---
_id: '10370'
abstract:
- lang: eng
text: Eukaryotic cells are densely packed with macromolecular complexes and intertwining
organelles, continually transported and reshaped. Intriguingly, organelles avoid
clashing and entangling with each other in such limited space. Mitochondria form
extensive networks constantly remodeled by fission and fusion. Here, we show that
mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of
mitochondria – via encounter with motile intracellular pathogens, via external
pressure applied by an atomic force microscope, or via cell migration across uneven
microsurfaces – results in the recruitment of the mitochondrial fission machinery,
and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria,
acts as a membrane-bound force sensor to recruit the fission machinery to mechanically
strained sites. Thus, mitochondria adapt to the environment by sensing and responding
to biomechanical cues. Our findings that mechanical triggers can be coupled to
biochemical responses in membrane dynamics may explain how organelles orderly
cohabit in the crowded cytoplasm.
article_number: e30292
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian Carsten Johannes
full_name: Helle, Sebastian Carsten Johannes
last_name: Helle
- first_name: Qian
full_name: Feng, Qian
last_name: Feng
- first_name: Mathias J
full_name: Aebersold, Mathias J
last_name: Aebersold
- first_name: Luca
full_name: Hirt, Luca
last_name: Hirt
- first_name: Raphael R
full_name: Grüter, Raphael R
last_name: Grüter
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Andrea
full_name: Sirianni, Andrea
last_name: Sirianni
- first_name: Serge
full_name: Mostowy, Serge
last_name: Mostowy
- first_name: Jess G
full_name: Snedeker, Jess G
last_name: Snedeker
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Tomaso
full_name: Zambelli, Tomaso
last_name: Zambelli
- first_name: Benoît
full_name: Kornmann, Benoît
last_name: Kornmann
citation:
ama: Helle SCJ, Feng Q, Aebersold MJ, et al. Mechanical force induces mitochondrial
fission. eLife. 2017;6. doi:10.7554/elife.30292
apa: Helle, S. C. J., Feng, Q., Aebersold, M. J., Hirt, L., Grüter, R. R., Vahid,
A., … Kornmann, B. (2017). Mechanical force induces mitochondrial fission. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.30292
chicago: Helle, Sebastian Carsten Johannes, Qian Feng, Mathias J Aebersold, Luca
Hirt, Raphael R Grüter, Afshin Vahid, Andrea Sirianni, et al. “Mechanical Force
Induces Mitochondrial Fission.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30292.
ieee: S. C. J. Helle et al., “Mechanical force induces mitochondrial fission,”
eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy
S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. 2017. Mechanical force
induces mitochondrial fission. eLife. 6, e30292.
mla: Helle, Sebastian Carsten Johannes, et al. “Mechanical Force Induces Mitochondrial
Fission.” ELife, vol. 6, e30292, eLife Sciences Publications, 2017, doi:10.7554/elife.30292.
short: S.C.J. Helle, Q. Feng, M.J. Aebersold, L. Hirt, R.R. Grüter, A. Vahid, A.
Sirianni, S. Mostowy, J.G. Snedeker, A. Šarić, T. Idema, T. Zambelli, B. Kornmann,
ELife 6 (2017).
date_created: 2021-11-29T08:51:38Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2021-11-29T09:28:14Z
day: '09'
ddc:
- '572'
doi: 10.7554/elife.30292
extern: '1'
external_id:
pmid:
- '29119945'
file:
- access_level: open_access
checksum: c35f42dcfb007f6d6c761a27e24c26d3
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T09:07:41Z
date_updated: 2021-11-29T09:07:41Z
file_id: '10372'
file_name: 2017_eLife_Helle.pdf
file_size: 6120157
relation: main_file
success: 1
file_date_updated: 2021-11-29T09:07:41Z
has_accepted_license: '1'
intvolume: ' 6'
keyword:
- general immunology and microbiology
- general biochemistry
- genetics and molecular biology
- general medicine
- general neuroscience
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://elifesciences.org/articles/30292
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical force induces mitochondrial fission
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: 6
year: '2017'
...
---
_id: '10373'
abstract:
- lang: eng
text: 'Electric charges are conserved. The same would be expected to hold for magnetic
charges, yet magnetic monopoles have never been observed. It is therefore surprising
that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations,
suggest that colloidal particles heated or cooled in certain polar or paramagnetic
solvents may behave as if they carry an electric/magnetic charge. Here, we present
numerical simulations that show that the field distribution around a pair of such
heated/cooled colloidal particles agrees quantitatively with the theoretical predictions
for a pair of oppositely charged electric or magnetic monopoles. However, in other
respects, the nonequilibrium colloidal particles do not behave as monopoles: They
cannot be moved by a homogeneous applied field. The numerical evidence for the
monopole-like fields around heated/cooled colloidal particles is crucial because
the experimental and numerical determination of forces between such colloidal
particles would be complicated by the presence of other effects, such as thermophoresis.'
acknowledgement: P.W. acknowledges many invaluable discussions with Martin Neumann,
Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge
financial support from the Austrian Academy of Sciences through a doctoral (DOC)
fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich
Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European
Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results
presented here have been achieved in part using the Vienna Scientific Cluster.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Wirnsberger, Peter
last_name: Wirnsberger
- first_name: Domagoj
full_name: Fijan, Domagoj
last_name: Fijan
- first_name: Roger A.
full_name: Lightwood, Roger A.
last_name: Lightwood
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical
evidence for thermally induced monopoles. Proceedings of the National Academy
of Sciences. 2017;114(19):4911-4914. doi:10.1073/pnas.1621494114
apa: Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., &
Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1621494114
chicago: Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph
Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2017. https://doi.org/10.1073/pnas.1621494114.
ieee: P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel,
“Numerical evidence for thermally induced monopoles,” Proceedings of the National
Academy of Sciences, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914,
2017.
ista: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017.
