---
_id: '10286'
abstract:
- lang: eng
text: 'In this paper, we evaluate clock signals generated in ring oscillators and
self-timed rings and the way their jitter can be transformed into random numbers.
We show that counting the periods of the jittery clock signal produces random
numbers of significantly better quality than the methods in which the jittery
signal is simply sampled (the case in almost all current methods). Moreover, we
use the counter values to characterize and continuously monitor the source of
randomness. However, instead of using the widely used statistical variance, we
propose to use Allan variance to do so. There are two main advantages: Allan variance
is insensitive to low frequency noises such as flicker noise that are known to
be autocorrelated and significantly less circuitry is required for its computation
than that used to compute commonly used variance. We also show that it is essential
to use a differential principle of randomness extraction from the jitter based
on the use of two identical oscillators to avoid autocorrelations originating
from external and internal global jitter sources and that this fact is valid for
both kinds of rings. Last but not least, we propose a method of statistical testing
based on high order Markov model to show the reduced dependencies when the proposed
randomness extraction is applied.'
article_processing_charge: No
article_type: original
author:
- first_name: Elie Noumon
full_name: Allini, Elie Noumon
last_name: Allini
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
- first_name: Oto
full_name: Petura, Oto
last_name: Petura
- first_name: Florent
full_name: Bernard, Florent
last_name: Bernard
- first_name: Marek
full_name: Laban, Marek
last_name: Laban
- first_name: Viktor
full_name: Fischer, Viktor
last_name: Fischer
citation:
ama: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and
monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242.
doi:10.13154/tches.v2018.i3.214-242
apa: Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer,
V. (2018). Evaluation and monitoring of free running oscillators serving as source
of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems.
International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242
chicago: Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek
Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems. International Association for Cryptologic Research,
2018. https://doi.org/10.13154/tches.v2018.i3.214-242.
ieee: E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer,
“Evaluation and monitoring of free running oscillators serving as source of randomness,”
IACR Transactions on Cryptographic Hardware and Embedded Systems, vol.
2018, no. 3. International Association for Cryptologic Research, pp. 214–242,
2018.
ista: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation
and monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.
mla: Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic
Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.
short: E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR
Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.
date_created: 2021-11-14T23:01:25Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-11-15T10:48:49Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/tches.v2018.i3.214-242
file:
- access_level: open_access
checksum: b816b848f046c48a8357700d9305dce5
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T10:27:29Z
date_updated: 2021-11-15T10:27:29Z
file_id: '10289'
file_name: 2018_IACR_Allini.pdf
file_size: 955755
relation: main_file
success: 1
file_date_updated: 2021-11-15T10:27:29Z
has_accepted_license: '1'
intvolume: ' 2018'
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 214-242
publication: IACR Transactions on Cryptographic Hardware and Embedded Systems
publication_identifier:
eissn:
- 2569-2925
publication_status: published
publisher: International Association for Cryptologic Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evaluation and monitoring of free running oscillators serving as source of
randomness
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2018
year: '2018'
...
---
_id: '10362'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) form gateways that control molecular exchange
between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules
and enable the selective transport of nuclear transport receptors with bound cargo.
The underlying mechanisms that establish these permeability properties remain
to be fully elucidated but require unstructured nuclear pore proteins rich in
Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical
modeling and in vitro approaches have provided a framework for explaining how
the FG network contributes to the barrier and transport properties of the NPC,
it remains unknown whether the number and/or the spatial positioning of different
FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes
to their collective properties and function. To begin to answer these questions,
we have used DNA origami to build a cylinder that mimics the dimensions of the
central transport channel and can house a specified number of FG-domains at specific
positions with easily tunable design parameters, such as grafting density and
topology. We find the overall morphology of the FG-domain assemblies to be dependent
on their chemical composition, determined by the type and density of FG-repeat,
and on their architectural confinement provided by the DNA cylinder, largely consistent
with here presented molecular dynamics simulations based on a coarse-grained polymer
model. In addition, high-speed atomic force microscopy reveals local and reversible
FG-domain condensation that transiently occludes the lumen of the DNA central
channel mimics, suggestive of how the NPC might establish its permeability properties.
acknowledgement: We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab
for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out
the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and
TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK
Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1,
and EP/M028100/1).
article_processing_charge: No
article_type: original
author:
- first_name: Patrick D. Ellis
full_name: Fisher, Patrick D. Ellis
last_name: Fisher
- first_name: Qi
full_name: Shen, Qi
last_name: Shen
- first_name: Bernice
full_name: Akpinar, Bernice
last_name: Akpinar
- first_name: Luke K.
full_name: Davis, Luke K.
last_name: Davis
- first_name: Kenny Kwok Hin
full_name: Chung, Kenny Kwok Hin
last_name: Chung
- first_name: David
full_name: Baddeley, David
last_name: Baddeley
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas J.
full_name: Melia, Thomas J.
last_name: Melia
- first_name: Bart W.
full_name: Hoogenboom, Bart W.
last_name: Hoogenboom
- first_name: Chenxiang
full_name: Lin, Chenxiang
last_name: Lin
- first_name: C. Patrick
full_name: Lusk, C. Patrick
last_name: Lusk
citation:
ama: Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for
organizing intrinsically disordered nucleoporins within nanopore confinement.
ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044
apa: Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley,
D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically
disordered nucleoporins within nanopore confinement. ACS Nano. American
Chemical Society. https://doi.org/10.1021/acsnano.7b08044
chicago: Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny
Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami
Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore
Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044.
ieee: P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing
intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano,
vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.
ista: Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia
TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for
organizing intrinsically disordered nucleoporins within nanopore confinement.
ACS Nano. 12(2), 1508–1518.
mla: Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing
Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano,
vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044.
short: P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley,
A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.
date_created: 2021-11-26T15:15:00Z
date_published: 2018-01-19T00:00:00Z
date_updated: 2021-11-26T15:57:02Z
day: '19'
doi: 10.1021/acsnano.7b08044
extern: '1'
external_id:
pmid:
- '29350911'
intvolume: ' 12'
issue: '2'
keyword:
- general physics and astronomy
language:
- iso: eng
month: '01'
oa_version: None
page: 1508-1518
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Programmable DNA origami platform for organizing intrinsically disordered
nucleoporins within nanopore confinement
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2018'
...
---
_id: '10360'
abstract:
- lang: eng
text: Mapping free-energy landscapes has proved to be a powerful tool for studying
reaction mechanisms. Many complex biomolecular assembly processes, however, have
remained challenging to access using this approach, including the aggregation
of peptides and proteins into amyloid fibrils implicated in a range of disorders.
Here, we generalize the strategy used to probe free-energy landscapes in protein
folding to determine the activation energies and entropies that characterize each
of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which
is associated with Alzheimer’s disease. Our results reveal that interactions between
monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation
fundamentally reverse the thermodynamic signature of this process relative to
primary nucleation, even though both processes generate aggregates from soluble
peptides. By mapping the energetic and entropic contributions along the reaction
trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results
from the enthalpic stabilization of adsorbing peptides in conformations amenable
to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.
acknowledgement: We thank B. Jönsson and I. André for helpful discussions. We acknowledge
financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge
(S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of
Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus
Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden
(S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg
Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science
Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust
(A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the
Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases
(C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).
article_processing_charge: No
article_type: original
author:
- first_name: Samuel I. A.
full_name: Cohen, Samuel I. A.
last_name: Cohen
- first_name: Risto
full_name: Cukalevski, Risto
last_name: Cukalevski
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Mattias
full_name: Törnquist, Mattias
last_name: Törnquist
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
citation:
ama: Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures
of oligomer generation in the aggregation of the amyloid-β peptide. Nature
Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x
apa: Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist,
M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of
oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry.
Springer Nature. https://doi.org/10.1038/s41557-018-0023-x
chicago: Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić,
Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell,
Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer
Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry.
Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x.
ieee: S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer
generation in the aggregation of the amyloid-β peptide,” Nature Chemistry,
vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.
ista: Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M,
Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures
of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry.
10(5), 523–531.
mla: Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer
Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry,
vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x.
short: S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M.
Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry
10 (2018) 523–531.
date_created: 2021-11-26T12:41:38Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2021-11-26T15:14:00Z
day: '26'
doi: 10.1038/s41557-018-0023-x
extern: '1'
external_id:
pmid:
- '29581486'
intvolume: ' 10'
issue: '5'
keyword:
- general chemical engineering
- general chemistry
language:
- iso: eng
month: '03'
oa_version: None
page: 523-531
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct thermodynamic signatures of oligomer generation in the aggregation
of the amyloid-β peptide
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10
year: '2018'
...
