Overall, we provide a way
to identify single-cell cross-protection between antibiotics and environmental
stressors from temporal gene expression data, and show how antibiotics can increase
bacterial fitness in changing environments. While gene expression changes to antibiotics
show a clear temporal structure at the population-level, it is unclear whether
this clear temporal order is followed by every single cell. Using dual-reporter
strains described in Chapter 3, we measured gene expression dynamics of promoter
pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that
the oxidative stress response and the DNA stress response showed little timing
variability and a clear temporal order under the antibiotic nitrofurantoin. In
contrast, the acid stress response under trimethoprim ran independently from all
other activated response programs including the DNA stress response, which showed
particularly high timing variability in this stress condition. In summary, this
approach provides insight into the temporal organization of gene expression programs
at the single-cell level and suggests dependencies between response programs and
the underlying variability-introducing mechanisms. Altogether, this work advances
our understanding of the diverse effects that antibiotics have on bacteria. These
results were obtained by taking into account gene expression dynamics, which allowed
us to identify general principles, molecular mechanisms, and dependencies between
genes. Our findings may have implications for infectious disease treatments, and
microbial communities in the human body and in nature. '
acknowledgement: 'First of all, I would like to express great gratitude to my PhD
supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom
to explore different scientific directions during this project, and follow the research
lines of my interest. I am thankful for constructive and often extensive discussions
and his support and commitment during the different stages of my PhD. I want to
thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest
and their valuable input to this project. Special thanks to Nassos for career guidance,
and for accepting me in his lab. A big thank you goes to the past, present and affiliated
members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová,
Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr,
Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed
working and discussing with you very much and I will miss our lengthy group meetings,
our inspiring journal clubs, and our common lunches. Special thanks to Bor for great
mental and professional support during the hard months of thesis writing, and to
Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial
Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and
collaborator Georg Rieckh for his enthusiasm and for getting so involved in these
projects, for his endurance and for his company throughout the years. Thanks to
the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular
I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange,
and enjoyable time together. Thanks to everybody who contributed to the cover for
Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh,
Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by
the graphic designer Martina Markus from the University of Cologne. Thanks to all
my office mates in the first floor Bertalanffy building throughout the years: for
ensuring a pleasant working atmosphere, and for your company! In general, I want
to thank all the people that make IST such a great environment, with the many possibilities
to shape our own social and research environment. I want to thank my family for
all kind of practical support during the years, and my second family in Argentina
for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being
great siblings, and to Helena and Valentin for the joy you brought to my life. My
deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and
for believing in me. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
citation:
ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862
apa: Mitosch, K. (2017). Timing, variability and cross-protection in bacteria
– insights from dynamic gene expression responses to antibiotics. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862
chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria –
Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of
Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862.
ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics,” Institute of Science and
Technology Austria, 2017.
ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. Institute of Science and
Technology Austria.
mla: Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.
short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and
Technology Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2023-09-07T12:00:26Z
day: '27'
ddc:
- '571'
- '579'
degree_awarded: PhD
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:th_862
file:
- access_level: closed
checksum: da3993c5f90f59a8e8623cc31ad501dd
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:48:51Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6210'
file_name: Thesis_KarinMitosch.docx
file_size: 6331071
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date_created: 2019-04-05T08:48:51Z
date_updated: 2020-07-14T12:48:09Z
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file_date_updated: 2020-07-14T12:48:09Z
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language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '113'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6831'
pubrep_id: '862'
related_material:
record:
- id: '2001'
relation: part_of_dissertation
status: public
- id: '666'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Timing, variability and cross-protection in bacteria – insights from dynamic
gene expression responses to antibiotics
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '819'
abstract:
- lang: eng
text: 'Contagious diseases must transmit from infectious to susceptible hosts in
order to reproduce. Whilst vectored pathogens can rely on intermediaries to find
new hosts for them, many infectious pathogens require close contact or direct
interaction between hosts for transmission. Hence, this means that conspecifics
are often the main source of infection for most animals and so, in theory, animals
should avoid conspecifics to reduce their risk of infection. Of course, in reality
animals must interact with one another, as a bare minimum, to mate. However, being
social provides many additional benefits and group living has become a taxonomically
diverse and widespread trait. How then do social animals overcome the issue of
increased disease? Over the last few decades, the social insects (ants, termites
and some bees and wasps) have become a model system for studying disease in social
animals. On paper, a social insect colony should be particularly susceptible to
disease, given that they often contain thousands of potential hosts that are closely
related and frequently interact, as well as exhibiting stable environmental conditions
that encourage microbial growth. Yet, disease outbreaks appear to be rare and
attempts to eradicate pest species using pathogens have failed time and again.
Evolutionary biologists investigating this observation have discovered that the
reduced disease susceptibility in social insects is, in part, due to collectively
performed disease defences of the workers. These defences act like a “social immune
system” for the colony, resulting in a per capita decrease in disease, termed
social immunity. Our understanding of social immunity, and its importance in relation
to the immunological defences of each insect, continues to grow, but there remain
many open questions. In this thesis I have studied disease defence in garden ants.
In the first data chapter, I use the invasive garden ant, Lasius neglectus, to
investigate how colonies mitigate lethal infections and prevent them from spreading
systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour
that uses endogenously produced acidic poison to kill diseased brood and to prevent
the pathogen from replicating. In the second experimental chapter, I continue
to study the use of poison in invasive garden ant colonies, finding that it is
sprayed prophylactically within the nest. However, this spraying has negative
effects on developing pupae when they have had their cocoons artificially removed.
Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon
spinning in this species. In the next experimental chapter, I investigated how
colony founding black garden ant queens (Lasius niger) prevent disease when a
co-foundress dies. I show that ant queens prophylactically perform undertaking
behaviours, similar to those performed by the workers in mature nests. When a
co-foundress was infected, these undertaking behaviours improved the survival
of the healthy queen. In the final data chapter, I explored how immunocompetence
(measured as antifungal activity) changes as incipient black garden ant colonies
grow and mature, from the solitary queen phase to colonies with several hundred
workers. Queen and worker antifungal activity varied throughout this time period,
but despite social immunity, did not decrease as colonies matured. In addition
to the above data chapters, this thesis includes two co-authored reviews. In the
first, we examine the state of the art in the field of social immunity and how
it might develop in the future. In the second, we identify several challenges
and open questions in the study of disease defence in animals. We highlight how
social insects offer a unique model to tackle some of these problems, as disease
defence can be studied from the cell to the society. '
acknowledgement: "ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely
spoilt to work in a lab with such good resources and I must thank the wonderful
Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help
and keeping the lab up and running. You guys will probably be the most missed once
I realise just how much work you have been saving me! For the same reason, I must
say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding
my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you
will be sorely missed now that I will have to take this task on myself. Of course,
I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing
and being a constant source of guidance and inspiration. You have given me the perfect
balance of independence and supervision. I cannot thank you enough for creating
such a great working environment and allowing me the freedom to follow my own research
questions. I have had so many exceptional opportunities – attending and presenting
at conferences all over the world, inviting me to write the ARE with you, going
to workshops in Panama and Switzerland, and even organising our own PhD course –
that I often think I must have had the best PhD in the world. You have taught me
so much and made me a scientist. I sincerely hope we get the chance to work together
again in the future. Thank you for everything. I must also thank my PhD Committee,
Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout
the duration of my PhD. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
citation:
ama: Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861
apa: Pull, C. (2017). Disease defence in garden ants. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861
chicago: Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science
and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861.
ieee: C. Pull, “Disease defence in garden ants,” Institute of Science and Technology
Austria, 2017.
ista: Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology
Austria.
mla: Pull, Christopher. Disease Defence in Garden Ants. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861.
short: C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-28T11:31:32Z
day: '26'
ddc:
- '576'
- '577'
- '578'
- '579'
- '590'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:th_861
file:
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checksum: 4993cdd5382295758ecc3ecbd2a9aaff
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month: '09'
oa: 1
oa_version: Published Version
page: '122'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6830'
pubrep_id: '861'
related_material:
record:
- id: '616'
relation: part_of_dissertation
status: public
- id: '806'
relation: part_of_dissertation
status: public
- id: '734'
relation: part_of_dissertation
status: public
- id: '732'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Disease defence in garden ants
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1528'
abstract:
- lang: eng
text: 'We consider N×N Hermitian random matrices H consisting of blocks of size
M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian
in the four moment matching sense, but their distribution varies from block to
block to form a block-band structure, with an essential band width M. We show
that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle
law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using
a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys
155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous
estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors
in the middle of the spectrum are fully delocalized.'
acknowledgement: "Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L.
Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access
funding provided by Institute of Science and Technology (IST Austria). The authors
are very grateful to the anonymous referees for careful reading and valuable comments,
which helped to improve the organization."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: Bao Z, Erdös L. Delocalization for a class of random block band matrices. Probability
Theory and Related Fields. 2017;167(3-4):673-776. doi:10.1007/s00440-015-0692-y
apa: Bao, Z., & Erdös, L. (2017). Delocalization for a class of random block
band matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-015-0692-y
chicago: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block
Band Matrices.” Probability Theory and Related Fields. Springer, 2017.
https://doi.org/10.1007/s00440-015-0692-y.
ieee: Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,”
Probability Theory and Related Fields, vol. 167, no. 3–4. Springer, pp.
673–776, 2017.
ista: Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices.
Probability Theory and Related Fields. 167(3–4), 673–776.
mla: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block
Band Matrices.” Probability Theory and Related Fields, vol. 167, no. 3–4,
Springer, 2017, pp. 673–776, doi:10.1007/s00440-015-0692-y.
short: Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.
date_created: 2018-12-11T11:52:32Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T09:42:12Z
day: '01'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1007/s00440-015-0692-y
ec_funded: 1
external_id:
isi:
- '000398842700004'
file:
- access_level: open_access
checksum: 67afa85ff1e220cbc1f9f477a828513c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:05Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4665'
file_name: IST-2016-489-v1+1_s00440-015-0692-y.pdf
file_size: 1615755
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 167'
isi: 1
issue: 3-4
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 673 - 776
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_identifier:
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '5644'
pubrep_id: '489'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Delocalization for a class of random block band matrices
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: 167
year: '2017'
...
---
_id: '169'
abstract:
- lang: eng
text: We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman
sums leads to an optimal covering exponent for S3.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Vinay
full_name: Kumaraswamy, Vinay
last_name: Kumaraswamy
- first_name: Rapael
full_name: Steiner, Rapael
last_name: Steiner
citation:
ama: Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering
exponent for S3. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx116
apa: Browning, T. D., Kumaraswamy, V., & Steiner, R. (2017). Twisted Linnik
implies optimal covering exponent for S3. International Mathematics Research
Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx116
chicago: Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik
Implies Optimal Covering Exponent for S3.” International Mathematics Research
Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx116.
ieee: T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal
covering exponent for S3,” International Mathematics Research Notices.
Oxford University Press, 2017.
ista: Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal
covering exponent for S3. International Mathematics Research Notices.
mla: Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent
for S3.” International Mathematics Research Notices, Oxford University
Press, 2017, doi:10.1093/imrn/rnx116.
short: T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research
Notices (2017).
date_created: 2018-12-11T11:44:59Z
date_published: 2017-06-19T00:00:00Z
date_updated: 2021-01-12T06:52:32Z
day: '19'
doi: 10.1093/imrn/rnx116
extern: '1'
external_id:
arxiv:
- '1609.06097'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.06097
month: '06'
oa: 1
oa_version: None
publication: International Mathematics Research Notices
publication_status: published
publisher: Oxford University Press
publist_id: '7752'
quality_controlled: '1'
status: public
title: Twisted Linnik implies optimal covering exponent for S3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '172'
abstract:
- lang: eng
text: We study strong approximation for some algebraic varieties over ℚ which are
defined using norm forms. This allows us to confirm a special case of a conjecture
due to Harpaz and Wittenberg.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Damaris
full_name: Schindler, Damaris
last_name: Schindler
citation:
ama: Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and
Wittenberg. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx252
apa: Browning, T. D., & Schindler, D. (2017). Strong approximation and a conjecture
of Harpaz and Wittenberg. International Mathematics Research Notices. Oxford
University Press. https://doi.org/10.1093/imrn/rnx252
chicago: Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a
Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices.
Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx252.
ieee: T. D. Browning and D. Schindler, “Strong approximation and a conjecture of
Harpaz and Wittenberg,” International Mathematics Research Notices. Oxford
University Press, 2017.
ista: Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz
and Wittenberg. International Mathematics Research Notices.
mla: Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture
of Harpaz and Wittenberg.” International Mathematics Research Notices,
Oxford University Press, 2017, doi:10.1093/imrn/rnx252.
short: T.D. Browning, D. Schindler, International Mathematics Research Notices (2017).
date_created: 2018-12-11T11:45:00Z
date_published: 2017-10-30T00:00:00Z
date_updated: 2021-01-12T06:52:45Z
day: '30'
doi: 10.1093/imrn/rnx252
extern: '1'
external_id:
arxiv:
- '1509.07744'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.07744
month: '10'
oa: 1
oa_version: None
publication: International Mathematics Research Notices
publication_status: published
publisher: Oxford University Press
publist_id: '7749'
quality_controlled: '1'
status: public
title: Strong approximation and a conjecture of Harpaz and Wittenberg
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '2016'
abstract:
- lang: eng
text: The Ising model is one of the simplest and most famous models of interacting
systems. It was originally proposed to model ferromagnetic interactions in statistical
physics and is now widely used to model spatial processes in many areas such as
ecology, sociology, and genetics, usually without testing its goodness-of-fit.
Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model.
The theory of Markov bases has been developed in algebraic statistics for exact
goodness-of-fit testing using a Monte Carlo approach. However, this beautiful
theory has fallen short of its promise for applications, because finding a Markov
basis is usually computationally intractable. We develop a Monte Carlo method
for exact goodness-of-fit testing for the Ising model which avoids computing a
Markov basis and also leads to a better connectivity of the Markov chain and hence
to a faster convergence. We show how this method can be applied to analyze the
spatial organization of receptors on the cell membrane.
article_processing_charge: No
arxiv: 1
author:
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
last_name: Martin Del Campo Sanchez
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306.
doi:10.1111/sjos.12251
apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017).
Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of
Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251
chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline
Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal
of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.
ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit
testing for the Ising model,” Scandinavian Journal of Statistics, vol.
44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.
ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for
the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell,
2017, pp. 285–306, doi:10.1111/sjos.12251.
short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian
Journal of Statistics 44 (2017) 285–306.
date_created: 2018-12-11T11:55:13Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-19T15:13:27Z
day: '01'
department:
- _id: GaTk
doi: 10.1111/sjos.12251
external_id:
arxiv:
- '1410.1242'
isi:
- '000400985000001'
intvolume: ' 44'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.1242
month: '06'
oa: 1
oa_version: Preprint
page: 285 - 306
publication: Scandinavian Journal of Statistics
publication_identifier:
issn:
- '03036898'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5060'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Exact goodness-of-fit testing for the Ising model
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 44
year: '2017'
...
---
_id: '202'
abstract:
- lang: eng
text: 'Restriction-modification (RM) represents the simplest and possibly the most
widespread mechanism of self/non-self discrimination in nature. In order to provide
bacteria with immunity against bacteriophages and other parasitic genetic elements,
RM systems rely on a balance between two enzymes: the restriction enzyme, which
cleaves non-self DNA at specific restriction sites, and the modification enzyme,
which tags the host’s DNA as self and thus protects it from cleavage. In this
thesis, I use population and single-cell level experiments in combination with
mathematical modeling to study different aspects of the interplay between RM systems,
bacteria and bacteriophages. First, I analyze how mutations in phage restriction
sites affect the probability of phage escape – an inherently stochastic process,
during which phages accidently get modified instead of restricted. Next, I use
single-cell experiments to show that RM systems can, with a low probability, attack
the genome of their bacterial host and that this primitive form of autoimmunity
leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally,
I investigate the nature of interactions between bacteria, RM systems and temperate
bacteriophages to find that, as a consequence of phage escape and its impact on
population dynamics, RM systems can promote acquisition of symbiotic bacteriophages,
rather than limit it. The results presented here uncover new fundamental biological
properties of RM systems and highlight their importance in the ecology and evolution
of bacteria, bacteriophages and their interactions.'
acknowledgement: "During my PhD studies, I received help from many people, all of
which unfortunately cannot be listed here. I thank them deeply and hope that I never
made them regret their kindness.\r\nI would like to express my deepest gratitude
to Călin Guet, who went far beyond his responsibilities as an advisor and was to
me also a great mentor and a friend. Călin never questioned my potential or lacked
compassion and I cannot thank him enough for cultivating in me an independent scientist.
I was amazed by his ability to recognize the most fascinating scientific problems
in objects of study that others would find mundane. I hope I adopted at least a
fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his
support and especially for giving me the best possible example of how one can practice
excellent science with humor and style. Working with Bruce was a true privilege.\r\nI
thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the
Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI
thank all our lab members: Tobias Bergmiller for his guidance, especially in the
first years of my research, and for being a good friend throughout; Remy Chait for
staying in the lab at unreasonable hours and for the good laughs at bad jokes we
shared; Anna Staron for supportively listening to my whines whenever I had to run
a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for
keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek
for always being nice to me, no matter how much bench space I took from her.\r\nI
thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing
the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics
analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical
modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally,
I would like to thank my family and especially my wife Edita, who sacrificed a lot
so that I can pursue my goals and dreams.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
citation:
ama: Pleska M. Biology of restriction-modification systems at the single-cell and
population level. 2017. doi:10.15479/AT:ISTA:th_916
apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916
chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell
and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.
ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell
and population level,” Institute of Science and Technology Austria, 2017.
ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria.
mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell
and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.
short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell
and Population Level, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:45:10Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-15T12:04:56Z
day: '01'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:th_916
file:
- access_level: open_access
checksum: 33cfb59674e91f82e3738396d3fb3776
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:48Z
date_updated: 2020-07-14T12:45:24Z
file_id: '4710'
file_name: IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf
file_size: 18569590
relation: main_file
- access_level: closed
checksum: dcc239968decb233e7f98cf1083d8c26
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:33:14Z
date_updated: 2020-07-14T12:45:24Z
file_id: '6204'
file_name: 2017_Pleska_Maros_Thesis.docx
file_size: 2801649
relation: source_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '126'
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7711'
pubrep_id: '916'
related_material:
record:
- id: '1243'
relation: part_of_dissertation
status: public
- id: '561'
relation: part_of_dissertation
status: public
- id: '457'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Biology of restriction-modification systems at the single-cell and population
level
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1336'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse the runtimes of EAs on many
illustrative problems. Here we apply this theory to a simple model of natural
evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the
time between occurrences of new mutations is much longer than the time it takes
for a mutated genotype to take over the population. In this situation, the population
only contains copies of one genotype and evolution can be modelled as a stochastic
process evolving one genotype by means of mutation and selection between the resident
and the mutated genotype. The probability of accepting the mutated genotype then
depends on the change in fitness. We study this process, SSWM, from an algorithmic
perspective, quantifying its expected optimisation time for various parameters
and investigating differences to a similar evolutionary algorithm, the well-known
(1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at
crossing fitness valleys and study an example where SSWM outperforms the (1+1)
EA by taking advantage of information on the fitness gradient.
