---
_id: '10429'
abstract:
- lang: eng
text: "The scalability of concurrent data structures and distributed algorithms
strongly depends on\r\nreducing the contention for shared resources and the costs
of synchronization and communication. We show how such cost reductions can be
attained by relaxing the strict consistency conditions required by sequential
implementations. In the first part of the thesis, we consider relaxation in the
context of concurrent data structures. Specifically, in data structures \r\nsuch
as priority queues, imposing strong semantics renders scalability impossible,
since a correct implementation of the remove operation should return only the
element with highest priority. Intuitively, attempting to invoke remove operations
concurrently creates a race condition. This bottleneck can be circumvented by
relaxing semantics of the affected data structure, thus allowing removal of the
elements which are no longer required to have the highest priority. We prove that
the randomized implementations of relaxed data structures provide provable guarantees
on the priority of the removed elements even under concurrency. Additionally,
we show that in some cases the relaxed data structures can be used to scale the
classical algorithms which are usually implemented with the exact ones. In the
second part, we study parallel variants of the stochastic gradient descent (SGD)
algorithm, which distribute computation among the multiple processors, thus reducing
the running time. Unfortunately, in order for standard parallel SGD to succeed,
each processor has to maintain a local copy of the necessary model parameter,
which is identical to the local copies of other processors; the overheads from
this perfect consistency in terms of communication and synchronization can negate
the speedup gained by distributing the computation. We show that the consistency
conditions required by SGD can be relaxed, allowing the algorithm to be more
flexible in terms of tolerating quantized communication, asynchrony, or even crash
faults, while its convergence remains asymptotically the same."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
citation:
ama: Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429
apa: Nadiradze, G. (2021). On achieving scalability through relaxation. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429
chicago: Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.
ieee: G. Nadiradze, “On achieving scalability through relaxation,” Institute of
Science and Technology Austria, 2021.
ista: Nadiradze G. 2021. On achieving scalability through relaxation. Institute
of Science and Technology Austria.
mla: Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.
short: G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science
and Technology Austria, 2021.
date_created: 2021-12-08T21:52:28Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2023-10-17T11:48:55Z
day: '09'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
doi: 10.15479/at:ista:10429
ec_funded: 1
file:
- access_level: open_access
checksum: 6bf14e9a523387328f016c0689f5e10e
content_type: application/pdf
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2021-12-09T17:47:49Z
file_id: '10436'
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success: 1
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checksum: 914d6c5ca86bd0add471971a8f4c4341
content_type: application/zip
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2022-03-28T12:55:12Z
file_id: '10437'
file_name: Thesis_Final_09_12_2021.zip
file_size: 2596924
relation: source_file
file_date_updated: 2022-03-28T12:55:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10432'
relation: part_of_dissertation
status: public
- id: '6673'
relation: part_of_dissertation
status: public
- id: '5965'
relation: part_of_dissertation
status: public
- id: '10435'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: On achieving scalability through relaxation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9733'
abstract:
- lang: eng
text: This thesis is the result of the research carried out by the author during
his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich
polaron model, specifically to its regime of strong coupling. This model, which
is rigorously introduced and discussed in the introduction, has been of great
interest in condensed matter physics and field theory for more than eighty years.
It is used to describe an electron interacting with the atoms of a solid material
(the strength of this interaction is modeled by the presence of a coupling constant
α in the Hamiltonian of the system). The particular regime examined here, which
is mathematically described by considering the limit α →∞, displays many interesting
features related to the emergence of classical behavior, which allows for a simplified
effective description of the system under analysis. The properties, the range
of validity and a quantitative analysis of the precision of such classical approximations
are the main object of the present work. We specify our investigation to the study
of the ground state energy of the system, its dynamics and its effective mass.
For each of these problems, we provide in the introduction an overview of the
previously known results and a detailed account of the original contributions
by the author.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
citation:
ama: Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733
apa: Feliciangeli, D. (2021). The polaron at strong coupling. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:9733
chicago: Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.
ieee: D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and
Technology Austria, 2021.
ista: Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science
and Technology Austria.
mla: Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science
and Technology Austria, 2021, doi:10.15479/at:ista:9733.
short: D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and
Technology Austria, 2021.
date_created: 2021-07-27T15:48:30Z
date_published: 2021-08-20T00:00:00Z
date_updated: 2024-03-06T12:30:44Z
day: '20'
ddc:
- '515'
- '519'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
- _id: JaMa
doi: 10.15479/at:ista:9733
ec_funded: 1
file:
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checksum: e88bb8ca43948abe060eb2d2fa719881
content_type: application/pdf
creator: dfelicia
date_created: 2021-08-19T14:03:48Z
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date_created: 2021-08-19T14:06:35Z
date_updated: 2022-03-10T12:13:57Z
file_id: '9945'
file_name: thesis.7z
file_size: 3771669
relation: source_file
file_date_updated: 2022-03-10T12:13:57Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9787'
relation: part_of_dissertation
status: public
- id: '9792'
relation: part_of_dissertation
status: public
- id: '9225'
relation: part_of_dissertation
status: public
- id: '9781'
relation: part_of_dissertation
status: public
- id: '9791'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: The polaron at strong coupling
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9992'
abstract:
- lang: eng
text: "Blood – this is what animals use to heal wounds fast and efficient. Plants
do not have blood circulation and their cells cannot move. However, plants have
evolved remarkable capacities to regenerate tissues and organs preventing further
damage. In my PhD research, I studied the wound healing in the Arabidopsis root.
I used a UV laser to ablate single cells in the root tip and observed the consequent
wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane
switch and subsequently adopted the cell type of the killed cell to replace it.
We termed this form of wound healing “restorative divisions”. This initial observation
triggered the questions of my PhD studies: How and why do cells orient their division
planes, how do they feel the wound and why does this happen only in inner adjacent
cells.\r\nFor answering these questions, I used a quite simple experimental setup:
5 day - old seedlings were stained with propidium iodide to visualize cell walls
and dead cells; ablation was carried out using a special laser cutter and a confocal
microscope. Adaptation of the novel vertical microscope system made it possible
to observe wounds in real time. This revealed that restorative divisions occur
at increased frequency compared to normal divisions. Additionally,\r\nthe major
plant hormone auxin accumulates in wound adjacent cells and drives the expression
of the wound-stress responsive transcription factor ERF115. Using this as a marker
gene for wound responses, we found that an important part of wound signalling
is the sensing of the collapse of the ablated cell. The collapse causes a radical
pressure drop, which results in strong tissue deformations. These deformations
manifest in an invasion of the now free spot specifically by the inner adjacent
cells within seconds, probably because of higher pressure of the inner tissues.
Long-term imaging revealed that those deformed cells continuously expand towards
the wound hole and that this is crucial for the restorative division. These wound-expanding
cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the
division. Experiments inhibiting cell expansion suggest that it is the biphasic
stretching that induces those MT arrays. Adapting the micromanipulator aspiration
system from animal scientists at our institute confirmed the hypothesis that stretching
influences microtubule stability. In conclusion, this shows that microtubules
react to tissue deformation\r\nand this facilitates the observed division plane
switch. This puts mechanical cues and tensions at the most prominent position
for explaining the growth and wound healing properties of plants. Hence, it shines
light onto the importance of understanding mechanical signal transduction. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
citation:
ama: Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992
apa: Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992
chicago: Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.
ieee: L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of
Science and Technology Austria, 2021.
ista: Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute
of Science and Technology Austria.
mla: Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.
short: L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of
Science and Technology Austria, 2021.
date_created: 2021-09-09T07:37:20Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2023-09-07T13:38:33Z
day: '13'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:9992
ec_funded: 1
file:
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checksum: c763064adaa720e16066c1a4f9682bbb
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: lhoermaye
date_created: 2021-09-09T07:29:48Z
date_updated: 2021-09-15T22:30:26Z
embargo_to: open_access
file_id: '9993'
file_name: Thesis_vupload.docx
file_size: 25179004
relation: source_file
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checksum: 53911b06e93d7cdbbf4c7f4c162fa70f
content_type: application/pdf
creator: lhoermaye
date_created: 2021-09-09T14:25:08Z
date_updated: 2021-09-15T22:30:26Z
embargo: 2021-09-09
file_id: '9996'
file_name: Thesis_vfinal_pdfa.pdf
file_size: 6246900
relation: main_file
file_date_updated: 2021-09-15T22:30:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '168'
project:
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6351'
relation: part_of_dissertation
status: public
- id: '6943'
relation: part_of_dissertation
status: public
- id: '8002'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Wound healing in the Arabidopsis root meristem
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9623'
abstract:
- lang: eng
text: "Cytoplasmic reorganizations are essential for morphogenesis. In large cells
like oocytes, these reorganizations become crucial in patterning the oocyte for
later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm
(ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization
with the contraction of the actomyosin cortex along the animal-vegetal axis of
the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER),
maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the
myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here
we have used the species Phallusia mammillata to investigate the changes in cell
shape that accompany these reorganizations and the mechanochemical mechanisms
underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV)
axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening
followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show
that the fast oscillation corresponds to a dynamic polarization of the actin cortex
as a result of a fertilization-induced increase in cortical tension in the oocyte
that triggers a rupture of the cortex at the animal pole and the establishment
of vegetal-directed cortical flows. These flows are responsible for the vegetal
accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion
of the VP, leading to CP formation, correlates with a relaxation of the vegetal
cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm
is a solid-like layer that buckles under compression forces arising from the contracting
actin cortex at the VP. Straightening of the myoplasm when actin flows stops,
facilitates the expansion of the VP and the CP. Altogether, our results present
a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation.
\r\n"
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
citation:
ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the
actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021.
doi:10.15479/at:ista:9623
apa: Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623
chicago: Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.
ieee: S. Caballero Mancebo, “Fertilization-induced deformations are controlled by
the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,”
Institute of Science and Technology Austria, 2021.
ista: Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria.
mla: Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.
short: S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by
the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes,
Institute of Science and Technology Austria, 2021.
date_created: 2021-07-01T14:50:17Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-09-07T13:33:27Z
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:9623
file:
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: scaballe
date_created: 2021-07-01T14:48:54Z
date_updated: 2022-07-02T22:30:06Z
embargo_to: open_access
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file_name: PhDThesis_SCM.docx
file_size: 131946790
relation: source_file
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creator: scaballe
date_created: 2021-07-01T14:46:25Z
date_updated: 2022-07-02T22:30:06Z
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has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '111'
publication_identifier:
isbn:
- 978-3-99078-012-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9750'
relation: part_of_dissertation
status: public
- id: '9006'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Fertilization-induced deformations are controlled by the actin cortex and a
mitochondria-rich subcortical layer in ascidian oocytes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10058'
abstract:
- lang: eng
text: 'Quantum information and computation has become a vast field paved with opportunities
for researchers and investors. As large multinational companies and international
funds are heavily investing in quantum technologies it is still a question which
platform is best suited for the task of realizing a scalable quantum processor.
In this work we investigate hole spins in Ge quantum wells. These hold great promise
as they possess several favorable properties: a small effective mass, a strong
spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine
noise. All these characteristics helped Ge hole spin qubits to evolve from a single
qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated
a qubit approach leveraging the large out-of-plane g-factors of heavy hole states
in Ge quantum dots. We found this qubit to be reproducibly operable at extremely
low magnetic field and at large speeds while maintaining coherence. This was possible
because large differences of g-factors in adjacent dots can be achieved in the
out-of-plane direction. In the in-plane direction the small g-factors, on the
other hand, can be altered very effectively by the confinement potentials. Here,
we found that this can even lead to a sign change of the g-factors. The resulting
g-factor difference alters the dynamics of the system drastically and produces
effects typically attributed to a spin-orbit induced spin-flip term. The investigations
carried out in this thesis give further insights into the possibilities of holes
in Ge and reveal new physical properties that need to be considered when designing
future spin qubit experiments.'