---
_id: '10357'
abstract:
- lang: eng
text: The misfolding and aggregation of proteins into linear fibrils is widespread
in human biology, for example, in connection with amyloid formation and the pathology
of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The
oligomeric species that are formed in the early stages of protein aggregation
are of great interest, having been linked with the cellular toxicity associated
with these conditions. However, these species are not characterized in any detail
experimentally, and their properties are not well understood. Many of these species
have been found to have approximately spherical morphology and to be held together
by hydrophobic interactions. We present here an analytical statistical mechanical
model of globular oligomer formation from simple idealized amphiphilic protein
monomers and show that this correlates well with Monte Carlo simulations of oligomer
formation. We identify the controlling parameters of the model, which are closely
related to simple quantities that may be fitted directly from experiment. We predict
that globular oligomers are unlikely to form at equilibrium in many polypeptide
systems but instead form transiently in the early stages of amyloid formation.
We contrast the globular model of oligomer formation to a well-established model
of linear oligomer formation, highlighting how the differing ensemble properties
of linear and globular oligomers offer a potential strategy for characterizing
oligomers from experimental measurements.
acknowledgement: We acknowledge support from the Schiff Foundation (A.J.D.), the Royal
Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse,
Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome
Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC
(T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research
leading to these results has received funding from the European Research Council
under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through
the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several
useful discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J.
full_name: Dear, Alexander J.
last_name: Dear
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics
of globular oligomer formation by protein molecules. The Journal of Physical
Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805
apa: Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T.
P. J. (2018). Statistical mechanics of globular oligomer formation by protein
molecules. The Journal of Physical Chemistry B. American Chemical Society.
https://doi.org/10.1021/acs.jpcb.8b07805
chicago: Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M.
Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer
Formation by Protein Molecules.” The Journal of Physical Chemistry B. American
Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805.
ieee: A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles,
“Statistical mechanics of globular oligomer formation by protein molecules,” The
Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society,
pp. 11721–11730, 2018.
ista: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical
mechanics of globular oligomer formation by protein molecules. The Journal of
Physical Chemistry B. 122(49), 11721–11730.
mla: Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation
by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no.
49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805.
short: A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal
of Physical Chemistry B 122 (2018) 11721–11730.
date_created: 2021-11-26T11:55:12Z
date_published: 2018-10-18T00:00:00Z
date_updated: 2021-11-26T12:40:02Z
day: '18'
doi: 10.1021/acs.jpcb.8b07805
extern: '1'
external_id:
pmid:
- '30336667'
intvolume: ' 122'
issue: '49'
keyword:
- materials chemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 11721-11730
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical mechanics of globular oligomer formation by protein molecules
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 122
year: '2018'
...
---
_id: '10359'
abstract:
- lang: eng
text: Biological membranes typically contain a large number of different components
dispersed in small concentrations in the main membrane phase, including proteins,
sugars, and lipids of varying geometrical properties. Most of these components
do not bind the cargo. Here, we show that such “inert” components can be crucial
for the precise control of cross-membrane trafficking. Using a statistical mechanics
model and molecular dynamics simulations, we demonstrate that the presence of
inert membrane components of small isotropic curvatures dramatically influences
cargo endocytosis, even if the total spontaneous curvature of such a membrane
remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically
included proteins and tethered sugars can, therefore, actively participate in
the control of the membrane trafficking of nanoscopic cargo. We find that even
a low-level expression of curved inert membrane components can determine the membrane
selectivity toward the cargo size and can be used to selectively target membranes
of certain compositions. Our results suggest a robust and general method of controlling
cargo trafficking by adjusting the membrane composition without needing to alter
the concentration of receptors or the average membrane curvature. This study indicates
that cells can prepare for any trafficking event by incorporating curved inert
components in either of the membrane leaflets.
acknowledgement: We acknowledge discussions with Giuseppe Battaglia as well as support
from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL
Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy
of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme
under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and
D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the
Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.).
We thank Claudia Flandoli for help with Figure 1.
article_processing_charge: No
article_type: original
author:
- first_name: Tine
full_name: Curk, Tine
last_name: Curk
- first_name: Peter
full_name: Wirnsberger, Peter
last_name: Wirnsberger
- first_name: Jure
full_name: Dobnikar, Jure
last_name: Dobnikar
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking
in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786
apa: Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018).
Controlling cargo trafficking in multicomponent membranes. Nano Letters.
American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786
chicago: Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela
Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters.
American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786.
ieee: T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling
cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18,
no. 9. American Chemical Society, pp. 5350–5356, 2018.
ista: Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo
trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.
mla: Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.”
Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56,
doi:10.1021/acs.nanolett.8b00786.
short: T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters
18 (2018) 5350–5356.
date_created: 2021-11-26T12:15:47Z
date_published: 2018-04-18T00:00:00Z
date_updated: 2021-11-26T15:14:08Z
day: '18'
doi: 10.1021/acs.nanolett.8b00786
extern: '1'
external_id:
pmid:
- '29667410'
intvolume: ' 18'
issue: '9'
keyword:
- mechanical engineering
- condensed matter physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.10147
month: '04'
oa: 1
oa_version: Preprint
page: 5350-5356
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Controlling cargo trafficking in multicomponent membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 18
year: '2018'
...
---
_id: '10358'
abstract:
- lang: eng
text: Probing reaction mechanisms of supramolecular processes in soft and biological
matter, such as protein aggregation, is inherently challenging. This is because
these processes involve multiple molecular mechanisms that are associated with
the rearrangement of large numbers of weak bonds, resulting in complex free energy
landscapes with many kinetic barriers. Reaction rate measurements at different
temperatures can offer unprecedented insights into the underlying molecular mechanisms.
However, to be able to interpret such measurements, a key challenge is to establish
which properties of the complex free energy landscapes are probed by the reaction
rate. Here, we present a reaction rate theory for supramolecular kinetics based
on Kramers theory of diffusive reactions over multiple kinetic barriers. We find
that reaction rates for protein aggregation are of the Arrhenius–Eyring type and
that the associated activation energies probe only one relevant barrier along
the respective free energy landscapes. We apply this advancement to interpret,
in experiments and in coarse-grained computer simulations, reaction rates of amyloid
aggregation in terms of molecular mechanisms and associated thermodynamic signatures.
These results suggest a practical extension of the concept of rate-determining
steps for complex supramolecular processes and establish a general platform for
probing the underlying energy landscape using kinetic measurements.
acknowledgement: We thank Claudia Flandoli for the help with illustrations.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Lucie X.
full_name: Liu, Lucie X.
last_name: Liu
- first_name: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Peter G.
full_name: Bolhuis, Peter G.
last_name: Bolhuis
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: 'Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate
theory for supramolecular kinetics: application to protein aggregation. Molecular
Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280'
apa: 'Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., &
Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application
to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280'
chicago: 'Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela
Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics:
Application to Protein Aggregation.” Molecular Physics. Taylor & Francis,
2018. https://doi.org/10.1080/00268976.2018.1474280.'
ieee: 'T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P.
J. Knowles, “Reaction rate theory for supramolecular kinetics: application to
protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor &
Francis, pp. 3055–3065, 2018.'
ista: 'Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction
rate theory for supramolecular kinetics: application to protein aggregation. Molecular
Physics. 116(21–22), 3055–3065.'
mla: 'Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics:
Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22,
Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.'
short: T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles,
Molecular Physics 116 (2018) 3055–3065.
date_created: 2021-11-26T12:08:02Z
date_published: 2018-05-24T00:00:00Z
date_updated: 2021-11-26T12:39:58Z
day: '24'
doi: 10.1080/00268976.2018.1474280
extern: '1'
external_id:
arxiv:
- '1803.04851'
intvolume: ' 116'
issue: 21-22
keyword:
- physical chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.04851
month: '05'
oa: 1
oa_version: Preprint
page: 3055-3065
publication: Molecular Physics
publication_identifier:
eissn:
- 1362-3028
issn:
- 0026-8976
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Reaction rate theory for supramolecular kinetics: application to protein aggregation'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2018'
...
---
_id: '10361'
abstract:
- lang: eng
text: Understanding how normally soluble peptides and proteins aggregate to form
amyloid fibrils is central to many areas of modern biomolecular science, ranging
from the development of functional biomaterials to the design of rational therapeutic
strategies against increasingly prevalent medical conditions such as Alzheimer's
and Parkinson's diseases. As such, there is a great need to develop models to
mechanistically describe how amyloid fibrils are formed from precursor peptides
and proteins. Here we review and discuss how ideas and concepts from chemical
reaction kinetics can help to achieve this objective. In particular, we show how
a combination of theory, experiments, and computer simulations, based on chemical
kinetics, provides a general formalism for uncovering, at the molecular level,
the mechanistic steps that underlie the phenomenon of amyloid fibril formation.
acknowledgement: "We acknowledge support from the Swiss National Science Foundation
(T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy
of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.);
the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology
and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances
and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results
has received funding from the European Research Council (ERC) under the\r\nEuropean
Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt
(337969)."