Numerical evidence for thermally induced monopoles. Proceedings of the National
Academy of Sciences. 114(19), 4911–4914.
mla: Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences, vol. 114, no. 19, National
Academy of Sciences, 2017, pp. 4911–14, doi:10.1073/pnas.1621494114.
short: P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel,
Proceedings of the National Academy of Sciences 114 (2017) 4911–4914.
date_created: 2021-11-29T09:28:24Z
date_published: 2017-04-24T00:00:00Z
date_updated: 2021-11-29T09:59:12Z
day: '24'
doi: 10.1073/pnas.1621494114
extern: '1'
external_id:
arxiv:
- '1610.06840'
pmid:
- '28439003'
intvolume: ' 114'
issue: '19'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/114/19/4911
month: '04'
oa: 1
oa_version: Published Version
page: 4911-4914
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Numerical evidence for thermally induced monopoles
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 114
year: '2017'
...
---
_id: '10374'
abstract:
- lang: eng
text: The formation of filaments from naturally occurring protein molecules is a
process at the core of a range of functional and aberrant biological phenomena,
such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's
disease. The macroscopic behaviour associated with such processes is remarkably
diverse, ranging from simple nucleated growth to highly cooperative processes
with a well-defined lagtime. Thus, conventionally, different molecular mechanisms
have been used to explain the self-assembly of different proteins. Here we show
that this range of behaviour can be quantitatively captured by a single unifying
Petri net that describes filamentous growth in terms of aggregate number and aggregate
mass concentrations. By considering general features associated with a particular
network connectivity, we are able to establish directly the rate-determining steps
of the overall aggregation reaction from the system's scaling behaviour. We illustrate
the power of this framework on a range of different experimental and simulated
aggregating systems. The approach is general and will be applicable to any future
extensions of the reaction network of filamentous self-assembly.
acknowledgement: The research leading to these results has received funding from the
European Research Council under the European Union's Seventh Framework Programme
(FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (SL, TPJK),
Sidney Sussex College Cambridge (GM), the Frances and Augusta Newman Foundation
(TPJK), the Biotechnology and Biological Science Research Council (TPJK), the Swedish
Research Council (SL), the Academy of Medical Sciences (AŠ), Wellcome Trust (AŠ),
and the Cambridge Centre for Misfolding Diseases (CMD, TPJK, MV).
article_processing_charge: No
article_type: original
author:
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Luke
full_name: Rajah, Luke
last_name: Rajah
- first_name: Samuel A. I.
full_name: Cohen, Samuel A. I.
last_name: Cohen
- first_name: Manuela
full_name: Pfammatter, Manuela
last_name: Pfammatter
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Erik
full_name: Hellstrand, Erik
last_name: Hellstrand
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Adriano
full_name: Aguzzi, Adriano
last_name: Aguzzi
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- 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: Meisl G, Rajah L, Cohen SAI, et al. Scaling behaviour and rate-determining
steps in filamentous self-assembly. Chemical Science. 2017;8(10):7087-7097.
doi:10.1039/c7sc01965c
apa: Meisl, G., Rajah, L., Cohen, S. A. I., Pfammatter, M., Šarić, A., Hellstrand,
E., … Knowles, T. P. J. (2017). Scaling behaviour and rate-determining steps in
filamentous self-assembly. Chemical Science. Royal Society of Chemistry.
https://doi.org/10.1039/c7sc01965c
chicago: Meisl, Georg, Luke Rajah, Samuel A. I. Cohen, Manuela Pfammatter, Anđela
Šarić, Erik Hellstrand, Alexander K. Buell, et al. “Scaling Behaviour and Rate-Determining
Steps in Filamentous Self-Assembly.” Chemical Science. Royal Society of
Chemistry, 2017. https://doi.org/10.1039/c7sc01965c.
ieee: G. Meisl et al., “Scaling behaviour and rate-determining steps in filamentous
self-assembly,” Chemical Science, vol. 8, no. 10. Royal Society of Chemistry,
pp. 7087–7097, 2017.
ista: Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK,
Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. 2017. Scaling behaviour
and rate-determining steps in filamentous self-assembly. Chemical Science. 8(10),
7087–7097.
mla: Meisl, Georg, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous
Self-Assembly.” Chemical Science, vol. 8, no. 10, Royal Society of Chemistry,
2017, pp. 7087–97, doi:10.1039/c7sc01965c.
short: G. Meisl, L. Rajah, S.A.I. Cohen, M. Pfammatter, A. Šarić, E. Hellstrand,
A.K. Buell, A. Aguzzi, S. Linse, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles,
Chemical Science 8 (2017) 7087–7097.
date_created: 2021-11-29T09:29:31Z
date_published: 2017-08-31T00:00:00Z
date_updated: 2021-11-29T10:00:00Z
day: '31'
ddc:
- '540'
doi: 10.1039/c7sc01965c
extern: '1'
external_id:
pmid:
- '29147538'
intvolume: ' 8'
issue: '10'
keyword:
- general chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/3.0/
main_file_link:
- open_access: '1'
url: https://pubs.rsc.org/en/content/articlelanding/2017/SC/C7SC01965C
month: '08'
oa: 1
oa_version: Published Version
page: 7087-7097
pmid: 1
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scaling behaviour and rate-determining steps in filamentous self-assembly
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2017'
...