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison
of natural and artificial evolution. Algorithmica. 2017;78(2):681-713.
doi:10.1007/s00453-016-0212-1
apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards
a runtime comparison of natural and artificial evolution. Algorithmica.
Springer. https://doi.org/10.1007/s00453-016-0212-1
chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova.
“Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica.
Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.
ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime
comparison of natural and artificial evolution,” Algorithmica, vol. 78,
no. 2. Springer, pp. 681–713, 2017.
ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime
comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.
mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial
Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713,
doi:10.1007/s00453-016-0212-1.
short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017)
681–713.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:14:42Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-016-0212-1
ec_funded: 1
external_id:
isi:
- '000400379500013'
file:
- access_level: open_access
checksum: 7873f665a0c598ac747c908f34cb14b9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:19Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4805'
file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf
file_size: 710206
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 681 - 713
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_identifier:
issn:
- '01784617'
publication_status: published
publisher: Springer
publist_id: '5931'
pubrep_id: '658'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards a runtime comparison of natural and artificial evolution
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: 78
year: '2017'
...
---
_id: '1337'
abstract:
- lang: eng
text: We consider the local eigenvalue distribution of large self-adjoint N×N random
matrices H=H∗ with centered independent entries. In contrast to previous works
the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence
the density of states is not the Wigner semicircle law. Its possible shapes are
described in the companion paper (Ajanki et al. in Quadratic Vector Equations
on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the
resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z))
solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki
et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095).
We prove a local law down to the smallest spectral resolution scale, and bulk
universality for both real symmetric and complex hermitian symmetry classes.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices.
Probability Theory and Related Fields. 2017;169(3-4):667-727. doi:10.1007/s00440-016-0740-2
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2017). Universality for general
Wigner-type matrices. Probability Theory and Related Fields. Springer.
https://doi.org/10.1007/s00440-016-0740-2
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for
General Wigner-Type Matrices.” Probability Theory and Related Fields. Springer,
2017. https://doi.org/10.1007/s00440-016-0740-2.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type
matrices,” Probability Theory and Related Fields, vol. 169, no. 3–4. Springer,
pp. 667–727, 2017.
ista: Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type
matrices. Probability Theory and Related Fields. 169(3–4), 667–727.
mla: Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.”
Probability Theory and Related Fields, vol. 169, no. 3–4, Springer, 2017,
pp. 667–727, doi:10.1007/s00440-016-0740-2.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields
169 (2017) 667–727.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:14:17Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: LaEr
doi: 10.1007/s00440-016-0740-2
ec_funded: 1
external_id:
isi:
- '000414358400002'
file:
- access_level: open_access
checksum: 29f5a72c3f91e408aeb9e78344973803
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:25Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4686'
file_name: IST-2017-657-v1+2_s00440-016-0740-2.pdf
file_size: 988843
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 169'
isi: 1
issue: 3-4
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 667 - 727
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '5930'
pubrep_id: '657'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universality for general Wigner-type matrices
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: 169
year: '2017'
...
---
_id: '1338'
abstract:
- lang: eng
text: We present a computer-aided programming approach to concurrency. The approach
allows programmers to program assuming a friendly, non-preemptive scheduler, and
our synthesis procedure inserts synchronization to ensure that the final program
works even with a preemptive scheduler. The correctness specification is implicit,
inferred from the non-preemptive behavior. Let us consider sequences of calls
that the program makes to an external interface. The specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We guarantee that
our synthesis does not introduce deadlocks and that the synchronization inserted
is optimal w.r.t. a given objective function. The solution is based on a finitary
abstraction, an algorithm for bounded language inclusion modulo an independence
relation, and generation of a set of global constraints over synchronization placements.
Each model of the global constraints set corresponds to a correctness-ensuring
synchronization placement. The placement that is optimal w.r.t. the given objective
function is chosen as the synchronization solution. We apply the approach to device-driver
programming, where the driver threads call the software interface of the device
and the API provided by the operating system. Our experiments demonstrate that
our synthesis method is precise and efficient. The implicit specification helped
us find one concurrency bug previously missed when model-checking using an explicit,
user-provided specification. We implemented objective functions for coarse-grained
and fine-grained locking and observed that different synchronization placements
are produced for our experiments, favoring a minimal number of synchronization
operations or maximum concurrency, respectively.
article_processing_charge: No
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Edmund
full_name: Clarke, Edmund
last_name: Clarke
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling
using synchronization synthesis. Formal Methods in System Design. 2017;50(2-3):97-139.
doi:10.1007/s10703-016-0256-5
apa: Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta,
R., & Tarrach, T. (2017). From non-preemptive to preemptive scheduling using
synchronization synthesis. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-016-0256-5
chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid
Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive
Scheduling Using Synchronization Synthesis.” Formal Methods in System Design.
Springer, 2017. https://doi.org/10.1007/s10703-016-0256-5.
ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using
synchronization synthesis,” Formal Methods in System Design, vol. 50, no.
2–3. Springer, pp. 97–139, 2017.
ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach
T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis.
Formal Methods in System Design. 50(2–3), 97–139.
mla: Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization
Synthesis.” Formal Methods in System Design, vol. 50, no. 2–3, Springer,
2017, pp. 97–139, doi:10.1007/s10703-016-0256-5.
short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta,
T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:13:51Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10703-016-0256-5
ec_funded: 1
external_id:
isi:
- '000399888900001'
file:
- access_level: open_access
checksum: 1163dfd997e8212c789525d4178b1653
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:05Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4985'
file_name: IST-2016-656-v1+1_s10703-016-0256-5.pdf
file_size: 1416170
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: 2-3
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 97 - 139
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '5929'
pubrep_id: '656'
quality_controlled: '1'
related_material:
record:
- id: '1729'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: From non-preemptive to preemptive scheduling using synchronization synthesis
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: 50
year: '2017'
...