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Johnny
full_name: Habchi, Johnny
last_name: Habchi
- first_name: Sean
full_name: Chia, Sean
last_name: Chia
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular
mechanisms and macroscopic measurements of amyloid fibril formation. Annual
Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322
apa: Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo,
M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms
and macroscopic measurements of amyloid fibril formation. Annual Review of
Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322
chicago: Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl,
Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical
Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid
Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews,
2018. https://doi.org/10.1146/annurev-physchem-050317-021322.
ieee: T. C. T. Michaels et al., “Chemical kinetics for bridging molecular
mechanisms and macroscopic measurements of amyloid fibril formation,” Annual
Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298,
2018.
ista: Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM,
Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic
measurements of amyloid fibril formation. Annual Review of Physical Chemistry.
69(1), 273–298.
mla: Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms
and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of
Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.
short: T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo,
C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.
date_created: 2021-11-26T12:52:12Z
date_published: 2018-02-28T00:00:00Z
date_updated: 2021-11-26T15:58:19Z
day: '28'
doi: 10.1146/annurev-physchem-050317-021322
extern: '1'
external_id:
pmid:
- '29490200'
intvolume: ' 69'
issue: '1'
keyword:
- physical and theoretical chemistry
language:
- iso: eng
month: '02'
oa_version: None
page: 273-298
pmid: 1
publication: Annual Review of Physical Chemistry
publication_identifier:
eissn:
- 1545-1593
issn:
- 0066-426X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chemical kinetics for bridging molecular mechanisms and macroscopic measurements
of amyloid fibril formation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 69
year: '2018'
...
---
_id: '10626'
abstract:
- lang: eng
text: "Owing to their wide tunability, multiple internal degrees of freedom, and
low disorder, graphene heterostructures are emerging as a promising experimental
platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal
activation gap measurements in dual graphite-gated monolayer graphene devices
fabricated in an edgeless Corbino geometry. In devices with substrate-induced
sublattice splitting, we find a tunable crossover between single- and multicomponent
FQH states in the zero energy Landau level. Activation gaps in the single-component
regime show excellent agreement with numerical calculations using a single broadening
parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps
are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered
state at integer filling ν=−4."
acknowledgement: We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for
discussing their unpublished data and for sharing the stack inversion technique.
The authors acknowledge further discussions of the results with I. Sodemann, M.
Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported
by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work
was performed at the National High Magnetic Field Laboratory, which is supported
by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State
of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative
conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges
the support of the Elings Prize Fellowship in Science of the California Nanosystems
Institute at the University of California, Santa Barbara. A. F. Y. acknowledges
the support of the David and Lucile Packard Foundation.
article_number: '226801'
article_processing_charge: No
article_type: original
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: H.
full_name: Zhou, H.
last_name: Zhou
- first_name: E. M.
full_name: Spanton, E. M.
last_name: Spanton
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: A. F.
full_name: Young, A. F.
last_name: Young
citation:
ama: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative
transport measurements of fractional quantum Hall energy gaps in edgeless graphene
devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801
apa: Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young,
A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy
gaps in edgeless graphene devices. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/physrevlett.121.226801
chicago: Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and
A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy
Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical
Society, 2018. https://doi.org/10.1103/physrevlett.121.226801.
ieee: H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young,
“Quantitative transport measurements of fractional quantum Hall energy gaps in
edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22.
American Physical Society, 2018.
ista: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative
transport measurements of fractional quantum Hall energy gaps in edgeless graphene
devices. Physical Review Letters. 121(22), 226801.
mla: Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional
Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters,
vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801.
short: H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young,
Physical Review Letters 121 (2018).
date_created: 2022-01-14T12:15:47Z
date_published: 2018-11-28T00:00:00Z
date_updated: 2022-01-14T13:48:35Z
day: '28'
doi: 10.1103/physrevlett.121.226801
extern: '1'
external_id:
arxiv:
- '1805.04199'
intvolume: ' 121'
issue: '22'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1805.04199
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative transport measurements of fractional quantum Hall energy gaps
in edgeless graphene devices
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 121
year: '2018'
...
---
_id: '10627'
abstract:
- lang: eng
text: We present a scanning probe technique for measuring the dynamics of individual
fluxoid transitions in multiply connected superconducting structures. In these
measurements, a small magnetic particle attached to the tip of a silicon cantilever
is scanned over a micron-size superconducting ring fabricated from a thin aluminum
film. We find that near the superconducting transition temperature of the aluminum,
the dissipation and frequency of the cantilever changes significantly at particular
locations where the tip-induced magnetic flux penetrating the ring causes the
two lowest-energy fluxoid states to become nearly degenerate. In this regime,
we show that changes in the cantilever frequency and dissipation are well-described
by a stochastic resonance (SR) process, wherein small oscillations of the cantilever
in the presence of thermally activated phase slips (TAPS) in the ring give rise
to a dynamical force that modifies the mechanical properties of the cantilever.
Using the SR model, we calculate the average fluctuation rate of the TAPS as a
function of temperature over a 32-dB range in frequency, and we compare it to
the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting
structures.
acknowledgement: "We are grateful to Nadya Mason for useful discussions. This work
was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649,
the Department of Physics and the Frederick Seitz Materials Research Laboratory
Central Facilities at the University of Illinois.\r\n"
article_number: '184501'
article_processing_charge: No
article_type: original
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Tyler R.
full_name: Naibert, Tyler R.
last_name: Naibert
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size
superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501
apa: Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip
dynamics in micron-size superconducting rings. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.97.184501
chicago: Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase
Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B.
American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.
ieee: H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in
micron-size superconducting rings,” Physical Review B, vol. 97, no. 18.
American Physical Society, 2018.
ista: Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size
superconducting rings. Physical Review B. 97(18), 184501.
mla: Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting
Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society,
2018, doi:10.1103/physrevb.97.184501.
short: H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).
date_created: 2022-01-14T13:48:47Z
date_published: 2018-05-08T00:00:00Z
date_updated: 2022-01-14T13:58:24Z
day: '08'
doi: 10.1103/physrevb.97.184501
extern: '1'
external_id:
arxiv:
- '1703.08184'
intvolume: ' 97'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.08184
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imaging phase slip dynamics in micron-size superconducting rings
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 97
year: '2018'
...
---
_id: '10883'
abstract:
- lang: eng
text: 'Solving parity games, which are equivalent to modal μ-calculus model checking,
is a central algorithmic problem in formal methods, with applications in reactive
synthesis, program repair, verification of branching-time properties, etc. Besides
the standard compu- tation model with the explicit representation of games, another
important theoretical model of computation is that of set-based symbolic algorithms.
Set-based symbolic algorithms use basic set operations and one-step predecessor
operations on the implicit description of games, rather than the explicit representation.
The significance of symbolic algorithms is that they provide scalable algorithms
for large finite-state systems, as well as for infinite-state systems with finite
quotient. Consider parity games on graphs with n vertices and parity conditions
with d priorities. While there is a rich literature of explicit algorithms for
parity games, the main results for set-based symbolic algorithms are as follows:
(a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic
space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations
and O(n) symbolic space. In this work, our contributions are as follows: (1) We
present a black-box set-based symbolic algorithm based on the explicit progress
measure algorithm. Two important consequences of our algorithm are as follows:
(a) a set-based symbolic algorithm for parity games that requires quasi-polynomially
many symbolic operations and O(n) symbolic space; and (b) any future improvement
in progress measure based explicit algorithms immediately imply an efficiency
improvement in our set-based symbolic algorithm for parity games. (2) We present
a set-based symbolic algorithm that requires quasi-polynomially many symbolic
operations and O(d · log n) symbolic space. Moreover, for the important special
case of d ≤ log n, our algorithm requires only polynomially many symbolic operations
and poly-logarithmic symbolic space.'
acknowledgement: 'A. S. is fully supported by the Vienna Science and Technology Fund
(WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund
(FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph
Games). For M.H the research leading to these results has received funding from
the European Research Council under the European Union’s Seventh Framework Programme
(FP/2007-2013) /ERC Grant Agreement no. 340506.'
alternative_title:
- EPiC Series in Computing
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based
symbolic algorithms for parity games. In: 22nd International Conference on
Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair;
2018:233-253. doi:10.29007/5z5k'
apa: 'Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial
set-based symbolic algorithms for parity games. In 22nd International Conference
on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57,
pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k'
chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander
Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd
International Conference on Logic for Programming, Artificial Intelligence and
Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.
ieee: K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial
set-based symbolic algorithms for parity games,” in 22nd International Conference
on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia,
2018, vol. 57, pp. 233–253.
ista: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based
symbolic algorithms for parity games. 22nd International Conference on Logic for
Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic
for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing,
vol. 57, 233–253.'
mla: Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms
for Parity Games.” 22nd International Conference on Logic for Programming,
Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53,
doi:10.29007/5z5k.
short: K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International
Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair,
2018, pp. 233–253.
conference:
end_date: 2018-11-21
location: Awassa, Ethiopia
name: 'LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning'
start_date: 2018-11-17
date_created: 2022-03-18T12:46:32Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2022-07-29T09:24:31Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29007/5z5k
ec_funded: 1
external_id:
arxiv:
- '1909.04983'
file:
- access_level: open_access
checksum: 1229aa8640bd6db610c85decf2265480
content_type: application/pdf
creator: dernst
date_created: 2022-05-17T07:51:08Z
date_updated: 2022-05-17T07:51:08Z
file_id: '11392'
file_name: 2018_EPiCs_Chatterjee.pdf
file_size: 720893
relation: main_file
success: 1
file_date_updated: 2022-05-17T07:51:08Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 233-253
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: 22nd International Conference on Logic for Programming, Artificial Intelligence
and Reasoning
publication_identifier:
issn:
- 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quasipolynomial set-based symbolic algorithms for parity games
type: conference
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 57
year: '2018'
...