---
_id: '10375'
abstract:
- lang: eng
text: 'Cellular membranes exhibit a large variety of shapes, strongly coupled to
their function. Many biological processes involve dynamic reshaping of membranes,
usually mediated by proteins. This interaction works both ways: while proteins
influence the membrane shape, the membrane shape affects the interactions between
the proteins. To study these membrane-mediated interactions on closed and anisotropically
curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as
a model system. We find that two particles on a closed system always attract each
other, and tend to align with the direction of largest curvature. Multiple particles
form arcs, or, at large enough numbers, a complete ring surrounding the vesicle
in its equatorial plane. The resulting vesicle shape resembles a snowman. Our
results indicate that these physical interactions on membranes with anisotropic
shapes can be exploited by cells to drive macromolecules to preferred regions
of cellular or intracellular membranes, and utilized to initiate dynamic processes
such as cell division. The same principle could be used to find the midplane of
an artificial vesicle, as a first step towards dividing it into two equal parts.'
acknowledgement: This work was supported by the Netherlands Organisation for Scientific
Research (NWO/OCW), as part of the Frontiers of Nanoscience program.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
citation:
ama: Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation
on fluid vesicles. Soft Matter. 2017;13(28):4924-4930. doi:10.1039/c7sm00433h
apa: Vahid, A., Šarić, A., & Idema, T. (2017). Curvature variation controls
particle aggregation on fluid vesicles. Soft Matter. Royal Society of Chemistry.
https://doi.org/10.1039/c7sm00433h
chicago: Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls
Particle Aggregation on Fluid Vesicles.” Soft Matter. Royal Society of
Chemistry, 2017. https://doi.org/10.1039/c7sm00433h.
ieee: A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation
on fluid vesicles,” Soft Matter, vol. 13, no. 28. Royal Society of Chemistry,
pp. 4924–4930, 2017.
ista: Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation
on fluid vesicles. Soft Matter. 13(28), 4924–4930.
mla: Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on
Fluid Vesicles.” Soft Matter, vol. 13, no. 28, Royal Society of Chemistry,
2017, pp. 4924–30, doi:10.1039/c7sm00433h.
short: A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930.
date_created: 2021-11-29T10:00:39Z
date_published: 2017-06-15T00:00:00Z
date_updated: 2021-11-29T10:33:36Z
day: '15'
doi: 10.1039/c7sm00433h
extern: '1'
external_id:
arxiv:
- '1703.00776'
pmid:
- '28677712'
intvolume: ' 13'
issue: '28'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
main_file_link:
- open_access: '1'
url: https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H
month: '06'
oa: 1
oa_version: Published Version
page: 4924-4930
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Curvature variation controls particle aggregation on fluid vesicles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 13
year: '2017'
...
---
_id: '10416'
abstract:
- lang: eng
text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck
reachability. The input is a graph where the edges are labeled with different
types of opening and closing parentheses, and the reachability information is
computed via paths whose parentheses are properly matched. We present new results
for Dyck reachability problems with applications to alias analysis and data-dependence
analysis. Our main contributions, that include improved upper bounds as well as
lower bounds that establish optimality guarantees, are as follows: First, we consider
Dyck reachability on bidirected graphs, which is the standard way of performing
field-sensitive points-to analysis. Given a bidirected graph with n nodes and
m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)),
where α(n) is the inverse Ackermann function, improving the previously known O(n2)
time bound; (ii) a matching lower bound that shows that our algorithm is optimal
wrt to worst-case complexity; and (iii) an optimal average-case upper bound of
O(m) time, improving the previously known O(m · logn) bound. Second, we consider
the problem of context-sensitive data-dependence analysis, where the task is to
obtain analysis summaries of library code in the presence of callbacks. Our algorithm
preprocesses libraries in almost linear time, after which the contribution of
the library in the complexity of the client analysis is only linear, and only
wrt the number of call sites. Third, we prove that combinatorial algorithms for
Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained
without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication,
which is a long-standing open problem. Thus we establish that the existing combinatorial
algorithms for Dyck reachability are (conditionally) optimal for general graphs.
We also show that the same hardness holds for graphs of constant treewidth. Finally,
we provide a prototype implementation of our algorithms for both alias analysis
and data-dependence analysis. Our experimental evaluation demonstrates that the
new algorithms significantly outperform all existing methods on the two problems,
over real-world benchmarks.'
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant
(279307: Graph Games).\r\n"
article_number: '30'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Bhavya
full_name: Choudhary, Bhavya
last_name: Choudhary
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence
and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158118
apa: 'Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck
reachability for data-dependence and Alias analysis. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158118'
chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal
Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.
ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability
for data-dependence and Alias analysis,” Proceedings of the ACM on Programming
Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability
for data-dependence and Alias analysis. Proceedings of the ACM on Programming
Languages. 2(POPL), 30.
mla: Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence
and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol.
2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.
short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming
Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:48Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:13Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158118
ec_funded: 1
external_id:
arxiv:
- '1910.00241'
file:
- access_level: open_access
checksum: faa3f7b3fe8aab84b50ed805c26a0ee5
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T08:06:28Z
date_updated: 2021-12-07T08:06:28Z
file_id: '10421'
file_name: 2017_ACMProgLang_Chatterjee.pdf
file_size: 460188
relation: main_file
success: 1
file_date_updated: 2021-12-07T08:06:28Z
has_accepted_license: '1'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5455'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Optimal Dyck reachability for data-dependence and Alias analysis
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: 2
year: '2017'
...
---
_id: '10417'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\n\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
partial order reduction. Proceedings of the ACM on Programming Languages.
2017;2(POPL). doi:10.1145/3158119
apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2017). Data-centric dynamic partial order reduction. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158119'
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2017. https://doi.org/10.1145/3158119.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
dynamic partial order reduction,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric
dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
2(POPL), 31.
mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for
Computing Machinery, 2017, doi:10.1145/3158119.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
of the ACM on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:16Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
arxiv:
- '1610.01188'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158119
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5448'
relation: earlier_version
status: public
- id: '5456'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '10418'
abstract:
- lang: eng
text: We present a new proof rule for proving almost-sure termination of probabilistic
programs, including those that contain demonic non-determinism. An important question
for a probabilistic program is whether the probability mass of all its diverging
runs is zero, that is that it terminates "almost surely". Proving that can be
hard, and this paper presents a new method for doing so. It applies directly to
the program's source code, even if the program contains demonic choice. Like others,
we use variant functions (a.k.a. "super-martingales") that are real-valued and
decrease randomly on each loop iteration; but our key innovation is that the amount
as well as the probability of the decrease are parametric. We prove the soundness
of the new rule, indicate where its applicability goes beyond existing rules,
and explain its connection to classical results on denumerable (non-demonic) Markov
chains.
acknowledgement: "McIver and Morgan are grateful to David Basin and the Information
Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during
part of which this work began. And thanks particularly to Andreas Lochbihler, who
shared with us the probabilistic termination problem that led to it. They acknowledge
the support of ARC grant DP140101119. Part of this work was carried out during the
Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs
Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden.
Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4."
article_number: '33'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Annabelle
full_name: Mciver, Annabelle
last_name: Mciver
- first_name: Carroll
full_name: Morgan, Carroll
last_name: Morgan
- first_name: Benjamin Lucien
full_name: Kaminski, Benjamin Lucien
last_name: Kaminski
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
citation:
ama: Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure
termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158121
apa: 'Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new
proof rule for almost-sure termination. Proceedings of the ACM on Programming
Languages. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3158121'
chicago: Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost
P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.
ieee: A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule
for almost-sure termination,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure
termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.
mla: Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for
Computing Machinery, 2017, doi:10.1145/3158121.
short: A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM
on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-07T00:00:00Z
date_updated: 2021-12-07T08:04:14Z
day: '07'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/3158121
external_id:
arxiv:
- '1711.03588'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158121
month: '12'
oa: 1
oa_version: Published Version
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new proof rule for almost-sure termination
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '1061'
abstract:
- lang: eng
text: 'Background: Metabolic engineering and synthetic biology of cyanobacteria
offer a promising sustainable alternative approach for fossil-based ethylene production,
by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly
into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis
sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce
ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae
pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the
ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene.
Results: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene
production through the integration of a codon-optimized version of the efe gene
under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5\''-AGGAGG-3\'')
as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased
ethylene production twofold by RBS screening and further investigated improving
ethylene production from a single gene copy of efe, using multiple tandem promoters
and by putting our best construct on an RSF1010-based broad-host-self-replicating
plasmid, which has a higher copy number than the genome. Moreover, to raise the
intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene
is formed, we constructed a glycogen-synthesis knockout mutant (glgC) and introduced
the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the
glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however,
surprisingly, ethylene production was lower in this strain than in the wild-type
background. Conclusion: Making use of different RBS sequences, production of ethylene
ranging over a 20-fold difference has been achieved. However, a further increase
of production through multiple tandem promoters and a broad-host plasmid was not
achieved speculating that the transcription strength and the gene copy number
are not the limiting factors in our system.'
article_number: '34'
article_processing_charge: No
author:
- first_name: Vinod
full_name: Veetil, Vinod
last_name: Veetil
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
citation:
ama: Veetil V, Angermayr A, Hellingwerf K. Ethylene production with engineered Synechocystis
sp PCC 6803 strains. Microbial Cell Factories. 2017;16(1). doi:10.1186/s12934-017-0645-5
apa: Veetil, V., Angermayr, A., & Hellingwerf, K. (2017). Ethylene production
with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories.
BioMed Central. https://doi.org/10.1186/s12934-017-0645-5
chicago: Veetil, Vinod, Andreas Angermayr, and Klaas Hellingwerf. “Ethylene Production
with Engineered Synechocystis Sp PCC 6803 Strains.” Microbial Cell Factories.
BioMed Central, 2017. https://doi.org/10.1186/s12934-017-0645-5.
ieee: V. Veetil, A. Angermayr, and K. Hellingwerf, “Ethylene production with engineered
Synechocystis sp PCC 6803 strains,” Microbial Cell Factories, vol. 16,
no. 1. BioMed Central, 2017.
ista: Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered
Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.
mla: Veetil, Vinod, et al. “Ethylene Production with Engineered Synechocystis Sp
PCC 6803 Strains.” Microbial Cell Factories, vol. 16, no. 1, 34, BioMed
Central, 2017, doi:10.1186/s12934-017-0645-5.
short: V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017).
date_created: 2018-12-11T11:49:56Z
date_published: 2017-02-23T00:00:00Z
date_updated: 2023-09-20T12:09:21Z
day: '23'
ddc:
- '579'
doi: 10.1186/s12934-017-0645-5
extern: '1'
external_id:
isi:
- '000397733000001'
pmid:
- '28231787'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:50Z
date_updated: 2018-12-12T10:16:50Z
file_id: '5240'
file_name: IST-2017-792-v1+1_s12934-017-0645-5.pdf
file_size: 1361313
relation: main_file
file_date_updated: 2018-12-12T10:16:50Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Microbial Cell Factories
publication_identifier:
issn:
- '14752859'
publication_status: published
publisher: BioMed Central
publist_id: '6325'
pubrep_id: '792'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ethylene production with engineered Synechocystis sp PCC 6803 strains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2017'
...
---
_id: '1062'
abstract:
- lang: eng
text: Mouse chromaffin cells (MCCs) generate action potential (AP) firing that regulates
the Ca2+‐dependent release of catecholamines (CAs). Recent findings indicate that
MCCs possess a variety of spontaneous firing modes that span from the common ‘tonic‐irregular’
to the less frequent ‘burst’ firing. This latter is evident in a small fraction
of MCCs but occurs regularly when Nav1.3/1.7 channels are made less available
or when the Slo1β2‐subunit responsible for BK channel inactivation is deleted.
Burst firing causes large increases of Ca2+‐entry and potentiates CA release by
∼3.5‐fold and thus may be a key mechanism for regulating MCC function. With the
aim to uncover a physiological role for burst‐firing we investigated the effects
of acidosis on MCC activity. Lowering the extracellular pH (pHo) from 7.4 to 7.0
and 6.6 induces cell depolarizations of 10–15 mV that generate repeated bursts.