---
_id: '13380'
abstract:
- lang: eng
text: Although dissipative self-assembly is ubiquitous in nature, where it gives
rise to structures and functions critical to life, examples of artificial systems
featuring this mode of self-assembly are rare. Here, we identify the presence
of ephemeral assemblies during seeded growth of gold nanoparticles. In this process,
hydrazine reduces Au(III) ions, which attach to the existing nanoparticles “seeds”.
The attachment is accompanied by a local increase in the concentration of a surfactant,
which therefore forms a bilayer on nanoparticle surfaces, inducing their assembly.
The resulting aggregates gradually disassemble as the surfactant concentration
throughout the solution equilibrates. The lifetimes of the out-of-equilibrium
aggregates depend on and can be controlled by the size of the constituent nanoparticles.
We demonstrate the utility of our out-of-equilibrium aggregates to form transient
reflective coatings on polar surfaces.
article_processing_charge: No
article_type: original
author:
- first_name: Michał
full_name: Sawczyk, Michał
last_name: Sawczyk
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Sawczyk M, Klajn R. Out-of-equilibrium aggregates and coatings during seeded
growth of metallic nanoparticles. Journal of the American Chemical Society.
2017;139(49):17973-17978. doi:10.1021/jacs.7b09111
apa: Sawczyk, M., & Klajn, R. (2017). Out-of-equilibrium aggregates and coatings
during seeded growth of metallic nanoparticles. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/jacs.7b09111
chicago: Sawczyk, Michał, and Rafal Klajn. “Out-of-Equilibrium Aggregates and Coatings
during Seeded Growth of Metallic Nanoparticles.” Journal of the American Chemical
Society. American Chemical Society, 2017. https://doi.org/10.1021/jacs.7b09111.
ieee: M. Sawczyk and R. Klajn, “Out-of-equilibrium aggregates and coatings during
seeded growth of metallic nanoparticles,” Journal of the American Chemical
Society, vol. 139, no. 49. American Chemical Society, pp. 17973–17978, 2017.
ista: Sawczyk M, Klajn R. 2017. Out-of-equilibrium aggregates and coatings during
seeded growth of metallic nanoparticles. Journal of the American Chemical Society.
139(49), 17973–17978.
mla: Sawczyk, Michał, and Rafal Klajn. “Out-of-Equilibrium Aggregates and Coatings
during Seeded Growth of Metallic Nanoparticles.” Journal of the American Chemical
Society, vol. 139, no. 49, American Chemical Society, 2017, pp. 17973–78,
doi:10.1021/jacs.7b09111.
short: M. Sawczyk, R. Klajn, Journal of the American Chemical Society 139 (2017)
17973–17978.
date_created: 2023-08-01T09:41:01Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-08-07T11:19:30Z
day: '01'
doi: 10.1021/jacs.7b09111
extern: '1'
external_id:
pmid:
- '29193964'
intvolume: ' 139'
issue: '49'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '12'
oa_version: None
page: 17973-17978
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Out-of-equilibrium aggregates and coatings during seeded growth of metallic
nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2017'
...
---
_id: '13381'
abstract:
- lang: eng
text: Self-assembly of inorganic nanoparticles has been used to prepare hundreds
of different colloidal crystals, but almost invariably with the restriction that
the particles must be densely packed. Here, we show that non–close-packed nanoparticle
arrays can be fabricated through the selective removal of one of two components
comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle
superlattices were prepared at the liquid-air interface, including several arrangements
that were previously unknown. Molecular dynamics simulations revealed the particular
role of the liquid in templating the formation of superlattices not achievable
through self-assembly in bulk solution. Second, upon stabilization, all of these
binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous
materials having the same chemical composition but differing in their nanoscale
architectures.
article_processing_charge: No
article_type: original
author:
- first_name: Thumu
full_name: Udayabhaskararao, Thumu
last_name: Udayabhaskararao
- first_name: Thomas
full_name: Altantzis, Thomas
last_name: Altantzis
- first_name: Lothar
full_name: Houben, Lothar
last_name: Houben
- first_name: Marc
full_name: Coronado-Puchau, Marc
last_name: Coronado-Puchau
- first_name: Judith
full_name: Langer, Judith
last_name: Langer
- first_name: Ronit
full_name: Popovitz-Biro, Ronit
last_name: Popovitz-Biro
- first_name: Luis M.
full_name: Liz-Marzán, Luis M.
last_name: Liz-Marzán
- first_name: Lela
full_name: Vuković, Lela
last_name: Vuković
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Sara
full_name: Bals, Sara
last_name: Bals
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Udayabhaskararao T, Altantzis T, Houben L, et al. Tunable porous nanoallotropes
prepared by post-assembly etching of binary nanoparticle superlattices. Science.
2017;358(6362):514-518. doi:10.1126/science.aan6046
apa: Udayabhaskararao, T., Altantzis, T., Houben, L., Coronado-Puchau, M., Langer,
J., Popovitz-Biro, R., … Klajn, R. (2017). Tunable porous nanoallotropes prepared
by post-assembly etching of binary nanoparticle superlattices. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.aan6046
chicago: Udayabhaskararao, Thumu, Thomas Altantzis, Lothar Houben, Marc Coronado-Puchau,
Judith Langer, Ronit Popovitz-Biro, Luis M. Liz-Marzán, et al. “Tunable Porous
Nanoallotropes Prepared by Post-Assembly Etching of Binary Nanoparticle Superlattices.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aan6046.
ieee: T. Udayabhaskararao et al., “Tunable porous nanoallotropes prepared
by post-assembly etching of binary nanoparticle superlattices,” Science,
vol. 358, no. 6362. American Association for the Advancement of Science, pp. 514–518,
2017.
ista: Udayabhaskararao T, Altantzis T, Houben L, Coronado-Puchau M, Langer J, Popovitz-Biro
R, Liz-Marzán LM, Vuković L, Král P, Bals S, Klajn R. 2017. Tunable porous nanoallotropes
prepared by post-assembly etching of binary nanoparticle superlattices. Science.
358(6362), 514–518.
mla: Udayabhaskararao, Thumu, et al. “Tunable Porous Nanoallotropes Prepared by
Post-Assembly Etching of Binary Nanoparticle Superlattices.” Science, vol.