---
_id: '1092'
abstract:
- lang: eng
text: 'A graphical model encodes conditional independence relations via the Markov
properties. For an undirected graph these conditional independence relations can
be represented by a simple polytope known as the graph associahedron, which can
be constructed as a Minkowski sum of standard simplices. We show that there is
an analogous polytope for conditional independence relations coming from a regular
Gaussian model, and it can be defined using multiinformation or relative entropy.
For directed acyclic graphical models we give a construction of this polytope
as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight
to construct a new ordering-based search algorithm for causal inference via directed
acyclic graphical models. '
author:
- first_name: Fatemeh
full_name: Mohammadi, Fatemeh
id: 2C29581E-F248-11E8-B48F-1D18A9856A87
last_name: Mohammadi
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Charles
full_name: Wang, Charles
last_name: Wang
- first_name: Josephine
full_name: Yu, Josephine
last_name: Yu
citation:
ama: Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic
graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93.
doi:10.1137/16M107894X
apa: Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra
from probabilistic graphical models. SIAM Journal on Discrete Mathematics.
SIAM. https://doi.org/10.1137/16M107894X
chicago: Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized
Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete
Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X.
ieee: F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from
probabilistic graphical models,” SIAM Journal on Discrete Mathematics,
vol. 32, no. 1. SIAM, pp. 64–93, 2018.
ista: Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic
graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93.
mla: Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical
Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018,
pp. 64–93, doi:10.1137/16M107894X.
short: F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics
32 (2018) 64–93.
date_created: 2018-12-11T11:50:06Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T06:48:13Z
day: '01'
doi: 10.1137/16M107894X
extern: '1'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.01814
month: '01'
oa: 1
oa_version: Preprint
page: 64-93
publication: SIAM Journal on Discrete Mathematics
publication_status: published
publisher: SIAM
publist_id: '6284'
quality_controlled: '1'
status: public
title: Generalized permutohedra from probabilistic graphical models
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2018'
...
---
_id: '11'
abstract:
- lang: eng
text: We report on a novel strategy to derive mean-field limits of quantum mechanical
systems in which a large number of particles weakly couple to a second-quantized
radiation field. The technique combines the method of counting and the coherent
state approach to study the growth of the correlations among the particles and
in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon
system of equations from the Nelson model with ultraviolet cutoff and possibly
massless scalar field. In particular, we prove the convergence of the reduced
density matrices (of the nonrelativistic particles and the field bosons) associated
with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon
equations in trace norm. Furthermore, we derive explicit bounds on the rate of
convergence of the one-particle reduced density matrix of the nonrelativistic
particles in Sobolev norm.
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: 'Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised
radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9'
apa: 'Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in
interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented
at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer.
https://doi.org/10.1007/978-3-030-01602-9_9'
chicago: Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.
ieee: 'N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction
with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits
of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.'
ista: 'Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction
with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems
vol. 270, 185–214.'
mla: Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp.
185–214, doi:10.1007/978-3-030-01602-9_9.
short: N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.
conference:
end_date: 2017-04-01
location: Munich, Germany
name: 'MaLiQS: Macroscopic Limits of Quantum Systems'
start_date: 2017-03-30
date_created: 2018-12-11T11:44:08Z
date_published: 2018-10-27T00:00:00Z
date_updated: 2021-01-12T06:48:16Z
day: '27'
department:
- _id: RoSe
doi: 10.1007/978-3-030-01602-9_9
ec_funded: 1
external_id:
arxiv:
- '1806.10843'
intvolume: ' 270'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.10843
month: '10'
oa: 1
oa_version: Preprint
page: 185 - 214
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_status: published
publisher: Springer
publist_id: '8045'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mean-field limits of particles in interaction with quantised radiation fields
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 270
year: '2018'
...
---
_id: '11063'
abstract:
- lang: eng
text: The total number of nuclear pore complexes (NPCs) per nucleus varies greatly
between different cell types and is known to change during cell differentiation
and cell transformation. However, the underlying mechanisms that control how many
nuclear transport channels are assembled into a given nuclear envelope remain
unclear. Here, we report that depletion of the NPC basket protein Tpr, but not
Nup153, dramatically increases the total NPC number in various cell types. This
negative regulation of Tpr occurs via a phosphorylation cascade of extracellular
signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein
kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin
(Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results
reveal a critical role of the Nup Tpr in coordinating signal transduction pathways
during cell proliferation and the dynamic organization of the nucleus.
article_processing_charge: No
article_type: original
author:
- first_name: Asako
full_name: McCloskey, Asako
last_name: McCloskey
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear
pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331.
doi:10.1101/gad.315523.118
apa: McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total
number of nuclear pore complexes per cell nucleus. Genes & Development.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118
chicago: McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the
Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development.
Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118.
ieee: A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of
nuclear pore complexes per cell nucleus,” Genes & Development, vol.
32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.
ista: McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear
pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331.
mla: McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes
per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring
Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.
short: A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.
date_created: 2022-04-07T07:45:30Z
date_published: 2018-09-18T00:00:00Z
date_updated: 2022-07-18T08:32:32Z
day: '18'
doi: 10.1101/gad.315523.118
extern: '1'
external_id:
pmid:
- '30228202'
intvolume: ' 32'
issue: 19-20
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.315523.118
month: '09'
oa: 1
oa_version: Published Version
page: 1321-1331
pmid: 1
publication: Genes & Development
publication_identifier:
issn:
- 0890-9369
- 1549-5477
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tpr regulates the total number of nuclear pore complexes per cell nucleus
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 32
year: '2018'
...
---
_id: '11064'
abstract:
- lang: eng
text: Biomarkers of aging can be used to assess the health of individuals and to
study aging and age-related diseases. We generate a large dataset of genome-wide
RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years
old to test whether signatures of aging are encoded within the transcriptome.
We develop an ensemble machine learning method that predicts age to a median error
of 4 years, outperforming previous methods used to predict age. The ensemble was
further validated by testing it on ten progeria patients, and our method is the
only one that predicts accelerated aging in these patients.
article_number: '221'
article_processing_charge: No
article_type: original
author:
- first_name: Jason G.
full_name: Fleischer, Jason G.
last_name: Fleischer
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Hsiao H.
full_name: Tsai, Hsiao H.
last_name: Tsai
- first_name: Swati
full_name: Tyagi, Swati
last_name: Tyagi
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- first_name: Maxim N.
full_name: Shokhirev, Maxim N.
last_name: Shokhirev
- first_name: Ling
full_name: Huang, Ling
last_name: Huang
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Saket
full_name: Navlakha, Saket
last_name: Navlakha
citation:
ama: Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome
of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6
apa: Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev,
M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal
fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6
chicago: Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz
Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting
Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology.
BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6.
ieee: J. G. Fleischer et al., “Predicting age from the transcriptome of human
dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018.
ista: Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L,
Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal
fibroblasts. Genome Biology. 19, 221.
mla: Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human
Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018,
doi:10.1186/s13059-018-1599-6.
short: J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev,
L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).
date_created: 2022-04-07T07:45:40Z
date_published: 2018-12-20T00:00:00Z
date_updated: 2022-07-18T08:32:34Z
day: '20'
doi: 10.1186/s13059-018-1599-6
extern: '1'
external_id:
pmid:
- '30567591'
intvolume: ' 19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s13059-018-1599-6
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1474-760X
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting age from the transcriptome of human dermal fibroblasts
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 19
year: '2018'
...
---
_id: '11508'
abstract:
- lang: eng
text: Distant luminous Lyman-α emitters (LAEs) are excellent targets for spectroscopic
observations of galaxies in the epoch of reionisation (EoR). We present deep high-resolution
(R = 5000) VLT/X-shooter observations, along with an extensive collection of photometric
data of COLA1, a proposed double peaked LAE at z = 6.6. We rule out the possibility
that COLA1’s emission line is an [OII] doublet at z = 1.475 on the basis of i)
the asymmetric red line-profile and flux ratio of the peaks (blue/red=0.31 ± 0.03)
and ii) an unphysical [OII]/Hα ratio ([OII]/Hα > 22). We show that COLA1’s observed
B-band flux is explained by a faint extended foreground LAE, for which we detect
Lyα and [OIII] at z = 2.142. We thus conclude that COLA1 is a real double-peaked
LAE at z = 6.593, the first discovered at z > 6. COLA1 is UV luminous (M1500 = −21.6 ± 0.3),
has a high equivalent width (EW0,Lyα = 120−40+50 Å) and very compact Lyα emission
(r50,Lyα = 0.33−0.04+0.07 kpc). Relatively weak inferred Hβ+[OIII] line-emission
from Spitzer/IRAC indicates an extremely low metallicity of Z < 1/20 Z⊙ or reduced
strength of nebular lines due to high escape of ionising photons. The small Lyα
peak separation of 220 ± 20 km s−1 implies a low HI column density and an ionising
photon escape fraction of ≈15 − 30%, providing the first direct evidence that
such galaxies contribute actively to the reionisation of the Universe at z > 6.
