---
_id: '8586'
abstract:
- lang: eng
text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights
into biological processes and structures within a native context. However, a major
challenge still lies in the efficient and reproducible preparation of adherent
cells for subsequent cryo-EM analysis. This is due to the sensitivity of many
cellular specimens to the varying seeding and culturing conditions required for
EM experiments, the often limited amount of cellular material and also the fragility
of EM grids and their substrate. Here, we present low-cost and reusable 3D printed
grid holders, designed to improve specimen preparation when culturing challenging
cellular samples directly on grids. The described grid holders increase cell culture
reproducibility and throughput, and reduce the resources required for cell culturing.
We show that grid holders can be integrated into various cryo-EM workflows, including
micro-patterning approaches to control cell seeding on grids, and for generating
samples for cryo-focused ion beam milling and cryo-electron tomography experiments.
Their adaptable design allows for the generation of specialized grid holders customized
to a large variety of applications.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: This work was supported by the Austrian Science Fund (FWF, P33367)
to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was
also supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the
BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi
Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing
our grid holders in different experimental setups and Daniel Gütl and the Kondrashov
group (IST Austria) for granting us repeated access to their 3D printers. We also
thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary
BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised
foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William
Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science)
for illustrating the graphical abstract.
article_number: '107633'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders
for improved cellular specimen preparation in cryo-electron microscopy. Journal
of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633
apa: Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed
cell culture grid holders for improved cellular specimen preparation in cryo-electron
microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633
chicago: Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur.
“3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation
in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier,
2020. https://doi.org/10.1016/j.jsb.2020.107633.
ieee: F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture
grid holders for improved cellular specimen preparation in cryo-electron microscopy,”
Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.
ista: Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid
holders for improved cellular specimen preparation in cryo-electron microscopy.
Journal of Structural Biology. 212(3), 107633.
mla: Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved
Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural
Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.
short: F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology
212 (2020).
corr_author: '1'
date_created: 2020-09-29T13:24:06Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2026-07-26T22:30:02Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2020.107633
external_id:
isi:
- '000600997800008'
pmid:
- '32987119'
file:
- access_level: open_access
checksum: c48cbf594e84fc2f91966ffaafc0918c
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:01:10Z
date_updated: 2020-12-10T14:01:10Z
file_id: '8937'
file_name: 2020_JourStrucBiology_Faessler.pdf
file_size: 7076870
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:01:10Z
has_accepted_license: '1'
intvolume: ' 212'
isi: 1
issue: '3'
keyword:
- electron microscopy
- cryo-EM
- EM sample preparation
- 3D printing
- cell culture
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '14592'
relation: used_in_publication
status: public
- id: '12491'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 3D printed cell culture grid holders for improved cellular specimen preparation
in cryo-electron microscopy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2020'
...
---
_id: '6418'
abstract:
- lang: eng
text: Males and females of Artemia franciscana, a crustacean commonly used in the
aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes,
but the nature and extent of differentiation of these chromosomes is unknown.
Here, we characterize the Z chromosome by detecting genomic regions that show
lower genomic coverage in female than in male samples, and regions that harbor
an excess of female-specific SNPs. We detect many Z-specific genes, which no longer
have homologs on the W, but also Z-linked genes that appear to have diverged very
recently from their existing W-linked homolog. We assess patterns of male and
female expression in two tissues with extensive morphological dimorphism, gonads,
and heads. In agreement with their morphology, sex-biased expression is common
in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased
genes, and seems to in fact have a mechanism of dosage compensation that leads
to equal expression in males and in females. Both of these patterns are contrary
to most ZW systems studied so far, making A. franciscana an excellent model for
investigating the interplay between the evolution of sexual dimorphism and dosage
compensation, as well as Z chromosome evolution in general.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene
expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome
biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053
apa: Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso,
B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053
chicago: Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger,
and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the
Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford
University Press, 2019. https://doi.org/10.1093/gbe/evz053.
ieee: A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso,
“Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University
Press, pp. 1033–1044, 2019.
ista: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased
gene expression and dosage compensation on the Artemia franciscana Z-chromosome.
Genome biology and evolution. 11(4), 1033–1044.
mla: Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation
on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution,
vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.
short: A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome
Biology and Evolution 11 (2019) 1033–1044.
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2025-04-14T07:41:21Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evz053
ec_funded: 1
external_id:
isi:
- '000476569800003'
file:
- access_level: open_access
checksum: 7d0ede297b6741f3dc89cd59017c7642
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:29:38Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6446'
file_name: 2019_GBE_Huylmans.pdf
file_size: 1256303
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1033-1044
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genome biology and evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '6060'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2019'
...
---
_id: '6442'
abstract:
- lang: eng
text: This paper investigates the use of fundamental solutions for animating detailed
linear water surface waves. We first propose an analytical solution for efficiently
animating circular ripples in closed form. We then show how to adapt the method
of fundamental solutions (MFS) to create ambient waves interacting with complex
obstacles. Subsequently, we present a novel wavelet-based discretization which
outperforms the state of the art MFS approach for simulating time-varying water
surface waves with moving obstacles. Our results feature high-resolution spatial
details, interactions with complex boundaries, and large open ocean domains. Our
method compares favorably with previous work as well as known analytical solutions.