358, no. 6362, American Association for the Advancement of Science, 2017, pp.
514–18, doi:10.1126/science.aan6046.
short: T. Udayabhaskararao, T. Altantzis, L. Houben, M. Coronado-Puchau, J. Langer,
R. Popovitz-Biro, L.M. Liz-Marzán, L. Vuković, P. Král, S. Bals, R. Klajn, Science
358 (2017) 514–518.
date_created: 2023-08-01T09:41:16Z
date_published: 2017-10-27T00:00:00Z
date_updated: 2023-08-07T11:25:00Z
day: '27'
doi: 10.1126/science.aan6046
extern: '1'
external_id:
pmid:
- '29074773'
intvolume: ' 358'
issue: '6362'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://repository.uantwerpen.be/docman/irua/8d722e/147242_2018_06_07.pdf
month: '10'
oa: 1
oa_version: Submitted Version
page: 514-518
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle
superlattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 358
year: '2017'
...
---
_id: '13382'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jan H.
full_name: van Esch, Jan H.
last_name: van Esch
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Sijbren
full_name: Otto, Sijbren
last_name: Otto
citation:
ama: van Esch JH, Klajn R, Otto S. Chemical systems out of equilibrium. Chemical
Society Reviews. 2017;46(18):5474-5475. doi:10.1039/c7cs90088k
apa: van Esch, J. H., Klajn, R., & Otto, S. (2017). Chemical systems out of
equilibrium. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c7cs90088k
chicago: Esch, Jan H. van, Rafal Klajn, and Sijbren Otto. “Chemical Systems out
of Equilibrium.” Chemical Society Reviews. Royal Society of Chemistry,
2017. https://doi.org/10.1039/c7cs90088k.
ieee: J. H. van Esch, R. Klajn, and S. Otto, “Chemical systems out of equilibrium,”
Chemical Society Reviews, vol. 46, no. 18. Royal Society of Chemistry,
pp. 5474–5475, 2017.
ista: van Esch JH, Klajn R, Otto S. 2017. Chemical systems out of equilibrium. Chemical
Society Reviews. 46(18), 5474–5475.
mla: van Esch, Jan H., et al. “Chemical Systems out of Equilibrium.” Chemical
Society Reviews, vol. 46, no. 18, Royal Society of Chemistry, 2017, pp. 5474–75,
doi:10.1039/c7cs90088k.
short: J.H. van Esch, R. Klajn, S. Otto, Chemical Society Reviews 46 (2017) 5474–5475.
date_created: 2023-08-01T09:41:30Z
date_published: 2017-09-08T00:00:00Z
date_updated: 2023-08-07T11:27:42Z
day: '08'
doi: 10.1039/c7cs90088k
extern: '1'
external_id:
pmid:
- '28884760'
intvolume: ' 46'
issue: '18'
keyword:
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/c7cs90088k
month: '09'
oa: 1
oa_version: Published Version
page: 5474-5475
pmid: 1
publication: Chemical Society Reviews
publication_identifier:
eissn:
- 1460-4744
issn:
- 0306-0012
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chemical systems out of equilibrium
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2017'
...
---
_id: '13383'
abstract:
- lang: eng
text: Two novel donor–acceptor Stenhouse adducts (DASAs) featuring the catechol
moiety were synthesized and characterized. Both compounds bind strongly to the
surfaces of magnetite nanoparticles. An adrenaline-derived DASA renders the particles
insoluble in all common solvents, likely because of poor solvation of the zwitterionic
isomer generated on the nanoparticle surfaces. Well-soluble nanoparticles were
successfully obtained using dopamine-derived DASA equipped with a long alkyl chain.
Upon its attachment to nanoparticles, this DASA undergoes an irreversible decoloration
reaction owing to the formation of the zwitterionic form. The reaction follows
first-order kinetics and proceeds more rapidly on large nanoparticles. Interestingly,
decoloration can be suppressed in the presence of free DASA molecules in solution
or at high nanoparticle concentrations.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Ahrens, Johannes
last_name: Ahrens
- first_name: Tong
full_name: Bian, Tong
last_name: Bian
- first_name: Tom
full_name: Vexler, Tom
last_name: Vexler
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Ahrens J, Bian T, Vexler T, Klajn R. Irreversible bleaching of donor-acceptor
stenhouse adducts on the surfaces of magnetite nanoparticles. ChemPhotoChem.
2017;1(5):230-236. doi:10.1002/cptc.201700009
apa: Ahrens, J., Bian, T., Vexler, T., & Klajn, R. (2017). Irreversible bleaching
of donor-acceptor stenhouse adducts on the surfaces of magnetite nanoparticles.
ChemPhotoChem. Wiley. https://doi.org/10.1002/cptc.201700009
chicago: Ahrens, Johannes, Tong Bian, Tom Vexler, and Rafal Klajn. “Irreversible
Bleaching of Donor-Acceptor Stenhouse Adducts on the Surfaces of Magnetite Nanoparticles.”
ChemPhotoChem. Wiley, 2017. https://doi.org/10.1002/cptc.201700009.
ieee: J. Ahrens, T. Bian, T. Vexler, and R. Klajn, “Irreversible bleaching of donor-acceptor
stenhouse adducts on the surfaces of magnetite nanoparticles,” ChemPhotoChem,
vol. 1, no. 5. Wiley, pp. 230–236, 2017.
ista: Ahrens J, Bian T, Vexler T, Klajn R. 2017. Irreversible bleaching of donor-acceptor
stenhouse adducts on the surfaces of magnetite nanoparticles. ChemPhotoChem. 1(5),
230–236.
mla: Ahrens, Johannes, et al. “Irreversible Bleaching of Donor-Acceptor Stenhouse
Adducts on the Surfaces of Magnetite Nanoparticles.” ChemPhotoChem, vol.
1, no. 5, Wiley, 2017, pp. 230–36, doi:10.1002/cptc.201700009.
short: J. Ahrens, T. Bian, T. Vexler, R. Klajn, ChemPhotoChem 1 (2017) 230–236.
date_created: 2023-08-01T09:41:43Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-08-07T12:08:05Z
day: '01'
doi: 10.1002/cptc.201700009
extern: '1'
intvolume: ' 1'
issue: '5'
keyword:
- Organic Chemistry
- Physical and Theoretical Chemistry
- Analytical Chemistry
language:
- iso: eng
month: '05'
oa_version: None
page: 230-236
publication: ChemPhotoChem
publication_identifier:
eissn:
- 2367-0932
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Irreversible bleaching of donor-acceptor stenhouse adducts on the surfaces
of magnetite nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2017'
...