Based on simple estimates, we find that COLA1 could have provided just enough
photons to reionise its own ≈0.3 pMpc (2.3 cMpc) bubble, allowing the blue Lyα
line to be observed. However, we also discuss alternative scenarios explaining
the detected double peaked nature of COLA1. Our results show that future high-resolution
observations of statistical samples of double peaked LAEs at z > 5 are a promising
probe of the occurrence of ionised regions around galaxies in the EoR.
acknowledgement: JM acknowledges the award of a Huygens PhD fellowship from Leiden
University. MG acknowledges support from NASA grant NNX17AK58G. APA, PhD::SPACE
fellow, acknowledges support from the FCT through the fellowship PD/BD/52706/2014.
Based on observations made with ESO Telescopes at the La Silla Paranal Observatory
under programme IDs 294.A-5018, 098.A-0819, 099.A-0254 and 0100.A-0213. We are grateful
for the excellent data-sets from the COSMOS and UltraVISTA survey teams. This research
was supported by the Munich Institute for Astro- and Particle Physics (MIAPP) of
the DFG cluster of excellence “Origin and Structure of the Universe”. We thank the
referee for their comments that improved the paper. We also thank Christoph Behrens,
Len Cowie, Koki Kakiichi, Peter Laursen, Charlotte Mason, Eros Vanzella, Lewis Weinberger
and Johannes Zabl for discussions. We have benefited from the public available programming
language Python, including the numpy, matplotlib, scipy and astropy packages (Hunter
2007; Astropy Collaboration 2013), the astronomical imaging tools Swarp (Bertin
2010) and ds9 and the Topcat analysis tool (Taylor 2013).
article_number: A136
article_processing_charge: No
article_type: original
author:
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: Max
full_name: Gronke, Max
last_name: Gronke
- first_name: Ana
full_name: Paulino-Afonso, Ana
last_name: Paulino-Afonso
- first_name: Mauro
full_name: Stefanon, Mauro
last_name: Stefanon
- first_name: Huub
full_name: Röttgering, Huub
last_name: Röttgering
citation:
ama: 'Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H.
Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly
contributing to the reionisation of the universe. Astronomy & Astrophysics.
2018;619. doi:10.1051/0004-6361/201833528'
apa: 'Matthee, J. J., Sobral, D., Gronke, M., Paulino-Afonso, A., Stefanon, M.,
& Röttgering, H. (2018). Confirmation of double peaked Lyα emission at z =
6.593: Witnessing a galaxy directly contributing to the reionisation of the universe.
Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833528'
chicago: 'Matthee, Jorryt J, David Sobral, Max Gronke, Ana Paulino-Afonso, Mauro
Stefanon, and Huub Röttgering. “Confirmation of Double Peaked Lyα Emission at
z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the
Universe.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833528.'
ieee: 'J. J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, and
H. Röttgering, “Confirmation of double peaked Lyα emission at z = 6.593: Witnessing
a galaxy directly contributing to the reionisation of the universe,” Astronomy
& Astrophysics, vol. 619. EDP Sciences, 2018.'
ista: 'Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering
H. 2018. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a
galaxy directly contributing to the reionisation of the universe. Astronomy &
Astrophysics. 619, A136.'
mla: 'Matthee, Jorryt J., et al. “Confirmation of Double Peaked Lyα Emission at
z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the
Universe.” Astronomy & Astrophysics, vol. 619, A136, EDP Sciences,
2018, doi:10.1051/0004-6361/201833528.'
short: J.J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, H. Röttgering,
Astronomy & Astrophysics 619 (2018).
date_created: 2022-07-06T11:14:23Z
date_published: 2018-11-19T00:00:00Z
date_updated: 2022-07-19T09:32:08Z
day: '19'
doi: 10.1051/0004-6361/201833528
extern: '1'
external_id:
arxiv:
- '1805.11621'
intvolume: ' 619'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: high-redshift / galaxies: formation / dark ages / reionization / first
stars / techniques: spectroscopic / intergalactic medium'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1805.11621
month: '11'
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: 'Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy
directly contributing to the reionisation of the universe'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 619
year: '2018'
...
---
_id: '11549'
abstract:
- lang: eng
text: We investigate the clustering properties of ∼7000 H β + [O III] and [O II]
narrowband-selected emitters at z ∼ 0.8–4.7 from the High-z Emission Line Survey.
We find clustering lengths, r0, of 1.5–4.0 h−1 Mpc and minimum dark matter halo
masses of 1010.7–12.1 M⊙ for our z = 0.8–3.2 H β + [O III] emitters and r0 ∼ 2.0–8.3
h−1 Mpc and halo masses of 1011.5–12.6 M⊙ for our z = 1.5–4.7 [O II] emitters.
We find r0 to strongly increase both with increasing line luminosity and redshift.
By taking into account the evolution of the characteristic line luminosity, L⋆(z),
and using our model predictions of halo mass given r0, we find a strong, redshift-independent
increasing trend between L/L⋆(z) and minimum halo mass. The faintest H β + [O III]
emitters are found to reside in 109.5 M⊙ haloes and the brightest emitters in
1013.0 M⊙ haloes. For [O II] emitters, the faintest emitters are found in 1010.5
M⊙ haloes and the brightest emitters in 1012.6 M⊙ haloes. A redshift-independent
stellar mass dependency is also observed where the halo mass increases from 1011
to 1012.5 M⊙ for stellar masses of 108.5 to 1011.5 M⊙, respectively. We investigate
the interdependencies of these trends by repeating our analysis in a Lline−Mstar
grid space for our most populated samples (H β + [O III] z = 0.84 and [O II] z
= 1.47) and find that the line luminosity dependency is stronger than the stellar
mass dependency on halo mass. For L > L⋆ emitters at all epochs, we find a relatively
flat trend with halo masses of 1012.5–13 M⊙, which may be due to quenching mechanisms
in massive haloes that is consistent with a transitional halo mass predicted by
models.
acknowledgement: We thank the anonymous referee for their useful comments and suggestions
that improved this study. AAK thanks Anahita Alavi and Irene Shivaei for useful
discussion in the making of this paper. AAK acknowledges that this work was supported
by NASA Headquarters under the NASA Earth and Space Science Fellowship Program –
Grant NNX16AO92H. DS acknowledges financial support from the Netherlands Organization
for Scientific Research (NWO) through a Veni fellowship and from Lancaster University
through an Early Career Internal Grant A100679. PNB is grateful for support from
STFC via grant STM001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the
ERC Advanced Grant DUSTYGAL (321334), and a Royal Society/Wolfson Merit award. JM
acknowledges the support of a Huygens PhD fellowship from Leiden University. BD
acknowledges financial support from NASA through the Astrophysics Data Analysis
Program (ADAP), grant number NNX12AE20G.
article_processing_charge: No
article_type: original
author:
- first_name: A A
full_name: Khostovan, A A
last_name: Khostovan
- first_name: D
full_name: Sobral, D
last_name: Sobral
- first_name: B
full_name: Mobasher, B
last_name: Mobasher
- first_name: P N
full_name: Best, P N
last_name: Best
- first_name: I
full_name: Smail, I
last_name: Smail
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: B
full_name: Darvish, B
last_name: Darvish
- first_name: H
full_name: Nayyeri, H
last_name: Nayyeri
- first_name: S
full_name: Hemmati, S
last_name: Hemmati
- first_name: J P
full_name: Stott, J P
last_name: Stott
citation:
ama: 'Khostovan AA, Sobral D, Mobasher B, et al. The clustering of H β + [O III]
and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar
mass. Monthly Notices of the Royal Astronomical Society. 2018;478(3):2999-3015.
doi:10.1093/mnras/sty925'
apa: 'Khostovan, A. A., Sobral, D., Mobasher, B., Best, P. N., Smail, I., Matthee,
J. J., … Stott, J. P. (2018). The clustering of H β + [O III] and [O II] emitters
since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices
of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty925'
chicago: 'Khostovan, A A, D Sobral, B Mobasher, P N Best, I Smail, Jorryt J Matthee,
B Darvish, H Nayyeri, S Hemmati, and J P Stott. “The Clustering of H β + [O III]
and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar
Mass.” Monthly Notices of the Royal Astronomical Society. Oxford University
Press, 2018. https://doi.org/10.1093/mnras/sty925.'
ieee: 'A. A. Khostovan et al., “The clustering of H β + [O III] and [O II]
emitters since z ∼ 5: Dependencies with line luminosity and stellar mass,” Monthly
Notices of the Royal Astronomical Society, vol. 478, no. 3. Oxford University
Press, pp. 2999–3015, 2018.'