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The author gratefully acknowledges support by the Austrian Science
Fund (FWF), grants No P30207, and the Nomis foundation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
citation:
ama: Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases. 2021. doi:10.15479/at:ista:10058
apa: Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in
2-dimensional Ge hole gases. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:10058
chicago: Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in
2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021.
https://doi.org/10.15479/at:ista:10058.
ieee: D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases,” Institute of Science and Technology Austria, 2021.
ista: Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases. Institute of Science and Technology Austria.
mla: Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional
Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.
short: D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional
Ge Hole Gases, Institute of Science and Technology Austria, 2021.
date_created: 2021-09-30T07:53:49Z
date_published: 2021-10-05T00:00:00Z
date_updated: 2023-09-08T11:41:08Z
day: '05'
ddc:
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- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:10058
file:
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date_updated: 2022-12-20T23:30:07Z
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file_name: PHD_Thesis_Jirovec_Source.zip
file_size: 32397600
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content_type: application/pdf
creator: djirovec
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date_updated: 2022-12-20T23:30:07Z
embargo: 2022-10-06
file_id: '10087'
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file_size: 26910829
relation: main_file
file_date_updated: 2022-12-20T23:30:07Z
has_accepted_license: '1'
keyword:
- qubits
- quantum computing
- holes
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8831'
relation: part_of_dissertation
status: public
- id: '10065'
relation: part_of_dissertation
status: public
- id: '10066'
relation: part_of_dissertation
status: public
- id: '8909'
relation: part_of_dissertation
status: public
- id: '5816'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole
gases
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9397'
abstract:
- lang: eng
text: Accumulation of interstitial fluid (IF) between embryonic cells is a common
phenomenon in vertebrate embryogenesis. Unlike other model systems, where these
accumulations coalesce into a large central cavity – the blastocoel, in zebrafish,
IF is more uniformly distributed between the deep cells (DC) before the onset
of gastrulation. This is likely due to the presence of a large extraembryonic
structure – the yolk cell (YC) at the position where the blastocoel typically
forms in other model organisms. IF has long been speculated to play a role in
tissue morphogenesis during embryogenesis, but direct evidence supporting such
function is still sparse. Here we show that the relocalization of IF to the interface
between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion
formation and migration along this interface, a key process in embryonic axis
formation. We further demonstrate that axial ME cell migration and IF relocalization
engage in a positive feedback loop, where axial ME migration triggers IF accumulation
ahead of the advancing axial ME tissue by mechanically compressing the overlying
epiblast cell layer. Upon compression, locally induced flow relocalizes the IF
through the porous epiblast tissue resulting in an IF accumulation ahead of the
leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation
and migration of the leading axial ME cells, thereby facilitating axial ME extension.
Our findings reveal a central role of dynamic IF relocalization in orchestrating
germ layer morphogenesis during gastrulation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
citation:
ama: Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is
required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397
apa: Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial
fluid is required for axial mesendoderm migration in zebrafish gastrulation.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397
chicago: Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial
Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.
ieee: K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid
is required for axial mesendoderm migration in zebrafish gastrulation,” Institute
of Science and Technology Austria, 2021.
ista: Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial
fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute
of Science and Technology Austria.
mla: Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial
Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.
short: K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid
Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute
of Science and Technology Austria, 2021.
date_created: 2021-05-17T12:31:30Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2023-09-07T13:32:32Z
day: '18'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: CaHe
- _id: GradSch
doi: 10.15479/at:ista:9397
file:
- access_level: closed
checksum: 7f98532f5324a0b2f3fa8de2967baa19
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: khuljev
date_created: 2021-05-17T12:29:12Z
date_updated: 2022-05-21T22:30:04Z
embargo_to: open_access
file_id: '9398'
file_name: KHuljev_Thesis_corrections.docx
file_size: 47799741
relation: source_file
- access_level: open_access
checksum: bf512f8a1e572a543778fc4b227c01ba
content_type: application/pdf
creator: khuljev
date_created: 2021-05-18T14:50:28Z
date_updated: 2022-05-21T22:30:04Z
embargo: 2022-05-20
file_id: '9401'
file_name: new_KHuljev_Thesis_corrections.pdf
file_size: 16542131
relation: main_file
file_date_updated: 2022-05-21T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '101'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- 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
title: Coordinated spatiotemporal reorganization of interstitial fluid is required
for axial mesendoderm migration in zebrafish gastrulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9562'
abstract:
- lang: eng
text: Left-right asymmetries can be considered a fundamental organizational principle
of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell
synaptic connection shows an input-side dependent asymmetry where the hemispheric
location of the presynaptic CA3 neuron determines the synaptic properties. Left-input
synapses terminating on apical dendrites in stratum radiatum have a higher density
of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1
and smaller areas with less often perforated PSDs. On the other hand, left-input
synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities
than right-input ones. Apical and basal synapses further employ different signaling
pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize
synaptic membrane proteins with high sensitivity and resolution, and has been
used to reveal the asymmetry at the electron microscopic level. However, it requires
time-consuming manual demarcation of the synaptic surface for quantitative measurements.
To facilitate the analysis of replica labeling, I first developed a software named
Darea, which utilizes deep-learning to automatize this demarcation. With Darea
I characterized the synaptic distribution of NMDA and AMPA receptors as well as
the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I
explored the role of GluN2B and its carboxy-terminus in the establishment of input-side
dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B
expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged
to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were
detected. We further discovered a previously unknown functional asymmetry of GluN2A,
which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus
plays a critical role in normal formation of input-side dependent asymmetry.
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
citation:
ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
2021. doi:10.15479/at:ista:9562'
apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated
by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis
by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562'
chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by
NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by
Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.'
ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,”
Institute of Science and Technology Austria, 2021.'
ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA
receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
Institute of Science and Technology Austria.'
mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA
Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.'
short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor
Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning,
Institute of Science and Technology Austria, 2021.'
date_created: 2021-06-17T14:10:47Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-09-11T12:55:53Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/at:ista:9562
file:
- access_level: open_access
checksum: 659df5518db495f679cb1df9e9bd1d94
content_type: application/pdf
creator: dkleindienst
date_created: 2021-06-17T14:03:14Z
date_updated: 2022-07-02T22:30:04Z
embargo: 2022-07-01
file_id: '9563'
file_name: Thesis.pdf
file_size: 77299142
relation: main_file
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checksum: 3bcf63a2b19e5b6663be051bea332748
content_type: application/zip
creator: dkleindienst
date_created: 2021-06-17T14:04:30Z
date_updated: 2022-07-02T22:30:04Z
embargo_to: open_access
file_id: '9564'
file_name: Thesis_source.zip
file_size: 369804895
relation: source_file
file_date_updated: 2022-07-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9756'
relation: part_of_dissertation
status: public
- id: '9437'
relation: part_of_dissertation
status: public
- id: '8532'
relation: part_of_dissertation
status: public
- id: '612'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B
C-terminus and high-throughput image analysis by Deep-Learning'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '8934'
abstract:
- lang: eng
text: "In this thesis, we consider several of the most classical and fundamental
problems in static analysis and formal verification, including invariant generation,
reachability analysis, termination analysis of probabilistic programs, data-flow
analysis, quantitative analysis of Markov chains and Markov decision processes,
and the problem of data packing in cache management.\r\nWe use techniques from
parameterized complexity theory, polyhedral geometry, and real algebraic geometry
to significantly improve the state-of-the-art, in terms of both scalability and
completeness guarantees, for the mentioned problems. In some cases, our results
are the first theoretical improvements for the respective problems in two or three
decades."
acknowledgement: 'The research was partially supported by an IBM PhD fellowship, a
Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences
(OeAW).'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: Goharshady AK. Parameterized and algebro-geometric advances in static program
analysis. 2021. doi:10.15479/AT:ISTA:8934
apa: Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in
static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934
chicago: Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances
in Static Program Analysis.” Institute of Science and Technology Austria, 2021.
https://doi.org/10.15479/AT:ISTA:8934.
ieee: A. K. Goharshady, “Parameterized and algebro-geometric advances in static
program analysis,” Institute of Science and Technology Austria, 2021.
ista: Goharshady AK. 2021. Parameterized and algebro-geometric advances in static
program analysis. Institute of Science and Technology Austria.
mla: Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances
in Static Program Analysis. Institute of Science and Technology Austria, 2021,
doi:10.15479/AT:ISTA:8934.
short: A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program
Analysis, Institute of Science and Technology Austria, 2021.
date_created: 2020-12-10T12:17:07Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-09-22T10:03:21Z
day: '01'
ddc:
- '005'
degree_awarded: PhD
department:
- _id: KrCh
- _id: GradSch
doi: 10.15479/AT:ISTA:8934
file:
- access_level: open_access
checksum: d1b9db3725aed34dadd81274aeb9426c
content_type: application/pdf
creator: akafshda
date_created: 2020-12-22T20:08:44Z
date_updated: 2021-12-23T23:30:04Z
embargo: 2021-12-22
file_id: '8969'
file_name: Thesis-pdfa.pdf
file_size: 5251507
relation: main_file
- access_level: closed
checksum: 1661df7b393e6866d2460eba3c905130
content_type: application/zip
creator: akafshda
date_created: 2020-12-22T20:08:50Z
date_updated: 2021-03-04T23:30:04Z
embargo_to: open_access
file_id: '8970'
file_name: source.zip
file_size: 10636756
relation: source_file
file_date_updated: 2021-12-23T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '278'
project:
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1386'
relation: part_of_dissertation
status: public
- id: '1437'
relation: part_of_dissertation
status: public
- id: '311'
relation: part_of_dissertation
status: public
- id: '6056'
relation: part_of_dissertation
status: public
- id: '6380'
relation: part_of_dissertation
status: public
- id: '639'
relation: part_of_dissertation
status: public
- id: '66'
relation: part_of_dissertation
status: public
- id: '6780'
relation: part_of_dissertation
status: public
- id: '6918'
relation: part_of_dissertation
status: public
- id: '7810'
relation: part_of_dissertation
status: public
- id: '6175'
relation: part_of_dissertation
status: public
- id: '6378'
relation: part_of_dissertation
status: public
- id: '6490'
relation: part_of_dissertation
status: public
- id: '7014'
relation: part_of_dissertation
status: public
- id: '8089'
relation: part_of_dissertation
status: public
- id: '8728'
relation: part_of_dissertation
status: public
- id: '7158'
relation: part_of_dissertation
status: public
- id: '5977'
relation: part_of_dissertation
status: public
- id: '6009'
relation: part_of_dissertation
status: public
- id: '6340'
relation: part_of_dissertation
status: public
- id: '949'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Parameterized and algebro-geometric advances in static program analysis
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10307'
abstract:
- lang: eng
text: Bacteria-host interactions represent a continuous trade-off between benefit
and risk. Thus, the host immune response is faced with a non-trivial problem –
accommodate beneficial commensals and remove harmful pathogens. This is especially
difficult as molecular patterns, such as lipopolysaccharide or specific surface
organelles such as pili, are conserved in both, commensal and pathogenic bacteria.
Type 1 pili, tightly regulated by phase variation, are considered an important
virulence factor of pathogenic bacteria as they facilitate invasion into host
cells. While invasion represents a de facto passive mechanism for pathogens to
escape the host immune response, we demonstrate a fundamental role of type 1 pili
as active modulators of the innate and adaptive immune response.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
citation:
ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021.
doi:10.15479/at:ista:10307
apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307
chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.
ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,”
Institute of Science and Technology Austria, 2021.
ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria.
mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.
short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response,
Institute of Science and Technology Austria, 2021.
date_created: 2021-11-18T15:05:06Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2023-09-07T13:34:38Z
day: '18'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
- _id: CaGu
- _id: GradSch
doi: 10.15479/at:ista:10307
file:
- access_level: open_access
checksum: b39c9e0ef18d0484d537a67551effd02
content_type: application/pdf
creator: ktomasek
date_created: 2021-11-18T15:07:31Z
date_updated: 2022-12-20T23:30:05Z
embargo: 2022-11-18
file_id: '10308'
file_name: ThesisTomasekKathrin.pdf
file_size: 13266088
relation: main_file
- access_level: closed
checksum: c0c440ee9e5ef1102a518a4f9f023e7c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: ktomasek
date_created: 2021-11-18T15:07:46Z
date_updated: 2022-12-20T23:30:05Z
embargo_to: open_access
file_id: '10309'
file_name: ThesisTomasekKathrin.docx
file_size: 7539509
relation: source_file
file_date_updated: 2022-12-20T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '73'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10316'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Pathogenic Escherichia coli hijack the host immune response
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10303'
abstract:
- lang: eng
text: 'Nitrogen is an essential macronutrient determining plant growth, development
and affecting agricultural productivity. Root, as a hub that perceives and integrates
local and systemic signals on the plant’s external and endogenous nitrogen resources,
communicates with other plant organs to consolidate their physiology and development
in accordance with actual nitrogen balance. Over the last years, numerous studies
demonstrated that these comprehensive developmental adaptations rely on the interaction
between pathways controlling nitrogen homeostasis and hormonal networks acting
globally in the plant body. However, molecular insights into how the information
about the nitrogen status is translated through hormonal pathways into specific
developmental output are lacking. In my work, I addressed so far poorly understood
mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment
of shoot growth and development after nitrate provision. Applying a combination
of molecular, cell, and developmental biology approaches, genetics and grafting
experiments as well as hormonal analytics, I identified and characterized an unknown
molecular framework orchestrating shoot development with a root nitrate sensory
system. '
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
citation:
ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303
apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303
chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.
ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science
and Technology Austria, 2021.
ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of
Science and Technology Austria.
mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.
short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science
and Technology Austria, 2021.
date_created: 2021-11-18T11:20:59Z
date_published: 2021-11-22T00:00:00Z
date_updated: 2023-09-19T14:42:45Z
day: '22'
ddc:
- '580'
- '581'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10303
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language:
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page: '139'
publication_identifier:
issn:
- 2663-337X
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publisher: Institute of Science and Technology Austria
related_material:
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- id: '47'
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status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Role of hormones in nitrate regulated growth
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image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9962'
abstract:
- lang: eng
text: The brain is one of the largest and most complex organs and it is composed
of billions of neurons that communicate together enabling e.g. consciousness.
The cerebral cortex is the largest site of neural integration in the central nervous
system. Concerted radial migration of newly born cortical projection neurons,
from their birthplace to their final position, is a key step in the assembly of
the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal
migration in vivo are however still unclear. Recent evidence suggests that distinct
signaling cues act cell-autonomously but differentially at certain steps during
the overall migration process. Moreover, functional analysis of genetic mosaics
(mutant neurons present in wild-type/heterozygote environment) using the MADM
(Mosaic Analysis with Double Markers) analyses in comparison to global knockout
also indicate a significant degree of non-cell-autonomous and/or community effects
in the control of cortical neuron migration. The interactions of cell-intrinsic
(cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely
unknown. In part of this thesis work we established a MADM-based experimental
strategy for the quantitative analysis of cell-autonomous gene function versus
non-cell-autonomous and/or community effects. The direct comparison of mutant
neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional
and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively
analyze non-cell-autonomous effects. Such analysis enable the high-resolution
analysis of projection neuron migration dynamics in distinct environments with
concomitant isolation of genomic and proteomic profiles. Using these experimental
paradigms and in combination with computational modeling we show and characterize
the nature of non-cell-autonomous effects to coordinate radial neuron migration.
Furthermore, this thesis discusses recent developments in neurodevelopment with
focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal
migration.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
citation:
ama: Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in
radial projection neuron migration. 2021. doi:10.15479/at:ista:9962
apa: Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous
effects in radial projection neuron migration. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:9962
chicago: Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous
Effects in Radial Projection Neuron Migration.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:9962.
ieee: A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration,” Institute of Science and Technology Austria,
2021.
ista: Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration. Institute of Science and Technology Austria.
mla: Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:9962.
short: A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration, Institute of Science and Technology Austria,
2021.
date_created: 2021-08-29T12:36:50Z
date_published: 2021-09-02T00:00:00Z
date_updated: 2023-09-22T09:58:30Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SiHi
doi: 10.15479/at:ista:9962
file:
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file_id: '9971'
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keyword:
- Neuronal migration
- Non-cell-autonomous
- Cell-autonomous
- Neurodevelopmental disease
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '182'
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8569'
relation: part_of_dissertation
status: public
- id: '960'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Cell-autonomous gene function and non-cell-autonomous effects in radial projection
neuron migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10083'
abstract:
- lang: eng
text: "Plant motions occur across a wide spectrum of timescales, ranging from seed
dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term
adaptation of gross architecture. Relatively fast motions include water-driven
growth as exemplified by root cell expansion under abiotic/biotic stresses or
during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered
by the phytohormone auxin. However, the cellular and molecular mechanisms are
still largely unknown. This thesis covers the studies about this topic as follows.
By taking advantage of microfluidics combined with live imaging, pharmaceutical
tools, and transgenic lines, we examined the kinetics of and causal relationship
among various auxininduced rapid cellular changes in root growth, apoplastic pH,
cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology.
We revealed that CMT reorientation and vacuolar constriction are the consequence
of growth itself instead of responding directly to auxin. In contrast, auxin induces
apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered
apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+
inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling.
To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined
microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct
a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway
is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we
uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface
signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during
auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly
activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract
instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and
TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and
TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore
the relation of two signaling pathways. Assisted with biochemistry and fluorescent
imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with
each other. The ability of TIR1/AFB binding to membrane lipid provides a basis
for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides,
transgenic analysis combined with genetic engineering and biochemistry showed
that vi\r\nthey do function in the same pathway. Particularly, auxin-induced
TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely,
TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling.
To follow the study of rapid growth regulation, we analyzed another rapid growth
regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid
and reversible growth inhibition caused by H + influx, highly resembling but not
dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression
of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1
hour, contributing to the sustained RALF1-triggered growth inhibition. These studies
collectively contribute to understanding rapid regulation on plant cell\r\ngrowth,
novel auxin signaling pathway as well as auxin-peptide crosstalk. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lanxin
full_name: Li, Lanxin
last_name: Li
citation:
ama: Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083
apa: Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083
chicago: Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of
Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.
ieee: L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science
and Technology Austria, 2021.
ista: Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science
and Technology Austria.
mla: Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of
Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.
short: L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science
and Technology Austria, 2021.
date_created: 2021-10-04T13:33:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2023-10-31T19:30:02Z
day: '06'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:10083
ec_funded: 1
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date_created: 2021-10-14T08:00:07Z
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creator: cchlebak
date_created: 2021-10-14T08:00:13Z
date_updated: 2022-12-20T23:30:03Z
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language:
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month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '442'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '9287'
relation: part_of_dissertation
status: public
- id: '8283'
relation: part_of_dissertation
status: public
- id: '8986'
relation: part_of_dissertation
status: public
- id: '6627'
relation: part_of_dissertation
status: public
- id: '10095'
relation: part_of_dissertation
status: public
- id: '10015'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Rapid cell growth regulation in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10293'
abstract:
- lang: eng
text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism
for explaining the evolution of cooperation among unrelated individuals. In contrast
to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally
cooperating by using their own experiences, indirect reciprocity is based on individuals’
reputations. If a player helps another, this increases the helper’s public standing,
benefitting them in the future. This lets cooperation in the population emerge
without individuals having to meet more than once. While the two modes of reciprocity
are intertwined, they are difficult to compare. Thus, they are usually studied
in isolation. Direct reciprocity can maintain cooperation with simple strategies,
and is robust against noise even when players do not remember more\r\nthan their
partner’s last action. Meanwhile, indirect reciprocity requires its successful
strategies, or social norms, to be more complex. Exhaustive search previously
identified eight such norms, called the “leading eight”, which excel at maintaining
cooperation. However, as the first result of this thesis, we show that the leading
eight break down once we remove the fundamental assumption that information is
synchronized and public, such that everyone agrees on reputations. Once we consider
a more realistic scenario of imperfect information, where reputations are private,
and individuals occasionally misinterpret or miss observations, the leading eight
do not promote cooperation anymore. Instead, minor initial disagreements can proliferate,
fragmenting populations into subgroups. In a next step, we consider ways to mitigate
this issue. We first explore whether introducing “generosity” can stabilize cooperation
when players use the leading eight strategies in noisy environments. This approach
of modifying strategies to include probabilistic elements for coping with errors
is known to work well in direct reciprocity. However, as we show here, it fails
for the more complex norms of indirect reciprocity. Imperfect information still
prevents cooperation from evolving. On the other hand, we succeeded to show in
this thesis that modifying the leading eight to use “quantitative assessment”,
i.e. tracking reputation scores on a scale beyond good and bad, and making overall
judgments of others based on a threshold, is highly successful, even when noise
increases in the environment. Cooperation can flourish when reputations\r\nare
more nuanced, and players have a broader understanding what it means to be “good.”
Finally, we present a single theoretical framework that unites the two modes of
reciprocity despite their differences. Within this framework, we identify a novel
simple and successful strategy for indirect reciprocity, which can cope with noisy
environments and has an analogue in direct reciprocity. We can also analyze decision
making when different sources of information are available. Our results help highlight
that for sustaining cooperation, already the most simple rules of reciprocity
can be sufficient."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
citation:
ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect
information. 2021. doi:10.15479/at:ista:10293
apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293
chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.
ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect
information,” Institute of Science and Technology Austria, 2021.
ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria.
mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:10293.
short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect
Information, Institute of Science and Technology Austria, 2021.
date_created: 2021-11-15T17:12:57Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2023-11-07T08:28:29Z
day: '17'
ddc:
- '519'
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrCh
doi: 10.15479/at:ista:10293
ec_funded: 1
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language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '171'
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _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_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9997'
relation: part_of_dissertation
status: public
- id: '2'
relation: part_of_dissertation
status: public
- id: '9402'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Evolution of cooperation via (in)direct reciprocity under imperfect information
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10135'
abstract:
- lang: eng
text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically
throughout their whole life and thereby flexibly adapt to ever-changing environmental
conditions. Plant hormones auxin and cytokinin are the main regulators of the
lateral root organogenesis. Additionally to their solo activities, the interaction
between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root
development and growth. In particular, cytokinin modulates auxin distribution
within the developing lateral root by affecting the endomembrane trafficking of
auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al.,
2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore,
it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational
level. Impact of cytokinin and other plant hormones on auxin transporters (including
PIN1) on the posttranslational level is described in detail in the introduction
part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights
into the molecular machinery underlying cytokinin effect on the endomembrane trafficking
in the plant cell, in particular on the PIN1 degradation, we conducted two large
proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical
proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin
treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A).
We found that DRP2A plays a role in cytokinin regulated processes during the plant
growth and that cytokinin treatment promotes destabilization of DRP2A protein.
However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In
the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial
role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation.
Altogether, we identified proteins, which bind to cytokinin and proteins that
in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation
pattern. By combining information from these two screens, we can pave our way
towards understanding of noncanonical cytokinin effects."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hana
full_name: Semerádová, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semerádová
citation:
ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135
apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:10135
chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:10135.
ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis,” Institute of Science and Technology
Austria, 2021.
ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria.
mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:10135.
short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology
Austria, 2021.
date_created: 2021-10-13T13:42:48Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-01-25T10:53:29Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10135
file:
- access_level: closed
checksum: ce7108853e6cec6224f17cd6429b51fe
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date_updated: 2022-12-20T23:30:05Z
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file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx
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date_created: 2021-10-27T07:45:57Z
date_updated: 2022-12-20T23:30:05Z
embargo: 2022-10-28
file_id: '10187'
file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf
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file_date_updated: 2022-12-20T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis.
publication_identifier:
isbn:
- 978-3-99078-014-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to
coordinate plant organogenesis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9728'
abstract:
- lang: eng
text: "Most real-world flows are multiphase, yet we know little about them compared
to their single-phase counterparts. Multiphase flows are more difficult to investigate
as their dynamics occur in large parameter space and involve complex phenomena
such as preferential concentration, turbulence modulation, non-Newtonian rheology,
etc. Over the last few decades, experiments in particle-laden flows have taken
a back seat in favour of ever-improving computational resources. However, computers
are still not powerful enough to simulate a real-world fluid with millions of
finite-size particles. Experiments are essential not only because they offer a
reliable way to investigate real-world multiphase flows but also because they
serve to validate numerical studies and steer the research in a relevant direction.
In this work, we have experimentally investigated particle-laden flows in pipes,
and in particular, examined the effect of particles on the laminar-turbulent transition
and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows,
an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic)
transition that occurs via localised turbulent structures called puffs is affected
by the addition of particles. In this study, in addition to this known transition,
we found a super-critical transition to a globally fluctuating state with increasing
particle concentration. At the same time, the Newtonian-type transition via puffs
is delayed to larger Reynolds numbers. At an even higher concentration, only the
globally fluctuating state is found. The dynamics of particle-laden flows are
hence determined by two competing instabilities that give rise to three flow regimes:
Newtonian-type turbulence at low, a particle-induced globally fluctuating state
at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect
of particles on turbulent drag is ambiguous, with studies reporting drag reduction,
no net change, and even drag increase. The ambiguity arises because, in addition
to particle concentration, particle shape, size, and density also affect the net
drag. Even similar particles might affect the flow dissimilarly in different Reynolds
number and concentration ranges. In the present study, we explored a wide range
of both Reynolds number and concentration, using spherical as well as cylindrical
particles. We found that the spherical particles do not reduce drag while the
cylindrical particles are drag-reducing within a specific Reynolds number interval.
The interval strongly depends on the particle concentration and the relative size
of the pipe and particles. Within this interval, the magnitude of drag reduction
reaches a maximum. These drag reduction maxima appear to fall onto a distinct
power-law curve irrespective of the pipe diameter and particle concentration,
and this curve can be considered as the maximum drag reduction asymptote for a
given fibre shape. Such an asymptote is well known for polymeric flows but had
not been identified for particle-laden flows prior to this work."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nishchal
full_name: Agrawal, Nishchal
id: 469E6004-F248-11E8-B48F-1D18A9856A87
last_name: Agrawal
citation:
ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe
flows. 2021. doi:10.15479/at:ista:9728
apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728
chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.
ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden
pipe flows,” Institute of Science and Technology Austria, 2021.
ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria.
mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.
short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows, Institute of Science and Technology Austria, 2021.
date_created: 2021-07-27T13:40:30Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2024-02-28T13:14:39Z
day: '29'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:9728
file:
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checksum: 77436be3563a90435024307b1b5ee7e8
content_type: application/x-zip-compressed
creator: nagrawal
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date_updated: 2022-07-29T22:30:05Z
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file_size: 22859658
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creator: nagrawal
date_created: 2021-07-28T13:32:05Z
date_updated: 2022-07-29T22:30:05Z
embargo: 2022-07-28
file_id: '9745'
file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf
file_size: 18658048
relation: main_file
file_date_updated: 2022-07-29T22:30:05Z
has_accepted_license: '1'
keyword:
- Drag Reduction
- Transition to Turbulence
- Multiphase Flows
- particle Laden Flows
- Complex Flows
- Experiments
- Fluid Dynamics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '118'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6189'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Transition to turbulence and drag reduction in particle-laden pipe flows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '7629'
abstract:
- lang: eng
text: "This thesis is based on three main topics: In the first part, we study convergence
of discrete gradient flow structures associated with regular finite-volume discretisations
of Fokker-Planck equations. We show evolutionary I convergence of the discrete
gradient flows to the L2-Wasserstein gradient flow corresponding to the solution
of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument,
we prove Mosco- and I-convergence results for discrete energy functionals, which
are of independent interest for convergence of equivalent gradient flow structures
in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric
graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein
distance, which is proved via a regularisation scheme for solutions of the continuity
equation, adapted to the peculiar geometric structure of metric graphs. Based
on those results, we show that the L2-Wasserstein space over a metric graph admits
a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn
the third part, we focus again on the discrete gradient flows, already encountered
in the first part. We propose a variational structure which extends the gradient
flow structure to Markov chains violating the detailed-balance conditions. Using
this structure, we characterise contraction estimates for the discrete heat flow
in terms of convexity of\r\ncorresponding path-dependent energy functionals. In
addition, we use this approach to derive several functional inequalities for said
functionals."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dominik L
full_name: Forkert, Dominik L
id: 35C79D68-F248-11E8-B48F-1D18A9856A87
last_name: Forkert
citation:
ama: Forkert DL. Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629
apa: Forkert, D. L. (2020). Gradient flows in spaces of probability measures
for finite-volume schemes, metric graphs and non-reversible Markov chains.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629
chicago: Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for
Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.
ieee: D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains,” Institute of Science
and Technology Austria, 2020.
ista: Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains. Institute of Science
and Technology Austria.
mla: Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for
Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.
short: D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume
Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science
and Technology Austria, 2020.
date_created: 2020-04-02T06:40:23Z
date_published: 2020-03-31T00:00:00Z
date_updated: 2023-09-07T13:03:12Z
day: '31'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: JaMa
doi: 10.15479/AT:ISTA:7629
ec_funded: 1
file:
- access_level: open_access
checksum: c814a1a6195269ca6fe48b0dca45ae8a
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T10:47:59Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7657'
file_name: Thesis_Forkert_PDFA.pdf
file_size: 3297129
relation: main_file
- access_level: closed
checksum: ceafb53f923d1b5bdf14b2b0f22e4a81
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-04-14T10:47:59Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7658'
file_name: Thesis_Forkert_source.zip
file_size: 1063908
relation: source_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '154'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: Gradient flows in spaces of probability measures for finite-volume schemes,
metric graphs and non-reversible Markov chains
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8574'
abstract:
- lang: eng
text: "This thesis concerns itself with the interactions of evolutionary and ecological
forces and the consequences on genetic diversity and the ultimate survival of
populations. It is important to understand what signals processes \r\nleave on
the genome and what we can infer from such data, which is usually abundant but
noisy. Furthermore, understanding how and when populations adapt or go extinct
is important for practical purposes, such as the genetic management of populations,
as well as for theoretical questions, since local adaptation can be the first
step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy
to approximate the demographic changes of a population in a simple setting, namely
the logistic growth model with immigration. We show that this method is not only
a powerful \r\ntool in physics but can be gainfully applied in an ecological framework.
We investigate how well it approximates the real \r\nbehavior of the system, and
find that is does so, even in unexpected situations. Finally, we illustrate how
it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution
of allele frequencies and population sizes in an infinite island model.\r\nWe
give conditions under which polygenic adaptation to a rare habitat is possible.
The model we use is based on the diffusion approximation, considers eco-evolutionary
feedback mechanisms (hard selection), and treats both \r\ndrift and environmental
fluctuations explicitly. We also look at limiting scenarios, for which we derive
analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation
tool to obtain patterns of diversity in a spatially explicit subdivided population,
in which the demographic history of each subpopulation can be specified. We compare
\r\nthe results to existing predictions, and explore the relative importance of
time and space under a variety of spatial arrangements and demographic histories,
such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook
to further research. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
citation:
ama: Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574
apa: Szep, E. (2020). Local adaptation in metapopulations. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574
chicago: Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science
and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.
ieee: E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology
Austria, 2020.
ista: Szep E. 2020. Local adaptation in metapopulations. Institute of Science and
Technology Austria.
mla: Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science
and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.
short: E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology
Austria, 2020.
date_created: 2020-09-28T07:33:38Z
date_published: 2020-09-20T00:00:00Z
date_updated: 2023-09-07T13:11:39Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:8574
file:
- access_level: open_access
checksum: 20e71f015fbbd78fea708893ad634ed0
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T07:25:35Z
date_updated: 2020-09-28T07:25:35Z
file_id: '8575'
file_name: thesis_EnikoSzep_final.pdf
file_size: 6354833
relation: main_file
success: 1
- access_level: closed
checksum: a8de2c14a1bb4e53c857787efbb289e1
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-09-28T07:25:37Z
date_updated: 2020-09-28T07:25:37Z
file_id: '8576'
file_name: thesisFiles_EnikoSzep.zip
file_size: 23020401
relation: source_file
file_date_updated: 2020-09-28T07:25:37Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '158'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Local adaptation in metapopulations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7514'
abstract:
- lang: eng
text: "We study the interacting homogeneous Bose gas in two spatial dimensions in
the thermodynamic limit at fixed density. We shall be concerned with some mathematical
aspects of this complicated problem in many-body quantum mechanics. More specifically,
we consider the dilute limit where the scattering length of the interaction potential,
which is a measure for the effective range of the potential, is small compared
to the average distance between the particles. We are interested in a setting
with positive (i.e., non-zero) temperature. After giving a survey of the relevant
literature in the field, we provide some facts and examples to set expectations
for the two-dimensional system. The crucial difference to the three-dimensional
system is that there is no Bose–Einstein condensate at positive temperature due
to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic
formula for the free energy holds similarly to the three-dimensional case.\r\nWe
motivate this formula by considering a toy model with δ interaction potential.
By restricting this model Hamiltonian to certain trial states with a quasi-condensate
we obtain an upper bound for the free energy that still has the quasi-condensate
fraction as a free parameter. When minimizing over the quasi-condensate fraction,
we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity,
which plays an important role in our rigorous contribution. The mathematically
rigorous result that we prove concerns the specific free energy in the dilute
limit. We give upper and lower bounds on the free energy in terms of the free
energy of the non-interacting system and a correction term coming from the interaction.
Both bounds match and thus we obtain the leading term of an asymptotic approximation
in the dilute limit, provided the thermal wavelength of the particles is of the
same order (or larger) than the average distance between the particles. The remarkable
feature of this result is its generality: the correction term depends on the interaction
potential only through its scattering length and it holds for all nonnegative
interaction potentials with finite scattering length that are measurable. In particular,
this allows to model an interaction of hard disks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
citation:
ama: Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514
apa: Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514
chicago: Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514.
ieee: S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute
of Science and Technology Austria, 2020.
ista: Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute
of Science and Technology Austria.
mla: Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.
short: S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute
of Science and Technology Austria, 2020.
date_created: 2020-02-24T09:17:27Z
date_published: 2020-02-24T00:00:00Z
date_updated: 2023-09-07T13:12:42Z
day: '24'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: RoSe
- _id: GradSch
doi: 10.15479/AT:ISTA:7514
ec_funded: 1
file:
- access_level: open_access
checksum: b4de7579ddc1dbdd44ff3f17c48395f6
content_type: application/pdf
creator: dernst
date_created: 2020-02-24T09:15:06Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7515'
file_name: thesis.pdf
file_size: 1563429
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checksum: ad7425867b52d7d9e72296e87bc9cb67
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-02-24T09:15:16Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7516'
file_name: thesis_source.zip
file_size: 2028038
relation: source_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '148'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7524'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: The free energy of a dilute two-dimensional Bose gas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8353'
abstract:
- lang: eng
text: "Mrp (Multi resistance and pH adaptation) are broadly distributed secondary
active antiporters that catalyze the transport of monovalent ions such as sodium
and potassium outside of the cell coupled to the inward translocation of protons.
Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG)
encoded in a single operon, whereas other antiporters catalyzing the same reaction
are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular
pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline
environments and for reduction of the intracellular concentration of toxic cations.
Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp
subunits have primary sequence similarity to essential redox-driven proton pumps,
such as respiratory complex I and membrane-bound hydrogenases. This similarity
reinforces the hypothesis that these present day redox-driven proton pumps are
descended from the Mrp antiporter. The Mrp structure serves as a model to understand
the yet obscure coupling mechanism between ion or electron transfer and proton
translocation in this large group of proteins. In the thesis, I am presenting
the purification, biochemical analysis, cryo-EM analysis and molecular structure
of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å
resolution. Numerous conditions were screened to purify Mrp to high homogeneity
and to obtain an appropriate distribution of single particles on cryo-EM grids
covered with a continuous layer of ultrathin carbon. A preferred particle orientation
problem was solved by performing a tilted data collection. The activity assays
showed the specific pH-dependent\r\nprofile of secondary active antiporters. The
molecular structure shows that Mrp is a dimer of seven-subunit protomers with
50 trans-membrane helices each. The dimer interface is built by many short and
tilted transmembrane helices, probably causing a thinning of the bacterial membrane.
The surface charge distribution shows an extraordinary asymmetry within each monomer,
revealing presumable proton and sodium translocation pathways. The two largest\r\nand
homologous Mrp subunits MrpA and MrpD probably translocate one proton each into
the cell. The sodium ion is likely being translocated in the opposite direction
within the small subunits along a ladder of charged and conserved residues. Based
on the structure, we propose a mechanism were the antiport activity is accomplished
via electrostatic interactions between the charged cations and key charged residues.
The flexible key TM helices coordinate these\r\nelectrostatic interactions, while
the membrane thinning between the monomers enables the translocation of sodium
across the charged membrane. The entire family of redox-driven proton pumps is
likely to perform their mechanism in a likewise manner."
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
acknowledgement: "I acknowledge the scientific service units of the IST Austria for
providing resources by the Life Science Facility, the Electron Microscopy Facility
and the high-performance computer cluster. Special thanks to the cryo-EM specialists
Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front
of the microscope and for supporting me to collect the data presented here. I also
want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from
Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian
Academy of Sciences."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Steiner, Julia
id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
last_name: Steiner
orcid: 0000-0003-0493-3775
citation:
ama: Steiner J. Biochemical and structural investigation of the Mrp antiporter,
an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353
apa: Steiner, J. (2020). Biochemical and structural investigation of the Mrp
antiporter, an ancestor of complex I. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:8353
chicago: Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter,
an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020.
https://doi.org/10.15479/AT:ISTA:8353.
ieee: J. Steiner, “Biochemical and structural investigation of the Mrp antiporter,
an ancestor of complex I,” Institute of Science and Technology Austria, 2020.
ista: Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter,
an ancestor of complex I. Institute of Science and Technology Austria.
mla: Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter,
an Ancestor of Complex I. Institute of Science and Technology Austria, 2020,
doi:10.15479/AT:ISTA:8353.
short: J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter,
an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-09T14:27:01Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2023-09-07T13:14:09Z
day: '09'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: LeSa
doi: 10.15479/AT:ISTA:8353
file:
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file_id: '8355'
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has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: None
page: '191'
project:
- _id: 26169496-B435-11E9-9278-68D0E5697425
grant_number: '24741'
name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex
I
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8284'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
title: Biochemical and structural investigation of the Mrp antiporter, an ancestor
of complex I
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8589'
abstract:
- lang: eng
text: The plant hormone auxin plays indispensable roles in plant growth and development.
An essential level of regulation in auxin action is the directional auxin transport
within cells. The establishment of auxin gradient in plant tissue has been attributed
to local auxin biosynthesis and directional intercellular auxin transport, which
both are controlled by various environmental and developmental signals. It is
well established that asymmetric auxin distribution in cells is achieved by polarly
localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights
into cellular mechanisms of PIN polarization obtained from the last decades, the
molecular mechanism and specific regulators mediating PIN polarization remains
elusive. In this thesis, we aim to find novel players in PIN subcellular polarity
regulation during Arabidopsis development. We first characterize the physiological
effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and
PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling
pathway in shoot gravitropism bending termination. In addition, we also explore
the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation
on PIN polarity. In Chapter 1, we give an overview of the current knowledge about
PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we
study the physiological effect of PA on shoot gravitropic bending. Our results
show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering
with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending
hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear
auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization
and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics
approach and identify the motor protein Myosin XI and its binding protein, the
MadB2 family, as an essential regulator of PIN polarity for auxin-canalization
related developmental processes. In Chapter 5, we demonstrate the vital role of
actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular
trafficking. Overall, the data presented in this PhD thesis brings novel insights
into the PIN polar localization regulation that resulted in the (re)establishment
of the polar auxin flow and gradient in response to environmental stimuli during
plant development.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: I also want to thank the China Scholarship Council for supporting
my study during the year from 2015 to 2019. I also want to thank IST facilities
– the Bioimaging facility, the media kitchen, the plant facility and all of the
campus services, for their support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
citation:
ama: Han H. Novel insights into PIN polarity regulation during Arabidopsis development.
2020. doi:10.15479/AT:ISTA:8589
apa: Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis
development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589
chicago: Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis
Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.
ieee: H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,”
Institute of Science and Technology Austria, 2020.
ista: Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis
development. Institute of Science and Technology Austria.
mla: Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis
Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.
short: H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development,
Institute of Science and Technology Austria, 2020.
date_created: 2020-09-30T14:50:51Z
date_published: 2020-09-30T00:00:00Z
date_updated: 2023-09-07T13:13:05Z
day: '30'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/AT:ISTA:8589
file:
- access_level: closed
checksum: c4bda1947d4c09c428ac9ce667b02327
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2020-09-30T14:50:20Z
date_updated: 2020-09-30T14:50:20Z
file_id: '8590'
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creator: dernst
date_created: 2020-09-30T14:49:59Z
date_updated: 2021-10-01T13:33:02Z
file_id: '8591'
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language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '164'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7643'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Novel insights into PIN polarity regulation during Arabidopsis development
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8155'
abstract:
- lang: eng
text: "In the thesis we focus on the interplay of the biophysics and evolution of
gene regulation. We start by addressing how the type of prokaryotic gene regulation
– activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional
crosstalk. We propose that regulatory interference caused by excess regulatory
proteins in the dense cellular medium – global crosstalk – could be a factor in
determining which type of gene regulatory network is evolutionarily preferred.
Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium
enhancer models that optimize so-called regulatory phenotypes. We find a class
of models that differ from standard thermodynamic equilibrium models by a single
parameter that notably increases the regulatory performance. Next chapter addresses
the question of genotype-phenotype-fitness maps of higher dimensional phenotypes.
We show that our biophysically realistic approach allows us to understand how
the mechanisms of promoter function constrain genotypephenotype maps, and how
they affect the evolutionary trajectories of promoters.\r\nIn the last chapter
we ask whether the intrinsic instability of gene duplication and amplification
provides a generic alternative to canonical gene regulation. Using mathematical
modeling, we show that amplifications can tune gene expression in many environments,
including those where transcription factor-based schemes are\r\nhard to evolve
or maintain. "
acknowledgement: For the duration of his PhD, Rok was a recipient of a DOC fellowship
of the Austrian Academy of Sciences.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
citation:
ama: Grah R. Gene regulation across scales – how biophysical constraints shape evolution.
2020. doi:10.15479/AT:ISTA:8155
apa: Grah, R. (2020). Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155
chicago: Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints
Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.
ieee: R. Grah, “Gene regulation across scales – how biophysical constraints shape
evolution,” Institute of Science and Technology Austria, 2020.
ista: Grah R. 2020. Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria.
mla: Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.
short: R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution, Institute of Science and Technology Austria, 2020.
date_created: 2020-07-23T09:51:28Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2023-09-07T13:13:27Z
day: '24'
ddc:
- '530'
- '570'
degree_awarded: PhD
department:
- _id: CaGu
- _id: GaTk
doi: 10.15479/AT:ISTA:8155
file:
- access_level: open_access
content_type: application/pdf
creator: rgrah
date_created: 2020-07-27T12:00:07Z
date_updated: 2020-07-27T12:00:07Z
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file_size: 16638998
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creator: rgrah
date_created: 2020-07-27T12:02:23Z
date_updated: 2020-07-30T13:04:55Z
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has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '310'
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7675'
relation: part_of_dissertation
status: public
- id: '7569'
relation: part_of_dissertation
status: public
- id: '7652'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Gene regulation across scales – how biophysical constraints shape evolution
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7460'
abstract:
- lang: eng
text: "Many methods for the reconstruction of shapes from sets of points produce
ordered simplicial complexes, which are collections of vertices, edges, triangles,
and their higher-dimensional analogues, called simplices, in which every simplex
gets assigned a real value measuring its size. This thesis studies ordered simplicial
complexes, with a focus on their topology, which reflects the connectedness of
the represented shapes and the presence of holes. We are interested both in understanding
better the structure of these complexes, as well as in developing algorithms for
applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure
for a simplex is the radius of the smallest empty circumsphere. Based on it, we
revisit Alpha and Wrap complexes and experimentally determine their probabilistic
properties for random data. Also, we prove the existence of tri-partitions, propose
algorithms to open and close holes, and extend the concepts from Euclidean to
Bregman geometries."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katharina
full_name: Ölsböck, Katharina
id: 4D4AA390-F248-11E8-B48F-1D18A9856A87
last_name: Ölsböck
orcid: 0000-0002-4672-8297
citation:
ama: Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460
apa: Ölsböck, K. (2020). The hole system of triangulated shapes. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460
chicago: Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.
ieee: K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science
and Technology Austria, 2020.
ista: Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science
and Technology Austria.
mla: Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.
short: K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science
and Technology Austria, 2020.
date_created: 2020-02-06T14:56:53Z
date_published: 2020-02-10T00:00:00Z
date_updated: 2023-09-07T13:15:30Z
day: '10'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: HeEd
- _id: GradSch
doi: 10.15479/AT:ISTA:7460
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description: latex source files, figures
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keyword:
- shape reconstruction
- hole manipulation
- ordered complexes
- Alpha complex
- Wrap complex
- computational topology
- Bregman geometry
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '155'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6608'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: The hole system of triangulated shapes
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7896'
abstract:
- lang: eng
text: "A search problem lies in the complexity class FNP if a solution to the given
instance of the problem can be verified efficiently. The complexity class TFNP
consists of all search problems in FNP that are total in the sense that a solution
is guaranteed to exist. TFNP contains a host of interesting problems from fields
such as algorithmic game theory, computational topology, number theory and combinatorics.
Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead,
one studies its syntactic subclasses which are defined based on the combinatorial
principle used to argue totality. Of particular interest is the subclass PPAD,
which contains important problems\r\nlike computing Nash equilibrium for bimatrix
games and computational counterparts of several fixed-point theorems as complete.