---
_id: '13384'
abstract:
- lang: eng
text: Although methane is a volatile gas, it can be efficiently trapped in ice,
which can then be readily set on fire. Beyond the curiosity of this “burning ice,”
caged methane is of great importance as one of the world's largest natural gas
resources. In these materials, known as clathrates, methane molecules are tightly
bound in nanometer-sized, regularly interspaced cages. Other inorganic materials,
such as the silica mineral chibaite, can similarly encapsulate methane and higher
hydrocarbons. Simple organic compounds have also been found to trap various organic
molecules upon crystallization.
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Klajn R. Clathrates grow up. Science. 2017;355(6328):912-912.
doi:10.1126/science.aam7927
apa: Samanta, D., & Klajn, R. (2017). Clathrates grow up. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.aam7927
chicago: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science.
American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam7927.
ieee: D. Samanta and R. Klajn, “Clathrates grow up,” Science, vol. 355, no.
6328. American Association for the Advancement of Science, pp. 912–912, 2017.
ista: Samanta D, Klajn R. 2017. Clathrates grow up. Science. 355(6328), 912–912.
mla: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science, vol.
355, no. 6328, American Association for the Advancement of Science, 2017, pp.
912–912, doi:10.1126/science.aam7927.
short: D. Samanta, R. Klajn, Science 355 (2017) 912–912.
date_created: 2023-08-01T09:41:55Z
date_published: 2017-03-03T00:00:00Z
date_updated: 2023-08-07T12:23:03Z
day: '03'
doi: 10.1126/science.aam7927
extern: '1'
external_id:
pmid:
- '28254902'
intvolume: ' 355'
issue: '6328'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa_version: None
page: 912-912
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clathrates grow up
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '13476'
abstract:
- lang: eng
text: Understanding ionizing fluxes of stellar populations is crucial for various
astrophysical problems including the epoch of reionization. Short-lived massive
stars are generally considered as the main stellar sources. We examine the potential
role of less massive stars that lose their envelope through interaction with a
binary companion. Here, we focus on the role of metallicity (Z). For this purpose
we used the evolutionary code MESA and created tailored atmosphere models with
the radiative transfer code CMFGEN. We show that typical progenitors, with initial
masses of 12 M⊙, produce hot and compact stars (~ 4 M⊙, 60–80 kK, ~1 R⊙). These
stripped stars copiously produce ionizing photons, emitting 60–85% and 30–60%
of their energy as HI and HeI ionizing radiation, for Z = 0.0001–0.02, respectively.
Their output is comparable to what massive stars emit during their Wolf-Rayet
phase, if we account for their longer lifetimes and the favorable slope of the
initial mass function. Their relative importance for reionization may be further
favored since they emit their photons with a time delay (~ 20 Myr after birth
in our fiducial model). This allows time for the dispersal of the birth clouds,
allowing the ionizing photons to escape into the intergalactic medium. At low
Z, we find that Roche stripping fails to fully remove the H-rich envelope, because
of the reduced opacity in the subsurface layers. This is in sharp contrast with
the assumption of complete stripping that is made in rapid population synthesis
simulations, which are widely used to simulate the binary progenitors of supernovae
and gravitational waves. Finally, we discuss the urgency to increase the observed
sample of stripped stars to test these models and we discuss how our predictions
can help to design efficient observational campaigns.
article_number: A11
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
citation:
ama: 'Götberg YLL, de Mink SE, Groh JH. Ionizing spectra of stars that lose their
envelope through interaction with a binary companion: Role of metallicity. Astronomy
& Astrophysics. 2017;608. doi:10.1051/0004-6361/201730472'
apa: 'Götberg, Y. L. L., de Mink, S. E., & Groh, J. H. (2017). Ionizing spectra
of stars that lose their envelope through interaction with a binary companion:
Role of metallicity. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201730472'
chicago: 'Götberg, Ylva Louise Linsdotter, S. E. de Mink, and J. H. Groh. “Ionizing
Spectra of Stars That Lose Their Envelope through Interaction with a Binary Companion:
Role of Metallicity.” Astronomy & Astrophysics. EDP Sciences, 2017.
https://doi.org/10.1051/0004-6361/201730472.'
ieee: 'Y. L. L. Götberg, S. E. de Mink, and J. H. Groh, “Ionizing spectra of stars
that lose their envelope through interaction with a binary companion: Role of
metallicity,” Astronomy & Astrophysics, vol. 608. EDP Sciences, 2017.'
ista: 'Götberg YLL, de Mink SE, Groh JH. 2017. Ionizing spectra of stars that lose
their envelope through interaction with a binary companion: Role of metallicity.
Astronomy & Astrophysics. 608, A11.'
mla: 'Götberg, Ylva Louise Linsdotter, et al. “Ionizing Spectra of Stars That Lose
Their Envelope through Interaction with a Binary Companion: Role of Metallicity.”
Astronomy & Astrophysics, vol. 608, A11, EDP Sciences, 2017, doi:10.1051/0004-6361/201730472.'
short: Y.L.L. Götberg, S.E. de Mink, J.H. Groh, Astronomy & Astrophysics 608
(2017).
date_created: 2023-08-03T10:15:09Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-08-09T11:27:06Z
day: '01'
doi: 10.1051/0004-6361/201730472
extern: '1'
external_id:
arxiv:
- '1701.07439'
intvolume: ' 608'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201730472
month: '12'
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: 'Ionizing spectra of stars that lose their envelope through interaction with
a binary companion: Role of metallicity'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 608
year: '2017'
...