ista: 'Khostovan AA, Sobral D, Mobasher B, Best PN, Smail I, Matthee JJ, Darvish
B, Nayyeri H, Hemmati S, Stott JP. 2018. The clustering of H β + [O III] and [O II]
emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly
Notices of the Royal Astronomical Society. 478(3), 2999–3015.'
mla: 'Khostovan, A. A., et al. “The Clustering of H β + [O III] and [O II] Emitters
since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices
of the Royal Astronomical Society, vol. 478, no. 3, Oxford University Press,
2018, pp. 2999–3015, doi:10.1093/mnras/sty925.'
short: A.A. Khostovan, D. Sobral, B. Mobasher, P.N. Best, I. Smail, J.J. Matthee,
B. Darvish, H. Nayyeri, S. Hemmati, J.P. Stott, Monthly Notices of the Royal Astronomical
Society 478 (2018) 2999–3015.
date_created: 2022-07-08T11:48:48Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2022-08-19T06:53:39Z
day: '01'
doi: 10.1093/mnras/sty925
extern: '1'
external_id:
arxiv:
- '1705.01101'
intvolume: ' 478'
issue: '3'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution'
- 'galaxies: haloes'
- 'galaxies: high-redshift'
- 'galaxies: star formation'
- 'cosmology: observations'
- large-scale structure of Universe
language:
- iso: eng
main_file_link:
- url: https://arxiv.org/abs/1705.01101
month: '08'
oa_version: Published Version
page: 2999-3015
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies
with line luminosity and stellar mass'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 478
year: '2018'
...
---
_id: '11557'
abstract:
- lang: eng
text: Deep narrow-band surveys have revealed a large population of faint Ly α emitters
(LAEs) in the distant Universe, but relatively little is known about the most
luminous sources (LLyα≳1042.7 erg s−1; LLyα≳L∗Lyα). Here we present the spectroscopic
follow-up of 21 luminous LAEs at z ∼ 2–3 found with panoramic narrow-band surveys
over five independent extragalactic fields (≈4 × 106 Mpc3 surveyed at z ∼ 2.2
and z ∼ 3.1). We use WHT/ISIS, Keck/DEIMOS, and VLT/X-SHOOTER to study these sources
using high ionization UV lines. Luminous LAEs at z ∼ 2–3 have blue UV slopes (β=−2.0+0.3−0.1)
and high Ly α escape fractions (50+20−15 per cent) and span five orders of magnitude
in UV luminosity (MUV ≈ −19 to −24). Many (70 per cent) show at least one high
ionization rest-frame UV line such as C IV, N V, C III], He II or O III], typically
blue-shifted by ≈100–200 km s−1 relative to Ly α. Their Ly α profiles reveal a
wide variety of shapes, including significant blue-shifted components and widths
from 200 to 4000 km s−1. Overall, 60 ± 11 per cent appear to be active galactic
nucleus (AGN) dominated, and at LLyα > 1043.3 erg s−1 and/or MUV < −21.5 virtually
all LAEs are AGNs with high ionization parameters (log U = 0.6 ± 0.5) and with
metallicities of ≈0.5 − 1 Z⊙. Those lacking signatures of AGNs (40 ± 11 per cent)
have lower ionization parameters (logU=−3.0+1.6−0.9 and log ξion = 25.4 ± 0.2)
and are apparently metal-poor sources likely powered by young, dust-poor ‘maximal’
starbursts. Our results show that luminous LAEs at z ∼ 2–3 are a diverse population
and that 2×L∗Lyα and 2×M∗UV mark a sharp transition in the nature of LAEs, from
star formation dominated to AGN dominated.
acknowledgement: 'We thank the anonymous reviewer for their timely and constructive
comments that greatly helped us to improve the manuscript. DS acknowledges financial
support from the Netherlands Organization for Scientific research (NWO) through
a Veni fellowship and from Lancaster University through an Early Career Internal
Grant A100679. JM acknowledges the support of a Huygens PhD fellowship from Leiden
University. BD acknowledges financial support from NASA through the Astrophysics
Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science
Foundation, grant number 1716907. IRS acknowledges support from the ERC Advanced
Grant DUSTYGAL (321334), STFC (ST/P000541/1), and a Royal Society/Wolfson Merit
Award. PNB is grateful for support from STFC via grant ST/M001229/1. We thank Anne
Verhamme, Kimihiko Nakajima, Ryan Trainor, Sangeeta Malhotra, Max Gronke, James
Rhoads, Fang Xia An, Matthew Hayes, Takashi Kojima, Mark Dijkstra, and Anne Jaskot
for many helpful and engaging discussions, particularly during the SnowCLAW Ly α
workshop. We thank Bruno Ribeiro, Stephane Charlot, and Joseph Caruana for comments
on the manuscript. The authors would also like to thank Ingrid Tengs, Meg Singleton,
Ali Khostovan, and Sara Perez for participating in part of the observations. We
also thank Joao Calhau, Leah Morabito, Sergio Santos, and Aayush Saxena for their
assistance with the narrow-band observations which allowed to select some of the
sour ces. Based on observations obtained with the William Herschel Telescope, program:
W16AN004; the Very Large Telescope, programs: 098.A-0819 & 099.A-0254; and the Keck
II telescope, program: C267D. Based on data products from observations made with
ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018,
294.A-5039, 092.A-0786, 093.A-0561, 097.A-0943, 098.A-0819, 099.A-0254 and 179.A-2005.
The authors acknowledge the award of service time (SW2014b20) on the WHT. WHT and
its service programme are operated on the island of La Palma by the Isaac Newton
Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de
Astrofisica de Canarias. The authors would also like to thank all the extremely
helpful observatory staff that have greatly contributed towards our observations,
particularly Fiona Riddick, Lilian Dominguez, Florencia Jimenez, and Ian Skillen.
We have benefited greatly from the publicly available programming language PYTHON,
including the NUMPY & SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al.
2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and
the TOPCAT analysis program (Taylor 2013). This research has made use of the VizieR
catalogue access tool, CDS, Strasbourg, France.'
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Behnam
full_name: Darvish, Behnam
last_name: Darvish
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: Philip N
full_name: Best, Philip N
last_name: Best
- first_name: Lara
full_name: Alegre, Lara
last_name: Alegre
- first_name: Huub
full_name: Röttgering, Huub
last_name: Röttgering
- first_name: Bahram
full_name: Mobasher, Bahram
last_name: Mobasher
- first_name: Ana
full_name: Paulino-Afonso, Ana
last_name: Paulino-Afonso
- first_name: Andra
full_name: Stroe, Andra
last_name: Stroe
- first_name: Iván
full_name: Oteo, Iván
last_name: Oteo
citation:
ama: 'Sobral D, Matthee JJ, Darvish B, et al. The nature of luminous Ly α emitters
at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices
of the Royal Astronomical Society. 2018;477(2):2817-2840. doi:10.1093/mnras/sty782'
apa: 'Sobral, D., Matthee, J. J., Darvish, B., Smail, I., Best, P. N., Alegre, L.,
… Oteo, I. (2018). The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor
starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical
Society. Oxford University Press. https://doi.org/10.1093/mnras/sty782'
chicago: 'Sobral, David, Jorryt J Matthee, Behnam Darvish, Ian Smail, Philip N Best,
Lara Alegre, Huub Röttgering, et al. “The Nature of Luminous Ly α Emitters at
z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices
of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty782.'
ieee: 'D. Sobral et al., “The nature of luminous Ly α emitters at z ∼ 2–3:
Maximal dust-poor starbursts and highly ionizing AGN,” Monthly Notices of the
Royal Astronomical Society, vol. 477, no. 2. Oxford University Press, pp.
2817–2840, 2018.'
ista: 'Sobral D, Matthee JJ, Darvish B, Smail I, Best PN, Alegre L, Röttgering H,
Mobasher B, Paulino-Afonso A, Stroe A, Oteo I. 2018. The nature of luminous Ly
α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly
Notices of the Royal Astronomical Society. 477(2), 2817–2840.'
mla: 'Sobral, David, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal
Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal
Astronomical Society, vol. 477, no. 2, Oxford University Press, 2018, pp.
2817–40, doi:10.1093/mnras/sty782.'
short: D. Sobral, J.J. Matthee, B. Darvish, I. Smail, P.N. Best, L. Alegre, H. Röttgering,
B. Mobasher, A. Paulino-Afonso, A. Stroe, I. Oteo, Monthly Notices of the Royal
Astronomical Society 477 (2018) 2817–2840.
date_created: 2022-07-12T07:18:02Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2022-08-19T07:01:08Z
day: '01'
doi: 10.1093/mnras/sty782
extern: '1'
external_id:
arxiv:
- '1802.10102'
intvolume: ' 477'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: active'
- 'galaxies: evolution'
- 'galaxies: high-redshift'
- 'galaxies: ISM'
- 'galaxies: starburst'
- 'cosmology: observations'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.10102
month: '06'
oa: 1
oa_version: Preprint
page: 2817-2840
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts
and highly ionizing AGN'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 477
year: '2018'
...