In the thesis, we undertake the study of averagecase hardness of TFNP, and in
particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness
of PPAD before a series of recent results showed how to achieve it using a cryptographic
primitive called program obfuscation.\r\nHowever, it is currently not known how
to construct program obfuscation from standard cryptographic assumptions. Therefore,
it is desirable to relax the assumption under which average-case hardness of PPAD
can be shown. In the thesis we take a step in this direction. First, we show that
assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to
factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average
in the random-oracle model. Then we strengthen this result to show that the average-case
hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform,
a well-known technique used to compile a public-coin interactive protocol into
a non-interactive one. As a corollary, we obtain average-case hardness for PPAD
in the random-oracle model assuming the worst-case hardness of #SAT. Moreover,
the above results can all be strengthened to obtain average-case hardness for
the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable
procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable,
we mean that every intermediate state of the computation includes a proof of its
correctness, and the proof can be updated and verified in polynomial time. Previous
constructions of such procedures relied on strong, non-standard assumptions. Instead,
we introduce a technique called recursive proof-merging to obtain the same from
weaker assumptions. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
citation:
ama: Kamath Hosdurg C. On the average-case hardness of total search problems. 2020.
doi:10.15479/AT:ISTA:7896
apa: Kamath Hosdurg, C. (2020). On the average-case hardness of total search
problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896
chicago: Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search
Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.
ieee: C. Kamath Hosdurg, “On the average-case hardness of total search problems,”
Institute of Science and Technology Austria, 2020.
ista: Kamath Hosdurg C. 2020. On the average-case hardness of total search problems.
Institute of Science and Technology Austria.
mla: Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.
short: C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems,
Institute of Science and Technology Austria, 2020.
date_created: 2020-05-26T14:08:55Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2023-09-07T13:15:55Z
day: '25'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrPi
doi: 10.15479/AT:ISTA:7896
ec_funded: 1
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creator: dernst
date_created: 2020-05-26T14:08:23Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7898'
file_name: Thesis_Kamath.zip
file_size: 15301529
relation: source_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '126'
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6677'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: On the average-case hardness of total search problems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7944'
abstract:
- lang: eng
text: "This thesis considers two examples of reconfiguration problems: flipping
edges in edge-labelled triangulations of planar point sets and swapping labelled
tokens placed on vertices of a graph. In both cases the studied structures – all
the triangulations of a given point set or all token placements on a given graph
– can be thought of as vertices of the so-called reconfiguration graph, in which
two vertices are adjacent if the corresponding structures differ by a single elementary
operation – by a flip of a diagonal in a triangulation or by a swap of tokens
on adjacent vertices, respectively. We study the reconfiguration of one instance
of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor
triangulations of point sets in which each edge has a unique label and a flip
transfers the label from the removed edge to the new edge, we prove a polynomial-time
testable condition, called the Orbit Theorem, that characterizes when two triangulations
of the same point set lie in the same connected component of the reconfiguration
graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot.
We additionally provide a polynomial time algorithm that computes a reconfiguring
flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties
of a certain high-dimensional cell complex that has the usual reconfiguration
graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph,
we make partial progress on the problem of finding shortest reconfiguration sequences.
We disprove the so-called Happy Leaf Conjecture and demonstrate the importance
of swapping tokens that are already placed at the correct vertices. We also prove
that a generalization of the problem to weighted coloured token swapping is NP-hard
on trees but solvable in polynomial time on paths and stars."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
citation:
ama: Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944
apa: Masárová, Z. (2020). Reconfiguration problems. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944
chicago: Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and
Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.
ieee: Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology
Austria, 2020.
ista: Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology
Austria.
mla: Masárová, Zuzana. Reconfiguration Problems. Institute of Science and
Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.
short: Z. Masárová, Reconfiguration Problems, Institute of Science and Technology
Austria, 2020.
date_created: 2020-06-08T00:49:46Z
date_published: 2020-06-09T00:00:00Z
date_updated: 2023-09-07T13:17:37Z
day: '09'
ddc:
- '516'
- '514'
degree_awarded: PhD
department:
- _id: HeEd
- _id: UlWa
doi: 10.15479/AT:ISTA:7944
file:
- access_level: open_access
checksum: df688bc5a82b50baee0b99d25fc7b7f0
content_type: application/pdf
creator: zmasarov
date_created: 2020-06-08T00:34:00Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7945'
file_name: THESIS_Zuzka_Masarova.pdf
file_size: 13661779
relation: main_file
- access_level: closed
checksum: 45341a35b8f5529c74010b7af43ac188
content_type: application/zip
creator: zmasarov
date_created: 2020-06-08T00:35:30Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7946'
file_name: THESIS_Zuzka_Masarova_SOURCE_FILES.zip
file_size: 32184006
relation: source_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
keyword:
- reconfiguration
- reconfiguration graph
- triangulations
- flip
- constrained triangulations
- shellability
- piecewise-linear balls
- token swapping
- trees
- coloured weighted token swapping
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: '160'
publication_identifier:
isbn:
- 978-3-99078-005-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7950'
relation: part_of_dissertation
status: public
- id: '5986'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Reconfiguration problems
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8341'
abstract:
- lang: eng
text: "One of the most striking hallmarks of the eukaryotic cell is the presence
of intracellular vesicles and organelles. Each of these membrane-enclosed compartments
has a distinct composition of lipids and proteins, which is essential for accurate
membrane traffic and homeostasis. Interestingly, their biochemical identities
are achieved with the help\r\nof small GTPases of the Rab family, which cycle
between GDP- and GTP-bound forms on the selected membrane surface. While this
activity switch is well understood for an individual protein, how Rab GTPases
collectively transition between states to generate decisive signal propagation
in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution
experiments with theoretical modeling to systematically study a minimal Rab5 activation
network from bottom-up. We find that positive feedback based on known molecular
interactions gives rise to bistable GTPase activity switching on system’s scale.
Furthermore, we determine that collective transition near the critical\r\npoint
is intrinsically stochastic and provide evidence that the inactive Rab5 abundance
on the membrane can shape the network response. Finally, we demonstrate that collective
switching can spread on the lipid bilayer as a traveling activation wave, representing
a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings
reveal new insights into the self-organization properties of signaling networks
away from chemical equilibrium. Our work highlights the importance of systematic
characterization of biochemical systems in well-defined physiological conditions.
This way, we were able to answer long-standing open questions in the field and
close the gap between regulatory processes on a molecular scale and emergent responses
on system’s level."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: NanoFab
acknowledgement: My thanks goes to the Loose lab members, BioImaging, Life Science
and Nanofabrication Facilities and the wonderful international community at IST
for sharing this experience with me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
citation:
ama: Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341
apa: Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341
chicago: Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.
ieee: U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute
of Science and Technology Austria, 2020.
ista: Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute
of Science and Technology Austria.
mla: Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.
short: U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute
of Science and Technology Austria, 2020.
date_created: 2020-09-08T08:53:53Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2023-09-07T13:17:06Z
day: '08'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MaLo
doi: 10.15479/AT:ISTA:8341
file:
- access_level: closed
checksum: 70871b335a595252a66c6bbf0824fb02
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-09-08T09:00:29Z
date_updated: 2021-09-16T12:49:12Z
file_id: '8342'
file_name: 2020_Urban_Bezeljak_Thesis_TeX.zip
file_size: 65246782
relation: source_file
- access_level: open_access
checksum: 59a62275088b00b7241e6ff4136434c7
content_type: application/pdf
creator: dernst
date_created: 2020-09-08T09:00:27Z
date_updated: 2021-09-16T12:49:12Z
file_id: '8343'
file_name: 2020_Urban_Bezeljak_Thesis.pdf
file_size: 31259058
relation: main_file
file_date_updated: 2021-09-16T12:49:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '215'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7580'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: In vitro reconstitution of a Rab activation switch
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8032'
abstract:
- lang: eng
text: "Algorithms in computational 3-manifold topology typically take a triangulation
as an input and return topological information about the underlying 3-manifold.
However, extracting the desired information from a triangulation (e.g., evaluating
an invariant) is often computationally very expensive. In recent years this complexity
barrier has been successfully tackled in some cases by importing ideas from the
theory of parameterized algorithms into the realm of 3-manifolds. Various computationally
hard problems were shown to be efficiently solvable for input triangulations that
are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial
parameter in the above context: we consider the treewidth of a compact, orientable
3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation
thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito
on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered
triangulations, we establish quantitative relations between the treewidth and
classical topological invariants of a 3-manifold. In particular, among other results,
we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold
is always within a constant factor of its Heegaard genus."
acknowledged_ssus:
- _id: E-Lib
- _id: CampIT
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
citation:
ama: Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020.
doi:10.15479/AT:ISTA:8032
apa: Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032
chicago: Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032.
ieee: K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute
of Science and Technology Austria, 2020.
ista: Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds.
Institute of Science and Technology Austria.
mla: Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.
short: K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute
of Science and Technology Austria, 2020.
date_created: 2020-06-26T10:00:36Z
date_published: 2020-06-26T00:00:00Z
date_updated: 2023-09-07T13:18:27Z
day: '26'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: UlWa
doi: 10.15479/AT:ISTA:8032
file:
- access_level: open_access
checksum: bd8be6e4f1addc863dfcc0fad29ee9c3
content_type: application/pdf
creator: khuszar
date_created: 2020-06-26T10:03:58Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8034'
file_name: Kristof_Huszar-Thesis.pdf
file_size: 2637562
relation: main_file
- access_level: closed
checksum: d5f8456202b32f4a77552ef47a2837d1
content_type: application/x-zip-compressed
creator: khuszar
date_created: 2020-06-26T10:10:06Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8035'
file_name: Kristof_Huszar-Thesis-source.zip
file_size: 7163491
relation: source_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: xviii+120
publication_identifier:
isbn:
- 978-3-99078-006-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6556'
relation: dissertation_contains
status: public
- id: '7093'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Jonathan
full_name: Spreer, Jonathan
last_name: Spreer
title: Combinatorial width parameters for 3-dimensional manifolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8358'
abstract:
- lang: eng
text: "During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like
structure at the center of the cell. This so-called Z-ring acts as a scaffold
recruiting several division-related proteins to mid-cell and plays a key role
in distributing proteins at the division site, a feature driven by the treadmilling
motion of FtsZ filaments around the septum. What regulates the architecture, dynamics
and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins
(Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy
and in vitro reconstitution experiments have helped to shed light into some of
the dynamic properties of these complex systems, but methods that allow to collect
and analyze large quantitative data sets of the underlying polymer dynamics are
still missing.\r\nHere, using an in vitro reconstitution approach, we studied
how different Zaps affect FtsZ filament dynamics and organization into large-scale
patterns, giving special emphasis to the role of the well-conserved protein ZapA.