---
_id: '13477'
abstract:
- lang: eng
text: Most massive stars, the progenitors of core-collapse supernovae, are in close
binary systems and may interact with their companion through mass transfer or
merging. We undertake a population synthesis study to compute the delay-time distribution
of core-collapse supernovae, that is, the supernova rate versus time following
a starburst, taking into account binary interactions. We test the systematic robustness
of our results by running various simulations to account for the uncertainties
in our standard assumptions. We find that a significant fraction, 15+9-8%, of
core-collapse supernovae are “late”, that is, they occur 50–200 Myr after birth,
when all massive single stars have already exploded. These late events originate
predominantly from binary systems with at least one, or, in most cases, with both
stars initially being of intermediate mass (4–8 M⊙). The main evolutionary channels
that contribute often involve either the merging of the initially more massive
primary star with its companion or the engulfment of the remaining core of the
primary by the expanding secondary that has accreted mass at an earlier evolutionary
stage. Also, the total number of core-collapse supernovae increases by 14+15-14%
because of binarity for the same initial stellar mass. The high rate implies that
we should have already observed such late core-collapse supernovae, but have not
recognized them as such. We argue that φ Persei is a likely progenitor and that
eccentric neutron star – white dwarf systems are likely descendants. Late events
can help explain the discrepancy in the delay-time distributions derived from
supernova remnants in the Magellanic Clouds and extragalactic type Ia events,
lowering the contribution of prompt Ia events. We discuss ways to test these predictions
and speculate on the implications for supernova feedback in simulations of galaxy
evolution.
article_number: A29
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: E.
full_name: Zapartas, E.
last_name: Zapartas
- first_name: S. E.
full_name: de Mink, S. E.
last_name: de Mink
- first_name: R. G.
full_name: Izzard, R. G.
last_name: Izzard
- first_name: S.-C.
full_name: Yoon, S.-C.
last_name: Yoon
- first_name: C.
full_name: Badenes, C.
last_name: Badenes
- 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: A.
full_name: de Koter, A.
last_name: de Koter
- first_name: C. J.
full_name: Neijssel, C. J.
last_name: Neijssel
- first_name: M.
full_name: Renzo, M.
last_name: Renzo
- first_name: A.
full_name: Schootemeijer, A.
last_name: Schootemeijer
- first_name: T. S.
full_name: Shrotriya, T. S.
last_name: Shrotriya
citation:
ama: Zapartas E, de Mink SE, Izzard RG, et al. Delay-time distribution of core-collapse
supernovae with late events resulting from binary interaction. Astronomy &
Astrophysics. 2017;601(A&A). doi:10.1051/0004-6361/201629685
apa: Zapartas, E., de Mink, S. E., Izzard, R. G., Yoon, S.-C., Badenes, C., Götberg,
Y. L. L., … Shrotriya, T. S. (2017). Delay-time distribution of core-collapse
supernovae with late events resulting from binary interaction. Astronomy &
Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201629685
chicago: Zapartas, E., S. E. de Mink, R. G. Izzard, S.-C. Yoon, C. Badenes, Ylva
Louise Linsdotter Götberg, A. de Koter, et al. “Delay-Time Distribution of Core-Collapse
Supernovae with Late Events Resulting from Binary Interaction.” Astronomy &
Astrophysics. EDP Sciences, 2017. https://doi.org/10.1051/0004-6361/201629685.
ieee: E. Zapartas et al., “Delay-time distribution of core-collapse supernovae
with late events resulting from binary interaction,” Astronomy & Astrophysics,
vol. 601, no. A&A. EDP Sciences, 2017.
ista: Zapartas E, de Mink SE, Izzard RG, Yoon S-C, Badenes C, Götberg YLL, de Koter
A, Neijssel CJ, Renzo M, Schootemeijer A, Shrotriya TS. 2017. Delay-time distribution
of core-collapse supernovae with late events resulting from binary interaction.
Astronomy & Astrophysics. 601(A&A), A29.
mla: Zapartas, E., et al. “Delay-Time Distribution of Core-Collapse Supernovae with
Late Events Resulting from Binary Interaction.” Astronomy & Astrophysics,
vol. 601, no. A&A, A29, EDP Sciences, 2017, doi:10.1051/0004-6361/201629685.
short: E. Zapartas, S.E. de Mink, R.G. Izzard, S.-C. Yoon, C. Badenes, Y.L.L. Götberg,
A. de Koter, C.J. Neijssel, M. Renzo, A. Schootemeijer, T.S. Shrotriya, Astronomy
& Astrophysics 601 (2017).
date_created: 2023-08-03T10:15:18Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-08-09T11:15:49Z
day: '01'
doi: 10.1051/0004-6361/201629685
extern: '1'
external_id:
arxiv:
- '1701.07032'
intvolume: ' 601'
issue: A&A
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201629685
month: '05'
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: Delay-time distribution of core-collapse supernovae with late events resulting
from binary interaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 601
year: '2017'
...
---
_id: '1351'
abstract:
- lang: eng
text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
simulation-based statistical testing-like methods. In this paper, we demonstrate
that we can replace this approach by a formal verification-like method that gives
higher assurance and scalability. We focus on Wagner’s weighted GRN model with
varying weights, which is used in evolutionary biology. In the model, weight parameters
represent the gene interaction strength that may change due to genetic mutations.
For a property of interest, we synthesise the constraints over the parameter space
that represent the set of GRNs satisfying the property. We experimentally show
that our parameter synthesis procedure computes the mutational robustness of GRNs—an
important problem of interest in evolutionary biology—more efficiently than the
classical simulation method. We specify the property in linear temporal logic.
We employ symbolic bounded model checking and SMT solving to compute the space
of GRNs that satisfy the property, which amounts to synthesizing a set of linear
constraints on the weights.
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787.
doi:10.1007/s00236-016-0278-x
apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov,
T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica.
Springer. https://doi.org/10.1007/s00236-016-0278-x
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking the evolution of gene regulatory networks,” Acta Informatica,
vol. 54, no. 8. Springer, pp. 765–787, 2017.
ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model
checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta
Informatica 54 (2017) 765–787.
date_created: 2018-12-11T11:51:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2025-05-28T11:57:04Z
day: '01'
ddc:
- '006'
- '576'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/s00236-016-0278-x
ec_funded: 1
external_id:
isi:
- '000414343200003'
file:
- access_level: open_access
checksum: 4e661d9135d7f8c342e8e258dee76f3e
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T15:57:29Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5841'
file_name: 2017_ActaInformatica_Giacobbe.pdf
file_size: 755241
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 765 - 787
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Acta Informatica
publication_identifier:
issn:
- '00015903'
publication_status: published
publisher: Springer
publist_id: '5898'
pubrep_id: '649'
quality_controlled: '1'
related_material:
record:
- id: '1835'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Model checking the evolution of gene regulatory networks
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: 54
year: '2017'
...