Bursts at pHo 6.6 lasted ∼330 ms, occurred at 1–2 Hz and caused an ∼7‐fold increase
of CA cumulative release. Burst firing originates from the inhibition of the pH‐sensitive
TASK‐1/TASK‐3 channels and from a 40% BK channel conductance reduction at pHo
7.0. The same pHo had little or no effect on Nav, Cav, Kv and SK channels that
support AP firing in MCCs. Burst firing of pHo 6.6 could be mimicked by mixtures
of the TASK‐1 blocker A1899 (300 nm) and BK blocker paxilline (300 nm) and could
be prevented by blocking L‐type channels by adding 3 μm nifedipine. Mixtures of
the two blockers raised cumulative CA‐secretion even more than low pHo (∼12‐fold),
showing that the action of protons on vesicle release is mainly a result of the
ionic conductance changes that increase Ca2+‐entry during bursts. Our data provide
direct evidence suggesting that MCCs respond to low pHo with sustained depolarization,
burst firing and enhanced CA‐secretion, thus mimicking the physiological response
of CCs to acute acidosis and hyperkalaemia generated during heavy exercise and
muscle fatigue.
article_processing_charge: No
author:
- first_name: Laura
full_name: Guarina, Laura
last_name: Guarina
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Valentina
full_name: Carabelli, Valentina
last_name: Carabelli
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
citation:
ama: Guarina L, Vandael DH, Carabelli V, Carbone E. Low pH inf o boosts burst firing
and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 2017;595(8):2587-2609.
doi:10.1113/JP273735
apa: Guarina, L., Vandael, D. H., Carabelli, V., & Carbone, E. (2017). Low pH
inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK
channels while preserving Cav1 channels in mouse chromaffin cells. Journal
of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP273735
chicago: Guarina, Laura, David H Vandael, Valentina Carabelli, and Emilio Carbone.
“Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1
and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” Journal
of Physiology. Wiley-Blackwell, 2017. https://doi.org/10.1113/JP273735.
ieee: L. Guarina, D. H. Vandael, V. Carabelli, and E. Carbone, “Low pH inf o boosts
burst firing and catecholamine release by blocking TASK-1 and BK channels while
preserving Cav1 channels in mouse chromaffin cells,” Journal of Physiology,
vol. 595, no. 8. Wiley-Blackwell, pp. 2587–2609, 2017.
ista: Guarina L, Vandael DH, Carabelli V, Carbone E. 2017. Low pH inf o boosts burst
firing and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 595(8), 2587–2609.
mla: Guarina, Laura, et al. “Low PH Inf o Boosts Burst Firing and Catecholamine
Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse
Chromaffin Cells.” Journal of Physiology, vol. 595, no. 8, Wiley-Blackwell,
2017, pp. 2587–609, doi:10.1113/JP273735.
short: L. Guarina, D.H. Vandael, V. Carabelli, E. Carbone, Journal of Physiology
595 (2017) 2587–2609.
date_created: 2018-12-11T11:49:56Z
date_published: 2017-04-15T00:00:00Z
date_updated: 2023-09-20T12:09:47Z
day: '15'
doi: 10.1113/JP273735
extern: '1'
external_id:
isi:
- '000399430300022'
intvolume: ' 595'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: '2587 - 2609 '
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6326'
quality_controlled: '1'
status: public
title: Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1
and BK channels while preserving Cav1 channels in mouse chromaffin cells
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 595
year: '2017'
...
---
_id: '1063'
abstract:
- lang: eng
text: Severe environmental change can drive a population extinct unless the population
adapts in time to the new conditions (“evolutionary rescue”). How does biparental
sexual reproduction influence the chances of population persistence compared to
clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele
model for adaptation in diploid species, where rescue is contingent on the establishment
of the mutant homozygote. Reproduction can occur by random mating, selfing, or
clonally. Random mating generates and destroys the rescue mutant; selfing is efficient
at generating it but at the same time depletes the heterozygote, which can lead
to a low mutant frequency in the standing genetic variation. Due to these (and
other) antagonistic effects, we find a nontrivial dependence of population survival
on the rate of sex/selfing, which is strongly influenced by the dominance coefficient
of the mutation before and after the environmental change. Importantly, since
mating with the wild‐type breaks the mutant homozygote up, a slow decay of the
wild‐type population size can impede rescue in randomly mating populations.
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
citation:
ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.
Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191
apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191
chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and
Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.
ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,”
Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.
ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. 71(4), 845–858.
mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal
Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58,
doi:10.1111/evo.13191.
short: H. Uecker, Evolution 71 (2017) 845–858.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2025-05-28T11:42:51Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.13191
ec_funded: 1
external_id:
isi:
- '000398545200003'
intvolume: ' 71'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2016/10/14/081042
month: '04'
oa: 1
oa_version: Submitted Version
page: 845 - 858
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6327'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary rescue in randomly mating, selfing, and clonal populations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '1065'
abstract:
- lang: eng
text: 'We consider the problem of reachability in pushdown graphs. We study the
problem for pushdown graphs with constant treewidth. Even for pushdown graphs
with treewidth 1, for the reachability problem we establish the following: (i)
the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem
would contradict the k-clique conjecture and imply faster combinatorial algorithms
for cliques in graphs.'
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: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information
Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003
apa: Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant
treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003
chicago: Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with
Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.
ieee: K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,”
Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.
ista: Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth.
Information Processing Letters. 122, 25–29.
mla: Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant
Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp.
25–29, doi:10.1016/j.ipl.2017.02.003.
short: K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:08:18Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: HeEd
doi: 10.1016/j.ipl.2017.02.003
ec_funded: 1
external_id:
isi:
- '000399506600005'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:17Z
date_updated: 2019-10-15T07:44:51Z
file_id: '4998'
file_name: IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf
file_size: 247657
relation: main_file
file_date_updated: 2019-10-15T07:44:51Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 25 - 29
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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: Information Processing Letters
publication_identifier:
issn:
- '00200190'
publication_status: published
publisher: Elsevier
publist_id: '6323'
pubrep_id: '991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pushdown reachability with constant treewidth
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 122
year: '2017'
...