We also present comparisons between our method and real world examples.
acknowledged_ssus:
- _id: ScienComp
article_number: '130'
article_processing_charge: No
author:
- first_name: Camille
full_name: Schreck, Camille
id: 2B14B676-F248-11E8-B48F-1D18A9856A87
last_name: Schreck
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation.
ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002
apa: Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for
water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002
chicago: Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions
for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002.
ieee: C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave
animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.
ista: Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave
animation. ACM Transactions on Graphics. 38(4), 130.
mla: Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.”
ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.
short: C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).
date_created: 2019-05-14T07:04:06Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2024-10-22T09:58:22Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ChWo
doi: 10.1145/3306346.3323002
ec_funded: 1
external_id:
isi:
- '000475740600104'
file:
- access_level: open_access
checksum: 1b737dfe3e051aba8f3f4ab1dceda673
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T07:03:55Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6443'
file_name: 2019_ACM_Schreck.pdf
file_size: 44328918
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/
scopus_import: '1'
status: public
title: Fundamental solutions for water wave animation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6859'
abstract:
- lang: eng
text: V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found
in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation
across theplasma membrane using the rotary-catalysis mechanism. They belong to
the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type
ATP synthasesin overall architecture. We solved cryo–electron microscopy structures
of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs,
in three rotationalstates and two substates. These structures indicate substantial
flexibility betweenV1and Voin a working enzyme, which results from mechanical
competition between centralshaft rotation and resistance from the peripheral stalks.
We also describedetails of adenosine diphosphate inhibition release, V1-Votorque
transmission, andproton translocation, which are relevant for the entire V-type
ATPase family.
acknowledged_ssus:
- _id: ScienComp
article_number: eaaw9144
article_processing_charge: No
author:
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus
thermophilus V/A-type ATPase. Science. 2019;365(6455). doi:10.1126/science.aaw9144
apa: Zhou, L., & Sazanov, L. A. (2019). Structure and conformational plasticity
of the intact Thermus thermophilus V/A-type ATPase. Science. AAAS. https://doi.org/10.1126/science.aaw9144
chicago: Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity
of the Intact Thermus Thermophilus V/A-Type ATPase.” Science. AAAS, 2019.
https://doi.org/10.1126/science.aaw9144.
ieee: L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the
intact Thermus thermophilus V/A-type ATPase,” Science, vol. 365, no. 6455.
AAAS, 2019.
ista: Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact
Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144.
mla: Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity
of the Intact Thermus Thermophilus V/A-Type ATPase.” Science, vol. 365,
no. 6455, eaaw9144, AAAS, 2019, doi:10.1126/science.aaw9144.
short: L. Zhou, L.A. Sazanov, Science 365 (2019).
date_created: 2019-09-07T19:04:45Z
date_published: 2019-08-23T00:00:00Z
date_updated: 2023-08-29T07:52:02Z
day: '23'
department:
- _id: LeSa
doi: 10.1126/science.aaw9144
external_id:
isi:
- '000482464000043'
pmid:
- '31439765'
intvolume: ' 365'
isi: 1
issue: '6455'
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/
scopus_import: '1'
status: public
title: Structure and conformational plasticity of the intact Thermus thermophilus
V/A-type ATPase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 365
year: '2019'
...
---
_id: '6978'
abstract:
- lang: eng
text: In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent
work, we study numerically the localized turbulence in pipe flow and elucidate
astate space structure that gives rise to transient chaos. Starting from the basin
boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence
of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe
homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which
wasconjectured in various earlier studies. By mapping the transverse intersections
between thestable and unstable manifold of a periodic orbit, we identify the gateways
that promote anescape from turbulence.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Akshunna
full_name: Dogra, Akshunna
last_name: Dogra
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401
apa: Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos
in streamwise-localized pipe flow turbulence. Physical Review Fluids. American
Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401
chicago: Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient
Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids.
American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401.
ieee: N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized
pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American
Physical Society, p. 102401, 2019.
ista: Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 4(10), 102401.
mla: Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized
Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American
Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.
short: N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.
date_created: 2019-11-04T10:04:01Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-30T07:20:03Z
day: '01'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.4.102401
external_id:
arxiv:
- '1810.02211'
isi:
- '000493510400001'
intvolume: ' 4'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.02211
month: '10'
oa: 1
oa_version: Preprint
page: '102401'
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of transient chaos in streamwise-localized pipe flow turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2019'
...
---
_id: '6848'
abstract:
- lang: eng
text: Proton-translocating transhydrogenase (also known as nicotinamide nucleotide
transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner
mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride
between NADH and NADP+, coupled to the translocation of one proton across the
membrane. Its main physiological function is the generation of NADPH, which is
a substrate in anabolic reactions and a regulator of oxidative status; however,
NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid
deficiency in humans and metabolic abnormalities in mice, similar to those observed
in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve
a rotation of around 180° of the entire NADP(H)-binding domain that alternately
participates in hydride transfer and proton-channel gating. However, owing to
the lack of high-resolution structures of intact NNT, the details of this process
remain unclear5,6. Here we present the cryo-electron microscopy structure of intact
mammalian NNT in different conformational states. We show how the NADP(H)-binding
domain opens the proton channel to the opposite sides of the membrane, and we
provide structures of these two states. We also describe the catalytically important
interfaces and linkers between the membrane and the soluble domains and their
roles in nucleotide exchange. These structures enable us to propose a revised
mechanism for a coupling process in NNT that is consistent with a large body of
previous biochemical work. Our results are relevant to the development of currently
unavailable NNT inhibitors, which may have therapeutic potential in ischaemia
reperfusion injury, metabolic syndrome and some cancers7,8,9.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: " We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their
assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing
was performed at the IST high-performance computing cluster.\r\nThis project has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement no. 665385."