For this purpose, we use high-resolution fluorescence microscopy combined with
novel image analysis workfows to study pattern organization and polymerization
dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three
diferent spatial scales: the large-scale organization of the membrane-bound filament
network, the underlying\r\npolymerization dynamics and the behavior of single
molecules.\r\nWe found that ZapA cooperatively increases the spatial order of
the filament network, binds only transiently to FtsZ filaments and has no effect
on filament length and treadmilling velocity. Our data provides a model for how
FtsZ-associated proteins can increase the precision and stability of the bacterial
cell division machinery in a\r\nswitch-like manner, without compromising filament
dynamics. Furthermore, we believe that our automated quantitative methods can
be used to analyze a large variety of dynamic cytoskeletal systems, using standard
time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments
in vitro or even inside the living cell.\r\n"
acknowledged_ssus:
- _id: Bio
acknowledgement: I should also express my gratitude to the bioimaging facility at
IST Austria, for their assistance with the TIRF setup over the years, and especially
to Christoph Sommer, who gave me a lot of input when I was starting to dive into
programming.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
citation:
ama: Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in
cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358
apa: Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling
filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358
chicago: Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling
Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of
Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.
ieee: P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments
in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and
Technology Austria, 2020.
ista: Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments
in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and
Technology Austria.
mla: Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments
in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science
and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358.
short: P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments
in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and
Technology Austria, 2020.
date_created: 2020-09-10T09:26:49Z
date_published: 2020-09-10T00:00:00Z
date_updated: 2023-09-07T13:18:51Z
day: '10'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: MaLo
doi: 10.15479/AT:ISTA:8358
file:
- access_level: open_access
checksum: 882f93fe9c351962120e2669b84bf088
content_type: application/pdf
creator: pcaldas
date_created: 2020-09-10T12:11:29Z
date_updated: 2020-09-10T12:11:29Z
file_id: '8364'
file_name: phd_thesis_pcaldas.pdf
file_size: 141602462
relation: main_file
success: 1
- access_level: closed
checksum: 70cc9e399c4e41e6e6ac445ae55e8558
content_type: application/x-zip-compressed
creator: pcaldas
date_created: 2020-09-10T12:18:17Z
date_updated: 2020-09-11T07:48:10Z
file_id: '8365'
file_name: phd_thesis_latex_pcaldas.zip
file_size: 450437458
relation: source_file
file_date_updated: 2020-09-11T07:48:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '135'
publication_identifier:
isbn:
- 978-3-99078-009-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7572'
relation: dissertation_contains
status: public
- id: '7197'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Organization and dynamics of treadmilling filaments in cytoskeletal networks
of FtsZ and its crosslinkers
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8332'
abstract:
- lang: eng
text: "Designing and verifying concurrent programs is a notoriously challenging,
time consuming, and error prone task, even for experts. This is due to the sheer
number of possible interleavings of a concurrent program, all of which have to
be tracked and accounted for in a formal proof. Inventing an inductive invariant
that captures all interleavings of a low-level implementation is theoretically
possible, but practically intractable. We develop a refinement-based verification
framework that provides mechanisms to simplify proof construction by decomposing
the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we
present a foundation for refinement reasoning over structured concurrent programs.
We introduce layered concurrent programs as a compact notation to represent multi-layer
refinement proofs. A layered concurrent program specifies a sequence of connected
concurrent programs, from most concrete to most abstract, such that common parts
of different programs are written exactly once. Each program in this sequence
is expressed as structured concurrent program, i.e., a program over (potentially
recursive) procedures, imperative control flow, gated atomic actions, structured
parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based
verifiers, which represent concurrent systems as flat transition relations. We
present a powerful refinement proof rule that decomposes refinement checking over
structured programs into modular verification conditions. Refinement checking
is supported by a new form of modular, parameterized invariants, called yield
invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn
a second line of work, we present two new reduction-based program transformations
that target asynchronous programs. These transformations reduce the number of
interleavings that need to be considered, thus reducing the complexity of invariants.
Synchronization simplifies the verification of asynchronous programs by introducing
the fiction, for proof purposes, that asynchronous operations complete synchronously.
Synchronization summarizes an asynchronous computation as immediate atomic effect.
Inductive sequentialization establishes sequential reductions that captures every
behavior of the original program up to reordering of coarse-grained commutative
actions. A sequential reduction of a concurrent program is easy to reason about
since it corresponds to a simple execution of the program in an idealized synchronous
environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur
approach is implemented the CIVL verifier, which has been successfully used for
the verification of several complex concurrent programs. In our methodology, the
overall correctness of a program is established piecemeal by focusing on the invariant
required for each refinement step separately. While the programmer does the creative
work of specifying the chain of programs and the inductive invariant justifying
each link in the chain, the tool automatically constructs the verification conditions
underlying each refinement step."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
citation:
ama: 'Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization.
2020. doi:10.15479/AT:ISTA:8332'
apa: 'Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization,
sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332'
chicago: 'Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization,
Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.'
ieee: 'B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,”
Institute of Science and Technology Austria, 2020.'
ista: 'Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization,
sequentialization. Institute of Science and Technology Austria.'
mla: 'Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization,
Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.'
short: 'B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization,
Institute of Science and Technology Austria, 2020.'
date_created: 2020-09-04T12:24:12Z
date_published: 2020-09-03T00:00:00Z
date_updated: 2023-09-13T08:45:08Z
day: '03'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:8332
file:
- access_level: open_access
checksum: 26fe261550f691280bda4c454bf015c7
content_type: application/pdf
creator: bkragl
date_created: 2020-09-04T12:17:47Z
date_updated: 2020-09-04T12:17:47Z
file_id: '8333'
file_name: kragl-thesis.pdf
file_size: 1348815
relation: main_file
- access_level: closed
checksum: b9694ce092b7c55557122adba8337ebc
content_type: application/zip
creator: bkragl
date_created: 2020-09-04T13:00:17Z
date_updated: 2020-09-04T13:00:17Z
file_id: '8335'
file_name: kragl-thesis.zip
file_size: 372312
relation: source_file
file_date_updated: 2020-09-04T13:00:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '120'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '133'
relation: part_of_dissertation
status: public
- id: '8012'
relation: part_of_dissertation
status: public
- id: '8195'
relation: part_of_dissertation
status: public
- id: '160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: 'Verifying concurrent programs: Refinement, synchronization, sequentialization'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8958'
abstract:
- lang: eng
text: "The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom
too many'' has been disavowed. Inspired by the possibility to experimentally manipulate
and enhance chemical reactivity in helium nanodroplets, we investigate the rotation
of coupled cold molecules in the presence of a many-body environment.\r\nIn this
thesis, we introduce new variational approaches to quantum impurities and apply
them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other
point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed
out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox,
we reveal the self-localization transition for the angulon quasiparticle. We show
that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath
coupling already at the mean-field level. The transition is accompanied by the
spherical-symmetry breaking of the angulon ground state and a discontinuity in
the first derivative of the ground-state energy. Moreover, the type of symmetry
breaking is dictated by the symmetry of the microscopic impurity-bath interaction,
which leads to a number of distinct self-localized states. \r\nFor the system
containing multiple impurities, by analogy with the bipolaron, we introduce the
biangulon quasiparticle describing two rotating molecules that align with respect
to each other due to the effective attractive interaction mediated by the excitations
of the bath. We study this system from the strong-coupling regime to the weak
molecule-bath interaction regime. We show that the molecules tend to have a strong
alignment in the ground state, the biangulon shows shifted angulon instabilities
and an additional spectral instability, where resonant angular momentum transfer
between the molecules and the bath takes place. Finally, we introduce a diagonalization
scheme that allows us to describe the transition from two separated angulons to
a biangulon as a function of the distance between the two molecules."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
citation:
ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment.
2020. doi:10.15479/AT:ISTA:8958
apa: Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body
environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958
chicago: Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.
ieee: X. Li, “Rotation of coupled cold molecules in the presence of a many-body
environment,” Institute of Science and Technology Austria, 2020.
ista: Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body
environment. Institute of Science and Technology Austria.
mla: Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.
short: X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body
Environment, Institute of Science and Technology Austria, 2020.
date_created: 2020-12-21T09:44:30Z
date_published: 2020-12-21T00:00:00Z
date_updated: 2023-09-20T11:30:58Z
day: '21'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: MiLe
doi: 10.15479/AT:ISTA:8958
ec_funded: 1
file:
- access_level: open_access
checksum: 3994c54a1241451d561db1d4f43bad30
content_type: application/pdf
creator: xli
date_created: 2020-12-22T10:55:56Z
date_updated: 2020-12-22T10:55:56Z
file_id: '8967'
file_name: THESIS_Xiang_Li.pdf
file_size: 3622305
relation: main_file
success: 1
- access_level: closed
checksum: 0954ecfc5554c05615c14de803341f00
content_type: application/x-zip-compressed
creator: xli
date_created: 2020-12-22T10:56:03Z
date_updated: 2020-12-30T07:18:03Z
file_id: '8968'
file_name: THESIS_Xiang_Li.zip
file_size: 4018859
relation: source_file
file_date_updated: 2020-12-30T07:18:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '125'
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5886'
relation: part_of_dissertation
status: public
- id: '8587'
relation: part_of_dissertation
status: public
- id: '1120'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
title: Rotation of coupled cold molecules in the presence of a many-body environment
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8386'
abstract:
- lang: eng
text: "Form versus function is a long-standing debate in various design-related
fields, such as architecture as well as graphic and industrial design. A good
design that balances form and function often requires considerable human effort
and collaboration among experts from different professional fields. Computational
design tools provide a new paradigm for designing functional objects. In computational
design, form and function are represented as mathematical\r\nquantities, with
the help of numerical and combinatorial algorithms, they can assist even novice
users in designing versatile models that exhibit their desired functionality.
This thesis presents three disparate research studies on the computational design
of functional objects: The appearance of 3d print—we optimize the volumetric material
distribution for faithfully replicating colored surface texture in 3d printing;
the dynamic motion of mechanical structures—\r\nour design system helps the novice
user to retarget various mechanical templates with different functionality to
complex 3d shapes; and a more abstract functionality, multistability—our algorithm
automatically generates models that exhibit multiple stable target poses. For
each of these cases, our computational design tools not only ensure the functionality
of the results but also permit the user aesthetic freedom over the form. Moreover,
fabrication constraints\r\nwere taken into account, which allow for the immediate
creation of physical realization via 3D printing or laser cutting."
acknowledged_ssus:
- _id: SSU
acknowledgement: The research in this thesis has received funding from the European
Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie
grant agreement No 642841 (DISTRO) and the European Research Council grant agreement
No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported
by Scientific Service Units (SSUs) at IST Austria.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
citation:
ama: Zhang R. Structure-aware computational design and its application to 3D printable
volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386
apa: Zhang, R. (2020). Structure-aware computational design and its application
to 3D printable volume scattering, mechanism, and multistability. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386
chicago: Zhang, Ran. “Structure-Aware Computational Design and Its Application to
3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science
and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.
ieee: R. Zhang, “Structure-aware computational design and its application to 3D
printable volume scattering, mechanism, and multistability,” Institute of Science
and Technology Austria, 2020.
ista: Zhang R. 2020. Structure-aware computational design and its application to
3D printable volume scattering, mechanism, and multistability. Institute of Science
and Technology Austria.
mla: Zhang, Ran. Structure-Aware Computational Design and Its Application to
3D Printable Volume Scattering, Mechanism, and Multistability. Institute of
Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.
short: R. Zhang, Structure-Aware Computational Design and Its Application to 3D
Printable Volume Scattering, Mechanism, and Multistability, Institute of Science
and Technology Austria, 2020.