---
_id: '1066'
abstract:
- lang: eng
text: "Simulation is an attractive alternative to language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. Simulation has also been extended in two orthogonal directions, namely,
(1) fair simulation, for simulation over specified set of infinite runs; and (2)
quantitative simulation, for simulation between weighted automata. While fair
trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial
time. For weighted automata, the (quantitative) language inclusion problem is
undecidable in general, whereas the (quantitative) simulation reduces to quantitative
games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we
study (quantitative) simulation for weighted automata with Büchi acceptance conditions,
i.e., we generalize fair simulation from non-weighted automata to weighted automata.
We show that imposing Büchi acceptance conditions on weighted automata changes
many fundamental properties of the simulation games, yet they still admit pseudo-polynomial
time algorithms."
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation
games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative
fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
“Quantitative Fair Simulation Games.” Information and Computation. Elsevier,
2017. https://doi.org/10.1016/j.ic.2016.10.006.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair
simulation games,” Information and Computation, vol. 254, no. 2. Elsevier,
pp. 143–166, 2017.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation
games. Information and Computation. 254(2), 143–166.
mla: Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information
and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation
254 (2017) 143–166.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:07:48Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.ic.2016.10.006
ec_funded: 1
external_id:
isi:
- '000402025600002'
intvolume: ' 254'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa_version: None
page: 143 - 166
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '6322'
quality_controlled: '1'
related_material:
record:
- id: '5428'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Quantitative fair simulation games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 254
year: '2017'
...
---
_id: '10663'
abstract:
- lang: eng
text: 'The superconducting state of matter enables one to observe quantum effects
on the macroscopic scale and hosts many fascinating phenomena. Topological defects
of the superconducting order parameter, such as vortices and fluxoid states in
multiply connected structures, are often the key ingredients of these phenomena.
This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for
investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures.
The technique relies on the magneto-mechanical coupling of a MFM cantilever to
the motion of fluxons. The novelty of the technique is that a magnetic particle
attached to the cantilever is used not only to sense the state of a SC structure,
but also as a primary source of the inhomogeneous magnetic field which induces
that state. Φ0-MFM enables us to map the transitions between tip-induced states
during a scan: at the positions of the tip, where the two lowest energy states
become degenerate, small oscillations of the tip drive the transitions between
these states, which causes a significant shift in the resonant frequency and dissipation
of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions
form concentric contours on a scan. We show that the changes in the cantilever
resonant frequency and dissipation are well-described by a stochastic resonance
(SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model
allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin
(LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR
model to qualitatively study the effects of a locally applied magnetic field on
the phase slip rate in rings containing constrictions. The states with multiple
vortices or winding numbers could be useful for the development of novel superconducting
devices, or the study of vortex interactions and interference effects. Using Φ0-MFM
allows us to induce, probe and control fluxoid states in thin wall structures
comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions
allow us to identify the underlying states and to investigate their energetics
and dynamics even in complicated structures.'
alternative_title:
- Graduate Dissertations and Theses at Illinois
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
citation:
ama: Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting
structures. 2017.
apa: Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting
structures. University of Illinois at Urbana-Champaign.
chicago: Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting
Structures.” University of Illinois at Urbana-Champaign, 2017.
ieee: H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting
structures,” University of Illinois at Urbana-Champaign, 2017.
ista: Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting
structures. University of Illinois at Urbana-Champaign.
mla: Polshyn, Hryhoriy. Magnetic Force Microscopy Studies of Mesoscopic Superconducting
Structures. University of Illinois at Urbana-Champaign, 2017.
short: H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting
Structures, University of Illinois at Urbana-Champaign, 2017.
date_created: 2022-01-25T14:54:14Z
date_published: 2017-09-18T00:00:00Z
date_updated: 2022-01-25T15:00:26Z
day: '18'
degree_awarded: PhD
extern: '1'
keyword:
- physics
- superconductivity
- magnetic force microscopy
- phase slips
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://hdl.handle.net/2142/99178
month: '09'
oa: 1
oa_version: Published Version
page: '103'
publication_status: published
publisher: University of Illinois at Urbana-Champaign
status: public
supervisor:
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
title: Magnetic force microscopy studies of mesoscopic superconducting structures
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2017'
...
---
_id: '1067'
abstract:
- lang: eng
text: Embryo morphogenesis relies on highly coordinated movements of different tissues.
However, remarkably little is known about how tissues coordinate their movements
to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements
first become apparent during “doming,” when the blastoderm begins to spread over
the yolk sac, a process involving coordinated epithelial surface cell layer expansion
and mesenchymal deep cell intercalations. Here, we find that active surface cell
expansion represents the key process coordinating tissue movements during doming.
By using a combination of theory and experiments, we show that epithelial surface
cells not only trigger blastoderm expansion by reducing tissue surface tension,
but also drive blastoderm thinning by inducing tissue contraction through radial
deep cell intercalations. Thus, coordinated tissue expansion and thinning during
doming relies on surface cells simultaneously controlling tissue surface tension
and radial tissue contraction.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Martin
full_name: Bock, Martin
last_name: Bock
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical
basis of coordinated tissue spreading in zebrafish gastrulation. Developmental
Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010
apa: Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg,
C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish
gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010
chicago: Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume
Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue
Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017.
https://doi.org/10.1016/j.devcel.2017.01.010.
ieee: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg,
“The physical basis of coordinated tissue spreading in zebrafish gastrulation,”
Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.
ista: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017.
The physical basis of coordinated tissue spreading in zebrafish gastrulation.
Developmental Cell. 40(4), 354–366.
mla: Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading
in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press,
2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010.
short: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg,
Developmental Cell 40 (2017) 354–366.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2023-09-20T12:06:27Z
day: '27'
ddc:
- '572'
- '597'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2017.01.010
ec_funded: 1
external_id:
isi:
- '000395368300007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:57Z
date_updated: 2018-12-12T10:10:57Z
file_id: '4849'
file_name: IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf
file_size: 6866187
relation: main_file
file_date_updated: 2018-12-12T10:10:57Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 354 - 366
project:
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Developmental Cell
publication_identifier:
issn:
- '15345807'
publication_status: published
publisher: Cell Press
publist_id: '6320'
pubrep_id: '869'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The physical basis of coordinated tissue spreading in zebrafish gastrulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2017'
...