article_processing_charge: No
article_type: letter_note
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
orcid: 0000-0002-6018-3422
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2
apa: Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial
proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019.
https://doi.org/10.1038/s41586-019-1519-2.
ieee: D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating
transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295,
2019.
ista: Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 573(7773), 291–295.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer
Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2.
short: D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.
date_created: 2019-09-04T06:21:41Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-07-26T22:30:45Z
day: '12'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-019-1519-2
ec_funded: 1
external_id:
isi:
- '000485415400061'
pmid:
- '31462775'
file:
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creator: lsazanov
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date_updated: 2020-11-26T16:33:44Z
file_id: '8821'
file_name: Manuscript_final_acc_withFigs_SI_opt_red.pdf
file_size: 3066206
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success: 1
file_date_updated: 2020-11-26T16:33:44Z
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intvolume: ' 573'
isi: 1
issue: '7773'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 291–295
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/
record:
- id: '8340'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Structure and mechanism of mitochondrial proton-translocating transhydrogenase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 573
year: '2019'
...
---
OA_place: publisher
_id: '6435'
abstract:
- lang: eng
text: "Social insect colonies tend to have numerous members which function together
like a single organism in such harmony that the term ``super-organism'' is often
used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells
of a metazoan, while the sterile worker caste corresponds to somatic cells. The
worker castes, like tissues, are\r\nin charge of all functions of a living being,
besides reproduction. The establishment of new super-organismal units\r\n(i.e.
new colonies) is accomplished by the co-dependent castes. The term oftentimes
goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation,
nutrient regulation and gas exchange of a social insect colony. Furthermore, we
assert that the super-organism has an immune system, and benefits from ``social
immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists
to resolve the apparent discrepancy between the expected high frequency of disease
outbreak amongst numerous, closely related tightly-interacting hosts, living in
stable and microbially-rich environments, against the exceptionally scarce epidemic
accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly
of behaviours which have evolved to effectively keep the pathogenic enemies of
a colony at bay. The field of social immunity has drawn interest, as it becomes
increasingly urgent to stop\r\nthe collapse of pollinator species and curb the
growth of invasive pests. In the past decade, several mechanisms of\r\nsocial
immune responses have been dissected, but many more questions remain open.\r\n\r\nI
present my work in two experimental chapters. In the first, I use invasive garden
ants (*Lasius neglectus*) to study how pathogen load and its distribution among
nestmates affect the grooming response of the group. Any given group of ants will
carry out the same total grooming work, but will direct their grooming effort
towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation,
the highest risk of transmission does not stem from grooming highly contaminated
ants, but instead, we suggest that the grooming response likely minimizes spore
loss to the environment, reducing contamination from inadvertent pickup from the
substrate.\r\n\r\nThe second is a comparative developmental approach. I follow
black garden ant queens (*Lasius niger*) and their colonies from mating flight,
through hibernation for a year. Colonies which grow fast from the start, have
a lower chance of survival through hibernation, and those which survive grow at
a lower pace later. This is true for colonies of naive\r\nand challenged queens.
Early pathogen exposure of the queens changes colony dynamics in an unexpected
way: colonies from exposed queens are more likely to grow slowly and recover in
numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental
chapters, this thesis includes a co-authored published review on organisational\r\nimmunity,
where we enlist the experimental evidence and theoretical framework on which this
hypothesis is built,\r\nidentify the caveats and underline how the field is ripe
to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative
efforts, one to develop an image-based tracker, and the second to develop a classifier
for ant\r\nbehaviour."
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
- _id: M-Shop
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
citation:
ama: Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen.
2019. doi:10.15479/AT:ISTA:6435
apa: Casillas Perez, B. E. (2019). Collective defenses of garden ants against
a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435
chicago: Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against
a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.
ieee: B. E. Casillas Perez, “Collective defenses of garden ants against a fungal
pathogen,” Institute of Science and Technology Austria, 2019.
ista: Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal
pathogen. Institute of Science and Technology Austria.
mla: Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a
Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435.
short: B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal
Pathogen, Institute of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-05-13T08:58:35Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2026-04-08T14:02:12Z
day: '07'
ddc:
- '570'
- '006'
- '578'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:6435
ec_funded: 1
file:
- access_level: open_access
checksum: 6daf2d2086111aa8fd3fbc919a3e2833
content_type: application/pdf
creator: casillas
date_created: 2019-05-13T09:16:20Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-05-08
file_id: '6438'
file_name: tesisDoctoradoBC.pdf
file_size: 3895187
relation: main_file
- access_level: closed
checksum: 3d221aaff7559a7060230a1ff610594f
content_type: application/zip
creator: casillas
date_created: 2019-05-13T09:16:20Z
date_updated: 2020-07-14T12:47:30Z
embargo_to: open_access
file_id: '6439'
file_name: tesisDoctoradoBC.zip
file_size: 7365118
relation: source_file
file_date_updated: 2021-02-11T11:17:15Z
has_accepted_license: '1'
keyword:
- Social Immunity
- Sanitary care
- Social Insects
- Organisational Immunity
- Colony development
- Multi-target tracking
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '183'
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1999'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Collective defenses of garden ants against a fungal pathogen
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
_id: '134'
abstract:
- lang: eng
text: "The current state of the art in real-time two-dimensional water wave simulation
requires developers to choose between efficient Fourier-based methods, which lack
interactions with moving obstacles, and finite-difference or finite element methods,
which handle environmental interactions but are significantly more expensive.