---
_id: '11558'
abstract:
- lang: eng
text: We present and explore deep narrow- and medium-band data obtained with the
Subaru and the Isaac Newton Telescopes in the ∼2 deg2 COSMOS field. We use these
data as an extremely wide, low-resolution (R ∼ 20–80) Integral Field Unit survey
to slice through the COSMOS field and obtain a large sample of ∼4000 Ly α emitters
(LAEs) from z ∼ 2 to 6 in 16 redshift slices (SC4K). We present new Ly α luminosity
functions (LFs) covering a comoving volume of ∼108 Mpc3. SC4K extensively complements
ultradeep surveys, jointly covering over 4 dex in Ly α luminosity and revealing
a global (2.5 < z < 6) synergy LF with α=−1.93+0.12−0.12, log10Φ∗Lyα=−3.45+0.22−0.29 Mpc−3,
and log10L∗Lyα=42.93+0.15−0.11 erg s−1. The Schechter component of the Ly α LF
reveals a factor ∼5 rise in L∗Lyα and a ∼7 × decline in Φ∗Lyα from z ∼ 2 to 6.
The data reveal an extra power-law (or Schechter) component above LLy α ≈ 1043.3 erg s−1
at z ∼ 2.2–3.5 and we show that it is partially driven by X-ray and radio active
galactic nucleus (AGN), as their Ly α LF resembles the excess. The power-law component
vanishes and/or is below our detection limits above z > 3.5, likely linked with
the evolution of the AGN population. The Ly α luminosity density rises by a factor
∼2 from z ∼ 2 to 3 but is then found to be roughly constant (1.1+0.2−0.2×1040 erg s−1 Mpc−3)
to z ∼ 6, despite the ∼0.7 dex drop in ultraviolet (UV) luminosity density. The
Ly α/UV luminosity density ratio rises from 4 ± 1 per cent to 30 ± 6 per cent
from z ∼ 2.2 to 6. Our results imply a rise of a factor of ≈2 in the global ionization
efficiency (ξion) and a factor ≈4 ± 1 in the Ly α escape fraction from z ∼ 2 to
6, hinting for evolution in both the typical burstiness/stellar populations and
even more so in the typical interstellar medium conditions allowing Ly α photons
to escape.
acknowledgement: "We thank the anonymous referee for their constructive comments that
helped us improve the manuscript. DS acknowledges the hospitality of the IAC and
a Severo Ochoa visiting grant. SS and JC acknowledge studentships from the Lancaster
University. JM acknowledges a Huygens PhD fellowship from Leiden University. APA
acknowledges financial support from the Science and Technology Foundation (FCT,
Portugal) through research grants UID/FIS/04434/2013 and fellowship PD/BD/52706/2014.
The authors thank Alyssa Drake, Kimihiko Nakajima, Yuichi Harikane, Max Gronke,
Irene Shivaei, Helmut Dannerbauer, Huub Rottgering, ¨ Marius Eide, and Masami Ouchi
for many engaging and stimulating discussions. We also thank Sara Perez, Alex Bennett,
and Tom Rose for their involvement in the early stages of this project. Based on
data products from observations made with European Southern Observatory (ESO) Telescopes
at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 097.A 0943,\r\n098.A-0819,
099.A-0254, and 179.A-2005 and on data products produced by TERAPIX and the Cambridge
Astronomy Survey Unit on behalf of the UltraVISTA consortium. Based on observations
using the WFC on the 2.5 m INT, as part of programmes 2013AN002, 2013BN008, 2014AC88,
2014AN002, 2014BN006, 2014BC118, and 2016AN001. The INT is operated on the island
of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los
Muchachos of the Instituto de Astrofisica de Canarias. This work is based in part
on data products produced at TERAPIX available at the Canadian Astronomy Data Centre
as part of the Canada–France– Hawaii Telescope Legacy Survey (CFHTLS), a collaborative
project of NRC and CNRS.\r\nWe are grateful to the CFHTLS, COSMOS-UltraVISTA, and
COSMOS survey teams. We are also unmeasurably thankful to the pioneering and continuous
work from previous Ly α surveys’ teams. Without these previous Ly α and the wider
reach legacy surveys, this research would have been impossible. We also thank the
VUDS team for making available spectroscopic redshifts from data obtained with VIMOS
at the European Southern Observatory Very Large Telescope, Paranal, Chile, under
Large Programme 185.A-0791. Finally, the authors acknowledge the unique value of
the publicly available programming language PYTHON, including the NUMPY and SCIPY
(Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter
2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program
(Taylor 2005). We publicly release a catalogue with all LAEs used in this paper
(SC4K), so it can be freely explored by the community (see five example entries
in Table A1)."
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: Sérgio
full_name: Santos, Sérgio
last_name: Santos
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Ana
full_name: Paulino-Afonso, Ana
last_name: Paulino-Afonso
- first_name: Bruno
full_name: Ribeiro, Bruno
last_name: Ribeiro
- first_name: João
full_name: Calhau, João
last_name: Calhau
- first_name: Ali A
full_name: Khostovan, Ali A
last_name: Khostovan
citation:
ama: 'Sobral D, Santos S, Matthee JJ, et al. Slicing COSMOS with SC4K: The evolution
of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly
Notices of the Royal Astronomical Society. 2018;476(4):4725-4752. doi:10.1093/mnras/sty378'
apa: 'Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Ribeiro, B., Calhau,
J., & Khostovan, A. A. (2018). Slicing COSMOS with SC4K: The evolution of
typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly
Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty378'
chicago: 'Sobral, David, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Bruno
Ribeiro, João Calhau, and Ali A Khostovan. “Slicing COSMOS with SC4K: The Evolution
of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly
Notices of the Royal Astronomical Society. Oxford University Press, 2018.
https://doi.org/10.1093/mnras/sty378.'
ieee: 'D. Sobral et al., “Slicing COSMOS with SC4K: The evolution of typical
Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6,” Monthly Notices
of the Royal Astronomical Society, vol. 476, no. 4. Oxford University Press,
pp. 4725–4752, 2018.'
ista: 'Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Ribeiro B, Calhau J, Khostovan
AA. 2018. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and
the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical
Society. 476(4), 4725–4752.'
mla: 'Sobral, David, et al. “Slicing COSMOS with SC4K: The Evolution of Typical
Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices
of the Royal Astronomical Society, vol. 476, no. 4, Oxford University Press,
2018, pp. 4725–52, doi:10.1093/mnras/sty378.'
short: D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, B. Ribeiro, J. Calhau,
A.A. Khostovan, Monthly Notices of the Royal Astronomical Society 476 (2018) 4725–4752.
date_created: 2022-07-12T10:41:08Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2022-08-19T07:04:45Z
day: '01'
doi: 10.1093/mnras/sty378
extern: '1'
external_id:
arxiv:
- '1712.04451'
intvolume: ' 476'
issue: '4'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution'
- 'galaxies: formation'
- 'galaxies: high-redshift'
- 'galaxies: luminosity function'
- mass function
- 'galaxies: statistics'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.04451
month: '06'
oa: 1
oa_version: Preprint
page: 4725-4752
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α
escape fraction from z ∼ 2 to 6'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 476
year: '2018'
...
---
_id: '11555'
abstract:
- lang: eng
text: We investigate the morphology of the [C II] emission in a sample of ‘normal’
star-forming galaxies at 5 < z < 7.2 in relation to their UV (rest-frame) counterpart.
We use new Atacama Large Millimetre/submillimetre Array (ALMA) observations of
galaxies at z ∼ 6–7, as well as a careful re-analysis of archival ALMA data. In
total 29 galaxies were analysed, 21 of which are detected in [C II]. For several
of the latter the [C II] emission breaks into multiple components. Only a fraction
of these [C II] components, if any, is associated with the primary UV systems,
while the bulk of the [C II] emission is associated either with fainter UV components,
or not associated with any UV counterpart at the current limits. By taking into
account the presence of all these components, we find that the L[CII]–SFR (star
formation rate) relation at early epochs is fully consistent with the local relation,
but it has a dispersion of 0.48 ± 0.07 dex, which is about two times larger than
observed locally. We also find that the deviation from the local L[CII]–SFR relation
has a weak anticorrelation with the EW(Ly α). The morphological analysis also
reveals that [C II] emission is generally much more extended than the UV emission.
As a consequence, these primordial galaxies are characterized by a [C II] surface
brightness generally much lower than expected from the local Σ[CII]−ΣSFR relation.