---
_id: '1072'
abstract:
- lang: eng
text: Given a finite set of points in Rn and a radius parameter, we study the Čech,
Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized
discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel
sets of generalized discrete Morse functions, we prove that the four complexes
are simple-homotopy equivalent by a sequence of simplicial collapses, which are
explicitly described by a single discrete gradient field.
acknowledgement: This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP),
by ESF under the ACAT Research Network Programme, by the Russian Government under
mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR
109 “Discretization in Geometry and Dynamics”.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions
of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991
apa: Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay
complexes. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/6991
chicago: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and
Delaunay Complexes.” Transactions of the American Mathematical Society.
American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.
ieee: U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,”
Transactions of the American Mathematical Society, vol. 369, no. 5. American
Mathematical Society, pp. 3741–3762, 2017.
ista: Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes.
Transactions of the American Mathematical Society. 369(5), 3741–3762.
mla: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay
Complexes.” Transactions of the American Mathematical Society, vol. 369,
no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.
short: U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society
369 (2017) 3741–3762.
date_created: 2018-12-11T11:49:59Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-09-20T12:05:56Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/6991
ec_funded: 1
external_id:
arxiv:
- '1312.1231'
isi:
- '000398030400024'
intvolume: ' 369'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.1231
month: '05'
oa: 1
oa_version: Preprint
page: 3741 - 3762
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '6311'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Morse theory of Čech and delaunay complexes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 369
year: '2017'
...
---
_id: '1073'
abstract:
- lang: eng
text: Let X and Y be finite simplicial sets (e.g. finite simplicial complexes),
both equipped with a free simplicial action of a finite group G. Assuming that
Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes
the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|;
the existence of such a map can be decided even for dimX≤2d+1. This yields the
first algorithm for deciding topological embeddability of a k-dimensional finite
simplicial complex into Rn under the condition k≤23n−1. More generally, we present
an algorithm that, given a lifting-extension problem satisfying an appropriate
stability assumption, computes the set of all homotopy classes of solutions. This
result is new even in the non-equivariant situation.
article_processing_charge: No
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
citation:
ama: Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension
problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6
apa: Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of
the lifting extension problem. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-016-9855-6
chicago: Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability
of the Lifting Extension Problem.” Discrete & Computational Geometry.
Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.
ieee: M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting
extension problem,” Discrete & Computational Geometry, vol. 54, no.
4. Springer, pp. 915–965, 2017.
ista: Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting
extension problem. Discrete & Computational Geometry. 54(4), 915–965.
mla: Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.”
Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017,
pp. 915–65, doi:10.1007/s00454-016-9855-6.
short: M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54
(2017) 915–965.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:01:28Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-016-9855-6
external_id:
isi:
- '000400072700008'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1307.6444
month: '06'
oa: 1
oa_version: Submitted Version
page: 915 - 965
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6309'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic solvability of the lifting extension problem
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1074'
abstract:
- lang: eng
text: Recently it has become feasible to detect long blocks of nearly identical
sequence shared between pairs of genomes. These IBD blocks are direct traces of
recent coalescence events and, as such, contain ample signal to infer recent demography.
Here, we examine sharing of such blocks in two-dimensional populations with local
migration. Using a diffusion approximation to trace genetic ancestry, we derive
analytical formulae for patterns of isolation by distance of IBD blocks, which
can also incorporate recent population density changes. We introduce an inference
scheme that uses a composite likelihood approach to fit these formulae. We then
extensively evaluate our theory and inference method on a range of scenarios using
simulated data. We first validate the diffusion approximation by showing that
the theoretical results closely match the simulated block sharing patterns. We
then demonstrate that our inference scheme can accurately and robustly infer dispersal
rate and effective density, as well as bounds on recent dynamics of population
density. To demonstrate an application, we use our estimation scheme to explore
the fit of a diffusion model to Eastern European samples in the POPRES data set.
We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last
centuries, combined with accelerating population growth, can explain the observed
exponential decay of block sharing with increasing pairwise sample distance.
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351.
doi:10.1534/genetics.116.196220
apa: Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography
from isolation by distance of long shared sequence blocks. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.116.196220
chicago: Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent
Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics.
Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.
ieee: H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from
isolation by distance of long shared sequence blocks,” Genetics, vol. 205,
no. 3. Genetics Society of America, pp. 1335–1351, 2017.
ista: Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.
mla: Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance
of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society
of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.
short: H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2025-05-28T11:42:51Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.196220
ec_funded: 1
external_id:
isi:
- '000395807200023'
intvolume: ' 205'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/early/2016/09/23/076810
month: '03'
oa: 1
oa_version: Preprint
page: 1335 - 1351
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6307'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Inferring recent demography from isolation by distance of long shared sequence
blocks
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '10745'
abstract:
- lang: eng
text: New ways to investigate and manipulate fluxoid and vortex states of mesoscopic
superconducting structures are of great interest. The states with multiple vortices
or winding numbers could be useful for the study of vortex interactions and interference
effects, the braiding of Majorana bound states by winding vortices, and the development
of novel superconducting devices. We demonstrate a methodology based on magnetic
force microscopy that allows us to induce, probe and control fluxoid states in
thin wall structures comprised of multiple loops. By using micro-magnet as a source
of inhomogeneous magnetic field, we can efficiently explore the configuration
space of fluxoid states. Scanning over the structure reveals the energy crossing
points of the lowest laying fluxoid states. This is due the strong interaction
of cantilever with thermally activated fluxoid transitions at points of degeneracy.