This paper attempts to bridge this long-standing gap between complexity and performance,
by proposing a new wave simulation method that can faithfully simulate wave interactions
with moving obstacles in real time while simultaneously preserving minute details
and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating
2D water waves directly compute the change in height of the water surface, a strategy
which imposes limitations based on the CFL condition (fast moving waves require
small time steps) and Nyquist's limit (small wave details require closely-spaced
simulation variables). This paper proposes a novel wavelet transformation that
discretizes the liquid motion in terms of amplitude-like functions that vary over
space, frequency, and direction, effectively generalizing Fourier-based methods
to handle local interactions. Because these new variables change much more slowly
over space than the original water height function, our change of variables drastically
reduces the limitations of the CFL condition and Nyquist limit, allowing us to
simulate highly detailed water waves at very large visual resolutions. Our discretization
is amenable to fast summation and easy to parallelize. We also present basic extensions
like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue
that our discretization provides a convenient set of variables for artistic manipulation,
which we illustrate with a novel wave-painting interface."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- SIGGRAPH
article_number: '94'
article_processing_charge: No
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Matthias
full_name: Mueller Fischer, Matthias
last_name: Mueller Fischer
- first_name: Nuttapong
full_name: Chentanez, Nuttapong
last_name: Chentanez
- first_name: Miles
full_name: Macklin, Miles
last_name: Macklin
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336
apa: Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M.,
& Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/3197517.3201336
chicago: Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez,
Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions
on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.
ieee: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and
C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol.
37, no. 4. ACM, 2018.
ista: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.
mla: Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics,
vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.
short: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C.
Wojtan, ACM Transactions on Graphics 37 (2018).
date_created: 2018-12-11T11:44:48Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2024-10-22T09:58:20Z
day: '30'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3197517.3201336
ec_funded: 1
external_id:
isi:
- '000448185000055'
file:
- access_level: open_access
checksum: db75ebabe2ec432bf41389e614d6ef62
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:59:23Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5744'
file_name: 2018_ACM_Jeschke.pdf
file_size: 22185016
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '7789'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/
scopus_import: '1'
status: public
title: Water surface wavelets
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2018'
...
---
_id: '44'
abstract:
- lang: eng
text: 'Recent realization of a kinetically constrained chain of Rydberg atoms by
Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation
of unusual revivals in the many-body quantum dynamics. In our previous work [C.
J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to
the existence of “quantum scarred” eigenstates in the many-body spectrum of the
experimentally realized model. Here, we present a detailed study of the eigenstate
properties of the same model. We find that the majority of the eigenstates exhibit
anomalous thermalization: the observable expectation values converge to their
Gibbs ensemble values, but parametrically slower compared to the predictions of
the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum,
we identify nonergodic eigenstates that strongly violate the ETH, whose number
grows polynomially with system size. Previously, the same eigenstates were identified
via large overlaps with certain product states, and were used to explain the revivals
observed in experiment. Here, we find that these eigenstates, in addition to highly
atypical expectation values of local observables, also exhibit subthermal entanglement
entropy that scales logarithmically with the system size. Moreover, we identify
an additional class of quantum scarred eigenstates, and discuss their manifestations
in the dynamics starting from initial product states. We use forward scattering
approximation to describe the structure and physical properties of quantum scarred
eigenstates. Finally, we discuss the stability of quantum scars to various perturbations.
We observe that quantum scars remain robust when the introduced perturbation is
compatible with the forward scattering approximation. In contrast, the perturbations
which most efficiently destroy quantum scars also lead to the restoration of “canonical”
thermalization.'
acknowledged_ssus:
- _id: ScienComp
article_number: '155134'
article_processing_charge: No
arxiv: 1
author:
- first_name: C J
full_name: Turner, C J
last_name: Turner
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: D A
full_name: Abanin, D A
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Z
full_name: Papić, Z
last_name: Papić
citation:
ama: 'Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates
in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability
to perturbations. Physical Review B. 2018;98(15). doi:10.1103/PhysRevB.98.155134'
apa: 'Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., & Papić, Z.
(2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown
of thermalization, and stability to perturbations. Physical Review B. American
Physical Society. https://doi.org/10.1103/PhysRevB.98.155134'
chicago: 'Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić.
“Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown
of Thermalization, and Stability to Perturbations.” Physical Review B.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.155134.'
ieee: 'C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum
scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization,
and stability to perturbations,” Physical Review B, vol. 98, no. 15. American
Physical Society, 2018.'
ista: 'Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred
eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization,
and stability to perturbations. Physical Review B. 98(15), 155134.'
mla: 'Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain:
Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical
Review B, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:10.1103/PhysRevB.98.155134.'
short: C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review
B 98 (2018).
date_created: 2018-12-11T11:44:19Z
date_published: 2018-10-22T00:00:00Z
date_updated: 2023-10-10T13:28:49Z
day: '22'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.98.155134
external_id:
arxiv:
- '1806.10933'
isi:
- '000447919100001'
intvolume: ' 98'
isi: 1
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.10933
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '8010'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown
of thermalization, and stability to perturbations'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '1087'
abstract:
- lang: eng
text: Using extensive direct numerical simulations, the dynamics of laminar-turbulent
fronts in pipe flow is investigated for Reynolds numbers between and 5500. We
here investigate the physical distinction between the fronts of weak and strong
slugs both by analysing the turbulent kinetic energy budget and by comparing the
downstream front motion to the advection speed of bulk turbulent structures. Our
study shows that weak downstream fronts travel slower than turbulent structures
in the bulk and correspond to decaying turbulence at the front. At the downstream
front speed becomes faster than the advection speed, marking the onset of strong
fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts
by feeding on the downstream laminar flow. Our study also suggests that temporal
fluctuations of production and dissipation at the downstream laminar-turbulent
front drive the dynamical switches between the two types of front observed up
to.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
arxiv: 1
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Dwight
full_name: Barkley, Dwight
last_name: Barkley
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts
in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14
apa: Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure
of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge
University Press. https://doi.org/10.1017/jfm.2017.14
chicago: Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure
of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge
University Press, 2017. https://doi.org/10.1017/jfm.2017.14.
ieee: B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent
fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University
Press, pp. 1045–1059, 2017.
ista: Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent
fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.
mla: Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.”
Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017,
pp. 1045–59, doi:10.1017/jfm.2017.14.
short: B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017)
1045–1059.
date_created: 2018-12-11T11:50:04Z
date_published: 2017-02-25T00:00:00Z
date_updated: 2025-06-04T08:35:11Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.14
ec_funded: 1
external_id:
arxiv:
- '1603.04077'
isi:
- '000394376400044'
intvolume: ' 813'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.04077
month: '02'
oa: 1
oa_version: Submitted Version
page: 1045 - 1059
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
publist_id: '6290'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Speed and structure of turbulent fronts in pipe flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 813
year: '2017'
...
---
_id: '1118'
abstract:
- lang: eng
text: Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation
during non-rapid eye movement sleep, immobility, and consummatory behavior. However,
whether temporally modulated synaptic excitation or inhibition underlies the ripples
is controversial. To address this question, we performed simultaneous recordings
of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local
field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs,
inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5.
Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with
SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated
that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly
distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons
provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition,
but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
article_processing_charge: No
author:
- first_name: Jian
full_name: Gan, Jian
id: 3614E438-F248-11E8-B48F-1D18A9856A87
last_name: Gan
- first_name: Shih-Ming
full_name: Weng, Shih-Ming
id: 2F9C5AC8-F248-11E8-B48F-1D18A9856A87
last_name: Weng
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. Phase-locked inhibition,
but not excitation, underlies hippocampal ripple oscillations in awake mice in
vivo. Neuron. 2017;93(2):308-314. doi:10.1016/j.neuron.2016.12.018
apa: Gan, J., Weng, S.-M., Pernia-Andrade, A., Csicsvari, J. L., & Jonas, P.
M. (2017). Phase-locked inhibition, but not excitation, underlies hippocampal
ripple oscillations in awake mice in vivo. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.12.018
chicago: Gan, Jian, Shih-Ming Weng, Alejandro Pernia-Andrade, Jozsef L Csicsvari,
and Peter M Jonas. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal
Ripple Oscillations in Awake Mice in Vivo.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2016.12.018.
ieee: J. Gan, S.-M. Weng, A. Pernia-Andrade, J. L. Csicsvari, and P. M. Jonas, “Phase-locked
inhibition, but not excitation, underlies hippocampal ripple oscillations in awake
mice in vivo,” Neuron, vol. 93, no. 2. Elsevier, pp. 308–314, 2017.
ista: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. 2017. Phase-locked
inhibition, but not excitation, underlies hippocampal ripple oscillations in awake
mice in vivo. Neuron. 93(2), 308–314.
mla: Gan, Jian, et al. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal
Ripple Oscillations in Awake Mice in Vivo.” Neuron, vol. 93, no. 2, Elsevier,
2017, pp. 308–14, doi:10.1016/j.neuron.2016.12.018.
short: J. Gan, S.-M. Weng, A. Pernia-Andrade, J.L. Csicsvari, P.M. Jonas, Neuron
93 (2017) 308–314.
date_created: 2018-12-11T11:50:15Z
date_published: 2017-01-18T00:00:00Z
date_updated: 2025-04-15T07:20:01Z
day: '18'
ddc:
- '571'
department:
- _id: PeJo
- _id: JoCs
doi: 10.1016/j.neuron.2016.12.018
ec_funded: 1
external_id:
isi:
- '000396428200010'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:56Z
date_updated: 2018-12-12T10:08:56Z
file_id: '4719'
file_name: IST-2017-752-v1+1_1-s2.0-S0896627316309606-main.pdf
file_size: 2738950
relation: main_file
file_date_updated: 2018-12-12T10:08:56Z
has_accepted_license: '1'
intvolume: ' 93'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 308 - 314
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '6244'
pubrep_id: '752'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations
in awake mice in vivo
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: 93
year: '2017'
...