These properties are likely a consequence of a combination of different effects,
namely gas metallicity, [C II] emission from obscured star-forming regions, strong
variations of the ionization parameter, and circumgalactic gas in accretion or
ejected by these primeval galaxies.
acknowledgement: "This paper makes use of the following ALMA data:\r\nADS/JAO.ALMA#2012.1.00719.S,
ADS/JAO.ALMA#2012.A.00040.S,\r\nADS/JAO.ALMA#2013.A.00433.S, ADS/JAO.ALMA#2011.0.00115.S,\r\nADS/JAO.ALMA#2012.1.00033.S,
ADS/JAO.ALMA#2012.1.00523.S,\r\nADS/JAO.ALMA#2013.1.00815.S, ADS/JAO.ALMA#2015.1.00834.S.,\r\nADS/JAO.ALMA#2015.1.01105.S,
AND ADS/JAO.ALMA#2016.1.01240.S\r\nwhich can be retrieved from the ALMA data archive:\r\nhttps://almascience.eso.org/
alma-data/archive. ALMA is a partnership of ESO (representing its member states),
NSF (USA) and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan),
in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated
by ESO, AUI/NRAO, and NAOJ. We are grateful to G. Jones to for providing his [C
II] flux maps. RM and SC acknowledge support by the Science and Technology Facilities
Council (STFC). RM acknowledges ERC Advanced Grant 695671 ‘QUENCH’. AF acknowledges
support from the ERC Advanced Grant INTERSTELLAR H2020/740120."
article_processing_charge: No
article_type: original
author:
- first_name: S
full_name: Carniani, S
last_name: Carniani
- first_name: R
full_name: Maiolino, R
last_name: Maiolino
- first_name: R
full_name: Amorin, R
last_name: Amorin
- first_name: L
full_name: Pentericci, L
last_name: Pentericci
- first_name: A
full_name: Pallottini, A
last_name: Pallottini
- first_name: A
full_name: Ferrara, A
last_name: Ferrara
- first_name: C J
full_name: Willott, C J
last_name: Willott
- first_name: R
full_name: Smit, R
last_name: Smit
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: D
full_name: Sobral, D
last_name: Sobral
- first_name: P
full_name: Santini, P
last_name: Santini
- first_name: M
full_name: Castellano, M
last_name: Castellano
- first_name: S
full_name: De Barros, S
last_name: De Barros
- first_name: A
full_name: Fontana, A
last_name: Fontana
- first_name: A
full_name: Grazian, A
last_name: Grazian
- first_name: L
full_name: Guaita, L
last_name: Guaita
citation:
ama: Carniani S, Maiolino R, Amorin R, et al. Kiloparsec-scale gaseous clumps and
star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society.
2018;478(1):1170-1184. doi:10.1093/mnras/sty1088
apa: Carniani, S., Maiolino, R., Amorin, R., Pentericci, L., Pallottini, A., Ferrara,
A., … Guaita, L. (2018). Kiloparsec-scale gaseous clumps and star formation at
z = 5–7. Monthly Notices of the Royal Astronomical Society. Oxford University
Press. https://doi.org/10.1093/mnras/sty1088
chicago: Carniani, S, R Maiolino, R Amorin, L Pentericci, A Pallottini, A Ferrara,
C J Willott, et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.”
Monthly Notices of the Royal Astronomical Society. Oxford University Press,
2018. https://doi.org/10.1093/mnras/sty1088.
ieee: S. Carniani et al., “Kiloparsec-scale gaseous clumps and star formation
at z = 5–7,” Monthly Notices of the Royal Astronomical Society, vol. 478,
no. 1. Oxford University Press, pp. 1170–1184, 2018.
ista: Carniani S, Maiolino R, Amorin R, Pentericci L, Pallottini A, Ferrara A, Willott
CJ, Smit R, Matthee JJ, Sobral D, Santini P, Castellano M, De Barros S, Fontana
A, Grazian A, Guaita L. 2018. Kiloparsec-scale gaseous clumps and star formation
at z = 5–7. Monthly Notices of the Royal Astronomical Society. 478(1), 1170–1184.
mla: Carniani, S., et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at
z = 5–7.” Monthly Notices of the Royal Astronomical Society, vol. 478,
no. 1, Oxford University Press, 2018, pp. 1170–84, doi:10.1093/mnras/sty1088.
short: S. Carniani, R. Maiolino, R. Amorin, L. Pentericci, A. Pallottini, A. Ferrara,
C.J. Willott, R. Smit, J.J. Matthee, D. Sobral, P. Santini, M. Castellano, S.
De Barros, A. Fontana, A. Grazian, L. Guaita, Monthly Notices of the Royal Astronomical
Society 478 (2018) 1170–1184.
date_created: 2022-07-11T08:05:42Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2022-08-19T06:58:06Z
day: '01'
doi: 10.1093/mnras/sty1088
extern: '1'
external_id:
arxiv:
- '1712.03985'
intvolume: ' 478'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution'
- 'galaxies: high-redshift'
- 'galaxies: ISM'
- 'galaxies: formation'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.03985
month: '07'
oa: 1
oa_version: Preprint
page: 1170-1184
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Kiloparsec-scale gaseous clumps and star formation at z = 5–7
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 478
year: '2018'
...
---
_id: '11584'
abstract:
- lang: eng
text: Observations show that star-forming galaxies reside on a tight 3D plane between
mass, gas-phase metallicity, and star formation rate (SFR), which can be explained
by the interplay between metal-poor gas inflows, SFR and outflows. However, different
metals are released on different time-scales, which may affect the slope of this
relation. Here, we use central, star-forming galaxies with Mstar = 109.0–10.5
M⊙ from the EAGLE hydrodynamical simulation to examine 3D relations between mass,
SFR, and chemical enrichment using absolute and relative C, N, O, and Fe abundances.
We show that the scatter is smaller when gas-phase α-enhancement is used rather
than metallicity. A similar plane also exists for stellar α-enhancement, implying
that present-day specific SFRs are correlated with long time-scale star formation
histories. Between z = 0 and 1, the α-enhancement plane is even more insensitive
to redshift than the plane using metallicity. However, it evolves at z > 1 due
to lagging iron yields. At fixed mass, galaxies with higher SFRs have star formation
histories shifted towards late times, are more α-enhanced, and this α-enhancement
increases with redshift as observed. These findings suggest that relations between
physical properties inferred from observations may be affected by systematic variations
in α-enhancements.
acknowledgement: We thank the anonymous referee for their constructive comments. JM
acknowledges the support of a Huygens PhD fellowship from Leiden University. We
thank Jarle Brinchmann, Rob Crain and David Sobral for discussions. We acknowledge
the use of the TOPCAT software (Taylor 2013) for assisting in rapid exploration
of multidimensional data sets and the use of PYTHON and its NUMPY, MATPLOTLIB, and
PANDAS packages.
article_processing_charge: No
article_type: original
author:
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Joop
full_name: Schaye, Joop
last_name: Schaye
citation:
ama: 'Matthee JJ, Schaye J. Star-forming galaxies are predicted to lie on a fundamental
plane of mass, star formation rate, and α-enhancement. Monthly Notices of the
Royal Astronomical Society: Letters. 2018;479(1):L34-L39. doi:10.1093/mnrasl/sly093'
apa: 'Matthee, J. J., & Schaye, J. (2018). Star-forming galaxies are predicted
to lie on a fundamental plane of mass, star formation rate, and α-enhancement.
Monthly Notices of the Royal Astronomical Society: Letters. Oxford University
Press. https://doi.org/10.1093/mnrasl/sly093'
chicago: 'Matthee, Jorryt J, and Joop Schaye. “Star-Forming Galaxies Are Predicted
to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.”
Monthly Notices of the Royal Astronomical Society: Letters. Oxford University
Press, 2018. https://doi.org/10.1093/mnrasl/sly093.'
ieee: 'J. J. Matthee and J. Schaye, “Star-forming galaxies are predicted to lie
on a fundamental plane of mass, star formation rate, and α-enhancement,” Monthly
Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1. Oxford
University Press, pp. L34–L39, 2018.'
ista: 'Matthee JJ, Schaye J. 2018. Star-forming galaxies are predicted to lie on
a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices
of the Royal Astronomical Society: Letters. 479(1), L34–L39.'
mla: 'Matthee, Jorryt J., and Joop Schaye. “Star-Forming Galaxies Are Predicted
to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.”
Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no.
1, Oxford University Press, 2018, pp. L34–39, doi:10.1093/mnrasl/sly093.'
short: 'J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society:
Letters 479 (2018) L34–L39.'
date_created: 2022-07-14T12:49:47Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2022-08-19T08:35:45Z
day: '01'
doi: 10.1093/mnrasl/sly093
extern: '1'
external_id:
arxiv:
- '1802.06786'
intvolume: ' 479'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: abundances'
- 'galaxies: evolution'
- 'galaxies: formation'
- 'galaxies: star formation'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.06786
month: '09'
oa: 1
oa_version: Preprint
page: L34 - L39
publication: 'Monthly Notices of the Royal Astronomical Society: Letters'
publication_identifier:
eissn:
- 1745-3933
issn:
- 1745-3925
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Star-forming galaxies are predicted to lie on a fundamental plane of mass,
star formation rate, and α-enhancement
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 479
year: '2018'
...