We show that measured patterns of fluxoid transitions allow to identify the states,
investigate their energetics, and manipulate them. Further, we show that the dynamics
of driven fluxoid transitions can be described by stochastic resonance model,
which provides a unique way of measuring fluxoid transition rate and related energy
barrier for chosen transitions even in complicated structures
alternative_title:
- Bulletin of the American Physical Society
article_number: P39.00011
article_processing_charge: No
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
full_name: Naibert, Tyler
last_name: Naibert
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: 'Polshyn H, Naibert T, Budakian R. Probing and controlling fluxoid states
in multiply-connected mesoscopic superconducting structures. In: APS March
Meeting 2017. Vol 62. American Physical Society; 2017.'
apa: 'Polshyn, H., Naibert, T., & Budakian, R. (2017). Probing and controlling
fluxoid states in multiply-connected mesoscopic superconducting structures. In
APS March Meeting 2017 (Vol. 62). New Orleans, LA, United States: American
Physical Society.'
chicago: Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling
Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In
APS March Meeting 2017, Vol. 62. American Physical Society, 2017.
ieee: H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid
states in multiply-connected mesoscopic superconducting structures,” in APS
March Meeting 2017, New Orleans, LA, United States, 2017, vol. 62, no. 4.
ista: 'Polshyn H, Naibert T, Budakian R. 2017. Probing and controlling fluxoid
states in multiply-connected mesoscopic superconducting structures. APS March
Meeting 2017. APS: American Physical Society, Bulletin of the American Physical
Society, vol. 62, P39.00011.'
mla: Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected
Mesoscopic Superconducting Structures.” APS March Meeting 2017, vol. 62,
no. 4, P39.00011, American Physical Society, 2017.
short: H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American
Physical Society, 2017.
conference:
end_date: 2017-03-17
location: New Orleans, LA, United States
name: 'APS: American Physical Society'
start_date: 2017-03-13
date_created: 2022-02-08T09:49:17Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2022-02-08T10:44:35Z
day: '01'
extern: '1'
intvolume: ' 62'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR17/Session/P39.11
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2017
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: ' Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting
structures'
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 62
year: '2017'
...
---
_id: '1075'
alternative_title:
- American Studies in Austria
author:
- first_name: Bernhard
full_name: Wenzl, Bernhard
id: 479E9046-F248-11E8-B48F-1D18A9856A87
last_name: Wenzl
citation:
ama: 'Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on
"The Vienna Frontier" In: Parker J, Poole R, eds. Austria
and America: 20th-Century Cross-Cultural Encounters. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London;
2017:73-80.'
apa: 'Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos
Reports on "The Vienna Frontier" In J. Parker & R. Poole
(Eds.), Austria and America: 20th-Century Cross-Cultural Encounters (Vol.
15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.'
chicago: 'Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos
Reports on "The Vienna Frontier"” In Austria and America:
20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph
Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.'
ieee: 'B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports
on "The Vienna Frontier",” in Austria and America: 20th-Century
Cross-Cultural Encounters, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag
Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.'
ista: 'Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports
on "The Vienna Frontier" In: Austria and America: 20th-Century
Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.'
mla: 'Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos
Reports on "The Vienna Frontier"” Austria and America: 20th-Century
Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, vol. 15,
LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.'
short: 'B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century
Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017,
pp. 73–80.'
date_created: 2018-12-11T11:50:00Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2021-01-12T06:48:06Z
day: '01'
ddc:
- '001'
editor:
- first_name: Joshua
full_name: Parker, Joshua
last_name: Parker
- first_name: Ralph
full_name: Poole, Ralph
last_name: Poole
extern: '1'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:06Z
date_updated: 2018-12-12T10:08:06Z
file_id: '4666'
file_name: IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf
file_size: 380624
relation: main_file
file_date_updated: 2018-12-12T10:08:06Z
has_accepted_license: '1'
intvolume: ' 15'
language:
- iso: eng
month: '02'
oa: 1
oa_version: None
page: 73 - 80
publication: 'Austria and America: 20th-Century Cross-Cultural Encounters'
publication_identifier:
isbn:
- 978-3643908124
publication_status: published
publisher: LIT Verlag Berlin-Münster-Wien-Zürich-London
publist_id: '6306'
status: public
title: 'An American in Allied-occupied Austria: John Dos Passos Reports on "The
Vienna Frontier"'
type: book_chapter
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2017'
...
---
_id: '1076'
abstract:
- lang: eng
text: Signatures of the Coulomb corrections in the photoelectron momentum distribution
during laser-induced ionization of atoms or ions in tunneling and multiphoton
regimes are investigated analytically in the case of a one-dimensional problem.
A high-order Coulomb-corrected strong-field approximation is applied, where the
exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov
state including the second-order corrections to the eikonal. Although without
high-order corrections our theory coincides with the known analytical R-matrix
(ARM) theory, we propose a simplified procedure for the matrix element derivation.
Rather than matching the eikonal Coulomb-Volkov wave function with the bound state
as in the ARM theory to remove the Coulomb singularity, we calculate the matrix
element via the saddle-point integration method by time as well as by coordinate,
and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron
momentum distribution with respect to the ARM theory due to high-order corrections
is analyzed for tunneling and multiphoton regimes. The relation of the quantum
corrections to the tunneling delay time is discussed.
article_number: '023403'
article_processing_charge: No
author:
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Jiří
full_name: Daněk, Jiří
last_name: Daněk
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Karen
full_name: Hatsagortsyan, Karen
last_name: Hatsagortsyan
- first_name: Christoph
full_name: Keitel, Christoph
last_name: Keitel
citation:
ama: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization
via a high-order Coulomb-corrected strong-field approximation. Physical Review
A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403
apa: Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C.
(2017). Strong-field ionization via a high-order Coulomb-corrected strong-field
approximation. Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403
chicago: Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan,
and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403.
ieee: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation,”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2.
American Physical Society, 2017.
ista: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation. Physical
Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.
mla: Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403.
short: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical
Review A - Atomic, Molecular, and Optical Physics 95 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:57:23Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.95.023403
ec_funded: 1
external_id:
isi:
- '000400571700011'
intvolume: ' 95'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.07018
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_identifier:
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
publist_id: '6305'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong-field ionization via a high-order Coulomb-corrected strong-field approximation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...