---
_id: '470'
abstract:
- lang: eng
text: This paper presents a method for simulating water surface waves as a displacement
field on a 2D domain. Our method relies on Lagrangian particles that carry packets
of water wave energy; each packet carries information about an entire group of
wave trains, as opposed to only a single wave crest. Our approach is unconditionally
stable and can simulate high resolution geometric details. This approach also
presents a straightforward interface for artistic control, because it is essentially
a particle system with intuitive parameters like wavelength and amplitude. Our
implementation parallelizes well and runs in real time for moderately challenging
scenarios.
acknowledged_ssus:
- _id: ScienComp
article_number: '103'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
orcid: 0000-0003-4330-8884
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics.
2017;36(4). doi:10.1145/3072959.3073678
apa: Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/3072959.3073678
chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions
on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678.
ieee: S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics,
vol. 36, no. 4. ACM, 2017.
ista: Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics.
36(4), 103.
mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions
on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678.
short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).
date_created: 2018-12-11T11:46:39Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2026-04-16T09:58:39Z
day: '01'
ddc:
- '006'
department:
- _id: ChWo
doi: 10.1145/3072959.3073678
ec_funded: 1
external_id:
isi:
- '000406432100071'
file:
- access_level: open_access
checksum: 82a3b2bfeee4ddef16ecc21675d1a48a
content_type: application/pdf
creator: wojtan
date_created: 2020-01-24T09:32:35Z
date_updated: 2020-07-14T12:46:34Z
file_id: '7359'
file_name: wavepackets_final.pdf
file_size: 13131683
relation: main_file
file_date_updated: 2020-07-14T12:46:34Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: ACM
publist_id: '7350'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Water wave packets
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 36
year: '2017'
...
---
_id: '804'
abstract:
- lang: eng
text: Polysaccharides (carbohydrates) are key regulators of a large number of cell
biological processes. However, precise biochemical or genetic manipulation of
these often complex structures is laborious and hampers experimental structure–function
studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool
to generate and test hypotheses on saccharide function. Yet, currently used MD
force fields often overestimate the aggregation propensity of polysaccharides,
affecting the usability of those simulations. Here we tested MARTINI, a popular
coarse-grained (CG) force field for biological macromolecules, for its ability
to accurately represent molecular forces between saccharides. To this end, we
calculated a thermodynamic solution property, the second virial coefficient of
the osmotic pressure (B22). Comparison with light scattering experiments revealed
a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing
at an imbalance of the nonbonded solute–solute, solute–water, and water–water
interactions. This finding also applies to smaller oligosaccharides which were
all found to aggregate in simulations even at moderate concentrations, well below
their solubility limit. Finally, we explored the influence of the Lennard-Jones
(LJ) interaction between saccharide molecules and propose a simple scaling of
the LJ interaction strength that makes MARTINI more reliable for the simulation
of saccharides.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.S.S. was supported by research fellowship 2811/1-1 from the German
Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF
187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and
Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje
Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions
and the IST Austria Scientific Computing Facility for support.
article_processing_charge: No
arxiv: 1
author:
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Felix
full_name: Deluweit, Felix
last_name: Deluweit
- first_name: Roger
full_name: Scherrers, Roger
last_name: Scherrers
- 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
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
citation:
ama: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming
the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374
apa: Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &
Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in
simulations of polysaccharides. Journal of Chemical Theory and Computation.
American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374
chicago: Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J
Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force
Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation.
American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374.
ieee: P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M.
K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations
of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13,
no. 10. American Chemical Society, pp. 5039–5053, 2017.
ista: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017.
Overcoming the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 13(10), 5039–5053.
mla: Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI
Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory
and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53,
doi:10.1021/acs.jctc.7b00374.
short: P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora,
Journal of Chemical Theory and Computation 13 (2017) 5039–5053.
corr_author: '1'
date_created: 2018-12-11T11:48:35Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2025-06-04T09:49:02Z
day: '10'
department:
- _id: CaHe
doi: 10.1021/acs.jctc.7b00374
external_id:
arxiv:
- '1704.03773'
isi:
- '000412965700036'
intvolume: ' 13'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.03773
month: '10'
oa: 1
oa_version: Submitted Version
page: 5039 - 5053
publication: Journal of Chemical Theory and Computation
publication_identifier:
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
publist_id: '6847'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming the limitations of the MARTINI force field in simulations of polysaccharides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '727'
abstract:
- lang: eng
text: 'Actin filaments polymerizing against membranes power endocytosis, vesicular
traffic, and cell motility. In vitro reconstitution studies suggest that the structure
and the dynamics of actin networks respond to mechanical forces. We demonstrate
that lamellipodial actin of migrating cells responds to mechanical load when membrane
tension is modulated. In a steady state, migrating cell filaments assume the canonical
dendritic geometry, defined by Arp2/3-generated 70° branch points. Increased tension
triggers a dense network with a broadened range of angles, whereas decreased tension
causes a shift to a sparse configuration dominated by filaments growing perpendicularly
to the plasma membrane. We show that these responses emerge from the geometry
of branched actin: when load per filament decreases, elongation speed increases
and perpendicular filaments gradually outcompete others because they polymerize
the shortest distance to the membrane, where they are protected from capping.
This network-intrinsic geometrical adaptation mechanism tunes protrusive force
in response to mechanical load.'
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Jan
full_name: Mueller, Jan
last_name: Mueller
- first_name: Gregory
full_name: Szep, Gregory
id: 4BFB7762-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Arnon
full_name: Lieber, Arnon
last_name: Lieber
- first_name: Christoph
full_name: Winkler, Christoph
last_name: Winkler
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: John
full_name: Small, John
last_name: Small
- first_name: Christian
full_name: Schmeiser, Christian
last_name: Schmeiser
- first_name: Kinneret
full_name: Keren, Kinneret
last_name: Keren
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Mueller J, Szep G, Nemethova M, et al. Load adaptation of lamellipodial actin
networks. Cell. 2017;171(1):188-200. doi:10.1016/j.cell.2017.07.051
apa: Mueller, J., Szep, G., Nemethova, M., de Vries, I., Lieber, A., Winkler, C.,
… Sixt, M. K. (2017). Load adaptation of lamellipodial actin networks. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2017.07.051
chicago: Mueller, Jan, Gregory Szep, Maria Nemethova, Ingrid de Vries, Arnon Lieber,
Christoph Winkler, Karsten Kruse, et al. “Load Adaptation of Lamellipodial Actin
Networks.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.051.
ieee: J. Mueller et al., “Load adaptation of lamellipodial actin networks,”
Cell, vol. 171, no. 1. Cell Press, pp. 188–200, 2017.
ista: Mueller J, Szep G, Nemethova M, de Vries I, Lieber A, Winkler C, Kruse K,
Small J, Schmeiser C, Keren K, Hauschild R, Sixt MK. 2017. Load adaptation of
lamellipodial actin networks. Cell. 171(1), 188–200.
mla: Mueller, Jan, et al. “Load Adaptation of Lamellipodial Actin Networks.” Cell,
vol. 171, no. 1, Cell Press, 2017, pp. 188–200, doi:10.1016/j.cell.2017.07.051.
short: J. Mueller, G. Szep, M. Nemethova, I. de Vries, A. Lieber, C. Winkler, K.
Kruse, J. Small, C. Schmeiser, K. Keren, R. Hauschild, M.K. Sixt, Cell 171 (2017)
188–200.
corr_author: '1'
date_created: 2018-12-11T11:48:10Z
date_published: 2017-09-21T00:00:00Z
date_updated: 2025-07-10T11:54:27Z
day: '21'
department:
- _id: MiSi
- _id: Bio
doi: 10.1016/j.cell.2017.07.051
ec_funded: 1
external_id:
isi:
- '000411331800020'
intvolume: ' 171'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 188 - 200
project:
- _id: 25AD6156-B435-11E9-9278-68D0E5697425
grant_number: LS13-029
name: Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
publist_id: '6951'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Load adaptation of lamellipodial actin networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2017'
...
---
_id: '1350'
abstract:
- lang: eng
text: "The hippocampal CA3 region plays a key role in learning and memory. Recurrent
CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion.
However, the\r\nsynaptic mechanisms of this network computation remain enigmatic.
To investigate these mechanisms, we combined functional connectivity analysis
with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal
neurons revealed that connectivity was sparse, spatially uniform, and highly enriched
in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary
connections were composed of one or two synaptic contacts, suggesting efficient
use of postsynaptic space. Real-size modeling indicated that CA3 networks with
sparse connectivity, disynaptic motifs, and single-contact connections robustly
generated pattern completion.Thus, macro- and microconnectivity contribute to
efficient\r\nmemory storage and retrieval in hippocampal networks."
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern
completion in the hippocampal CA3 network. Science. 2016;353(6304):1117-1123.
doi:10.1126/science.aaf1836
apa: Guzmán, J., Schlögl, A., Frotscher, M., & Jonas, P. M. (2016). Synaptic
mechanisms of pattern completion in the hippocampal CA3 network. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf1836
chicago: Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic
Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science.
American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf1836.
ieee: J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms
of pattern completion in the hippocampal CA3 network,” Science, vol. 353,
no. 6304. American Association for the Advancement of Science, pp. 1117–1123,
2016.
ista: Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern
completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123.
mla: Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal
CA3 Network.” Science, vol. 353, no. 6304, American Association for the
Advancement of Science, 2016, pp. 1117–23, doi:10.1126/science.aaf1836.
short: J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123.
corr_author: '1'
date_created: 2018-12-11T11:51:31Z
date_published: 2016-09-09T00:00:00Z
date_updated: 2025-09-22T08:12:10Z
day: '09'
ddc:
- '570'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.1126/science.aaf1836
ec_funded: 1
external_id:
isi:
- '000382626800045'
file:
- access_level: open_access
checksum: 89caefa4e181424cbf0aecc835fcc5ec
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:27Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4945'
file_name: IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf
file_size: 19408143
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 353'
isi: 1
issue: '6304'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Preprint
page: 1117 - 1123
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5899'
pubrep_id: '823'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synaptic mechanisms of pattern completion in the hippocampal CA3 network
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 353
year: '2016'
...
---
_id: '1363'
abstract:
- lang: eng
text: When aiming to seamlessly integrate a fluid simulation into a larger scenario
(like an open ocean), careful attention must be paid to boundary conditions. In
particular, one must implement special "non-reflecting" boundary conditions,
which dissipate out-going waves as they exit the simulation. Unfortunately, the
state of the art in non-reflecting boundary conditions (perfectly-matched layers,
or PMLs) only permits trivially simple inflow/outflow conditions, so there is
no reliable way to integrate a fluid simulation into a more complicated environment
like a stormy ocean or a turbulent river. This paper introduces the first method
for combining nonreflecting boundary conditions based on PMLs with inflow/outflow
boundary conditions that vary arbitrarily throughout space and time. Our algorithm
is a generalization of stateof- the-art mean-flow boundary conditions in the computational
fluid dynamics literature, and it allows for seamless integration of a fluid simulation
into much more complicated environments. Our method also opens the door for previously-unseen
postprocess effects like retroactively changing the location of solid obstacles,
and locally increasing the visual detail of a pre-existing simulation.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: 'We thank the IST Austria Visual Computing group for helpful feedback
throughout the project. '
alternative_title:
- ACM Transactions on Graphics
article_number: '96'
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid
re-simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925963'
apa: 'Bojsen-Hansen, M., & Wojtan, C. (2016). Generalized non-reflecting boundaries
for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA,
USA: ACM. https://doi.org/10.1145/2897824.2925963'
chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries
for Fluid Re-Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925963.
ieee: M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for
fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol.
35, no. 4.
ista: Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for
fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.
mla: Bojsen-Hansen, Morten, and Chris Wojtan. Generalized Non-Reflecting Boundaries
for Fluid Re-Simulation. Vol. 35, no. 4, 96, ACM, 2016, doi:10.1145/2897824.2925963.
short: M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
corr_author: '1'
date_created: 2018-12-11T11:51:35Z
date_published: 2016-07-11T00:00:00Z
date_updated: 2025-09-22T07:43:01Z
day: '11'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2897824.2925963
ec_funded: 1
external_id:
isi:
- '000380112400066'
file:
- access_level: open_access
checksum: 140b5532f0a2a006a0149cab7c73c17c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:00Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4981'
file_name: IST-2016-631-v1+2_a96-bojsen-hansen.pdf
file_size: 12422760
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
publication_status: published
publisher: ACM
publist_id: '5879'
pubrep_id: '631'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generalized non-reflecting boundaries for fluid re-simulation
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: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2016'
...
---
_id: '2944'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This study has made use of the computational resources provided by
IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk).
The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk).
S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation,
St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in
the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).
article_processing_charge: No
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for
modular inference problems with many parameters: the example of migration rates.
. Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013.
https://doi.org/10.1111/mec.12165.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002,
2013.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. . Molecular Ecology. 22(4), 987–1002.'
mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference
Problems with Many Parameters: The Example of Migration Rates. .” Molecular
Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.
corr_author: '1'
date_created: 2018-12-11T12:00:28Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2025-09-29T13:25:36Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.12165
external_id:
isi:
- '000314220900008'
intvolume: ' 22'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 987 - 1002
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3788'
quality_controlled: '1'
related_material:
record:
- id: '9758'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Approximate Bayesian computation for modular inference problems with many
parameters: the example of migration rates. '
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 22
year: '2013'
...
---
_id: '2962'
abstract:
- lang: eng
text: The choice of summary statistics is a crucial step in approximate Bayesian
computation (ABC). Since statistics are often not sufficient, this choice involves
a trade-off between loss of information and reduction of dimensionality. The latter
may increase the efficiency of ABC. Here, we propose an approach for choosing
summary statistics based on boosting, a technique from the machine learning literature.
We consider different types of boosting and compare them to partial least squares
regression as an alternative. To mitigate the lack of sufficiency, we also propose
an approach for choosing summary statistics locally, in the putative neighborhood
of the true parameter value. We study a demographic model motivated by the re-introduction
of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are
the mean and standard deviation across microsatellites of the scaled ancestral
mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to
matings per breeding season (ω). By simulation, we assess the properties of the
posterior distribution obtained with the various methods. According to our criteria,
ABC with summary statistics chosen locally via boosting with the L2-loss performs
best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find
that most of the variation across loci of the ancestral mutation rate u is between
7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access
to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent
estimates.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
citation:
ama: Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary
statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047.
doi:10.1534/genetics.112.143164
apa: Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach
for choosing summary statistics in approximate Bayesian computation. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.112.143164
chicago: Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach
for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics.
Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164.
ieee: S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing
summary statistics in approximate Bayesian computation,” Genetics, vol.
192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.
ista: Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing
summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.
mla: Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics
in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics
Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.
short: S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.
corr_author: '1'
date_created: 2018-12-11T12:00:34Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2025-09-30T08:06:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.112.143164
external_id:
isi:
- '000310793900018'
pmid:
- '22960215'
intvolume: ' 192'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/
month: '11'
oa: 1
oa_version: Submitted Version
page: 1027 - 1047
pmid: 1
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3763'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A novel approach for choosing summary statistics in approximate Bayesian computation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 192
year: '2012'
...