date_created: 2020-09-14T01:04:53Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2023-09-22T09:49:31Z
day: '14'
ddc:
- '003'
degree_awarded: PhD
department:
- _id: BeBi
doi: 10.15479/AT:ISTA:8386
ec_funded: 1
file:
- access_level: closed
checksum: edcf578b6e1c9b0dd81ff72d319b66ba
content_type: application/x-zip-compressed
creator: rzhang
date_created: 2020-09-14T01:02:59Z
date_updated: 2020-09-14T12:18:43Z
file_id: '8388'
file_name: Thesis_Ran.zip
file_size: 1245800191
relation: source_file
- access_level: open_access
checksum: 817e20c33be9247f906925517c56a40d
content_type: application/pdf
creator: rzhang
date_created: 2020-09-15T12:51:53Z
date_updated: 2020-09-15T12:51:53Z
file_id: '8396'
file_name: PhD_thesis_Ran Zhang_20200915.pdf
file_size: 161385316
relation: main_file
success: 1
file_date_updated: 2020-09-15T12:51:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '148'
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '486'
relation: part_of_dissertation
status: public
- id: '1002'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
title: Structure-aware computational design and its application to 3D printable volume
scattering, mechanism, and multistability
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7996'
abstract:
- lang: eng
text: "Quantum computation enables the execution of algorithms that have exponential
complexity. This might open the path towards the synthesis of new materials or
medical drugs, optimization of transport or financial strategies etc., intractable
on even the fastest classical computers. A quantum computer consists of interconnected
two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide,
there are ongoing efforts to find the qubit architecture which will unite quantum
error correction compatible single and two qubit fidelities, long distance qubit
to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest
in this race, demonstrating an algorithm running on 53 coupled qubits, but still
the fidelities are not even close to those required for realizing a single logical
qubit. emiconductor qubits offer extremely good characteristics, but they are
currently investigated across different platforms. Uniting those good characteristics
into a single platform might be a big step towards the quantum computer realization.\r\nHere
we describe the implementation of a hole spin qubit hosted in a Ge hut wire double
quantum dot. The high and tunable spin-orbit coupling together with a heavy hole
state character is expected to allow fast spin manipulation and long coherence
times. Furthermore large lever arms, for hut wire devices, should allow good coupling
to superconducting resonators enabling efficient long distance spin to spin coupling
and a sensitive gate reflectometry spin readout. The developed cryogenic setup
(printed circuit board sample holders, filtering, high-frequency wiring) enabled
us to perform low temperature spin dynamics experiments. Indeed, we measured the
fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz,
while the dephasing times of 130 ns oppose the long decoherence predictions. In
order to further investigate this, a double quantum dot gate was connected directly
to a lumped element\r\nresonator which enabled gate reflectometry readout. The
vanishing inter-dot transition signal, for increasing external magnetic field,
revealed the spin nature of the measured quantity."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
citation:
ama: Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive
spin sensing. 2020. doi:10.15479/AT:ISTA:7996
apa: Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires
and dispersive spin sensing. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:7996
chicago: Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and
Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.
ieee: J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive
spin sensing,” Institute of Science and Technology Austria, 2020.
ista: Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive
spin sensing. Institute of Science and Technology Austria.
mla: Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and
Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020,
doi:10.15479/AT:ISTA:7996.
short: J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive
Spin Sensing, Institute of Science and Technology Austria, 2020.
date_created: 2020-06-22T09:22:23Z
date_published: 2020-06-22T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '22'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GeKa
doi: 10.15479/AT:ISTA:7996
file:
- access_level: closed
checksum: 467e52feb3e361ce8cf5fe8d5c254ece
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-06-22T09:22:04Z
date_updated: 2020-07-14T12:48:07Z
file_id: '7997'
file_name: JK_thesis_latex_source_files.zip
file_size: 392794743
relation: main_file
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checksum: 1de716bf110dbd77d383e479232bf496
content_type: application/pdf
creator: dernst
date_created: 2020-06-22T09:21:29Z
date_updated: 2020-07-14T12:48:07Z
file_id: '7998'
file_name: PhD_thesis_JK_pdfa.pdf
file_size: 28453247
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '178'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1328'
relation: part_of_dissertation
status: public
- id: '7541'
relation: part_of_dissertation
status: public
- id: '77'
relation: part_of_dissertation
status: public
- id: '23'
relation: part_of_dissertation
status: public
- id: '840'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8390'
abstract:
- lang: eng
text: "Deep neural networks have established a new standard for data-dependent feature
extraction pipelines in the Computer Vision literature. Despite their remarkable
performance in the standard supervised learning scenario, i.e. when models are
trained with labeled data and tested on samples that follow a similar distribution,
neural networks have been shown to struggle with more advanced generalization
abilities, such as transferring knowledge across visually different domains, or
generalizing to new unseen combinations of known concepts. In this thesis we argue
that, in contrast to the usual black-box behavior of neural networks, leveraging
more structured internal representations is a promising direction\r\nfor tackling
such problems. In particular, we focus on two forms of structure. First, we tackle
modularity: We show that (i) compositional architectures are a natural tool for
modeling reasoning tasks, in that they efficiently capture their combinatorial
nature, which is key for generalizing beyond the compositions seen during training.
We investigate how to to learn such models, both formally and experimentally,
for the task of abstract visual reasoning. Then, we show that (ii) in some settings,
modularity allows us to efficiently break down complex tasks into smaller, easier,
modules, thereby improving computational efficiency; We study this behavior in
the context of generative models for colorization, as well as for small objects
detection. Secondly, we investigate the inherently layered structure of representations
learned by neural networks, and analyze its role in the context of transfer learning
and domain adaptation across visually\r\ndissimilar domains. "
acknowledged_ssus:
- _id: CampIT
- _id: ScienComp
acknowledgement: Last but not least, I would like to acknowledge the support of the
IST IT and scientific computing team for helping provide a great work environment.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Amélie
full_name: Royer, Amélie
id: 3811D890-F248-11E8-B48F-1D18A9856A87
last_name: Royer
orcid: 0000-0002-8407-0705
citation:
ama: Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning
models. 2020. doi:10.15479/AT:ISTA:8390
apa: Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible
Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390
chicago: Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible
Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.
ieee: A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep
Learning models,” Institute of Science and Technology Austria, 2020.
ista: Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible
Deep Learning models. Institute of Science and Technology Austria.
mla: Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible
Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.
short: A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep
Learning Models, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-14T13:42:09Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2023-10-16T10:04:02Z
day: '14'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ChLa
doi: 10.15479/AT:ISTA:8390
file:
- access_level: open_access
checksum: c914d2f88846032f3d8507734861b6ee
content_type: application/pdf
creator: dernst
date_created: 2020-09-14T13:39:14Z
date_updated: 2020-09-14T13:39:14Z
file_id: '8391'
file_name: 2020_Thesis_Royer.pdf
file_size: 30224591
relation: main_file
success: 1
- access_level: closed
checksum: ae98fb35d912cff84a89035ae5794d3c
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-09-14T13:39:17Z
date_updated: 2020-09-14T13:39:17Z
file_id: '8392'
file_name: thesis_sources.zip
file_size: 74227627
relation: main_file
file_date_updated: 2020-09-14T13:39:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '197'
publication_identifier:
isbn:
- 978-3-99078-007-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7936'
relation: part_of_dissertation
status: public
- id: '7937'
relation: part_of_dissertation
status: public
- id: '8193'
relation: part_of_dissertation
status: public
- id: '8092'
relation: part_of_dissertation
status: public
- id: '911'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Leveraging structure in Computer Vision tasks for flexible Deep Learning models
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7196'
abstract:
- lang: eng
text: 'In this thesis we study certain mathematical aspects of evolution. The two
primary forces that drive an evolutionary process are mutation and selection.
Mutation generates new variants in a population. Selection chooses among the variants
depending on the reproductive rates of individuals. Evolutionary processes are
intrinsically random – a new mutation that is initially present in the population
at low frequency can go extinct, even if it confers a reproductive advantage.
The overall rate of evolution is largely determined by two quantities: the probability
that an invading advantageous mutation spreads through the population (called
fixation probability) and the time until it does so (called fixation time). Both
those quantities crucially depend not only on the strength of the invading mutation
but also on the population structure. In this thesis, we aim to understand how
the underlying population structure affects the overall rate of evolution. Specifically,
we study population structures that increase the fixation probability of advantageous
mutants (called amplifiers of selection). Broadly speaking, our results are of
three different types: We present various strong amplifiers, we identify regimes
under which only limited amplification is feasible, and we propose population
structures that provide different tradeoffs between high fixation probability
and short fixation time.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196
apa: Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196
chicago: Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196.
ieee: J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science
and Technology Austria, 2020.
ista: Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of
Science and Technology Austria.
mla: Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.
short: J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science
and Technology Austria, 2020.
date_created: 2019-12-20T12:26:36Z
date_published: 2020-01-12T00:00:00Z
date_updated: 2023-10-17T12:29:46Z
day: '12'
ddc:
- '519'
degree_awarded: PhD
department:
- _id: KrCh
- _id: GradSch
doi: 10.15479/AT:ISTA:7196
file:
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checksum: 451f8e64b0eb26bf297644ac72bfcbe9
content_type: application/zip
creator: jtkadlec
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page: '144'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: dissertation_contains
status: public
- id: '5751'
relation: dissertation_contains
status: public
- id: '7212'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: A role of graphs in evolutionary processes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8156'
abstract:
- lang: eng
text: 'We present solutions to several problems originating from geometry and discrete
mathematics: existence of equipartitions, maps without Tverberg multiple points,
and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological
approach to these type of questions. However, for the specific problems we consider
it had yielded only partial or no results. We get our results by complementing
equivariant obstruction theory with other techniques from topology and geometry.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
citation:
ama: Avvakumov S. Topological methods in geometry and discrete mathematics. 2020.
doi:10.15479/AT:ISTA:8156
apa: Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156
chicago: Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156.
ieee: S. Avvakumov, “Topological methods in geometry and discrete mathematics,”
Institute of Science and Technology Austria, 2020.
ista: Avvakumov S. 2020. Topological methods in geometry and discrete mathematics.
Institute of Science and Technology Austria.
mla: Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156.
short: S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute
of Science and Technology Austria, 2020.
date_created: 2020-07-23T09:51:29Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2023-12-18T10:51:01Z
day: '24'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: UlWa
doi: 10.15479/AT:ISTA:8156
file:
- access_level: closed
content_type: application/zip
creator: savvakum
date_created: 2020-07-27T12:44:51Z
date_updated: 2020-07-27T12:44:51Z
file_id: '8178'
file_name: source.zip
file_size: 1061740
relation: source_file
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content_type: application/pdf
creator: savvakum
date_created: 2020-07-27T12:46:53Z
date_updated: 2020-07-27T12:46:53Z
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file_size: 1336501
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success: 1
file_date_updated: 2020-07-27T12:46:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '119'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8182'
relation: part_of_dissertation
status: public
- id: '8183'
relation: part_of_dissertation
status: public
- id: '8185'
relation: part_of_dissertation
status: public
- id: '8184'
relation: part_of_dissertation
status: public
- id: '6355'
relation: part_of_dissertation
status: public
- id: '75'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: Topological methods in geometry and discrete mathematics
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8366'
abstract:
- lang: eng
text: "Fabrication of curved shells plays an important role in modern design, industry,
and science. Among their remarkable properties are, for example, aesthetics of
organic shapes, ability to evenly distribute loads, or efficient flow separation.
They find applications across vast length scales ranging from sky-scraper architecture
to microscopic devices. But, at\r\nthe same time, the design of curved shells
and their manufacturing process pose a variety of challenges. In this thesis,
they are addressed from several perspectives. In particular, this thesis presents
approaches based on the transformation of initially flat sheets into the target
curved surfaces. This involves problems of interactive design of shells with nontrivial
mechanical constraints, inverse design of complex structural materials, and data-driven
modeling of delicate and time-dependent physical properties. At the same time,
two newly-developed self-morphing mechanisms targeting flat-to-curved transformation
are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold
bent glass panelizations. Originally flat glass panels are bent into frames and
remain stressed. This is a cost-efficient fabrication approach compared to hot
bending, when glass panels are shaped plastically. However such constructions
are prone to breaking during bending, and it is highly\r\nnontrivial to navigate
the design space, keeping the panels fabricable and aesthetically pleasing at
the same time. We introduce an interactive design system for cold bent glass façades,
while previously even offline optimization for such scenarios has not been sufficiently
developed. Our method is based on a deep learning approach providing quick\r\nand
high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication
of smaller objects of scales below 1 m, can also greatly benefit from shaping
originally flat sheets. In this respect, we designed new self-morphing shell mechanisms
transforming from an initial flat state to a doubly curved state with high precision
and detail. Our so-called CurveUps demonstrate the encodement of the geometric
information\r\ninto the shell. Furthermore, we explored the frontiers of programmable
materials and showed how temporal information can additionally be encoded into
a flat shell. This allows prescribing deformation sequences for doubly curved
surfaces and, thus, facilitates self-collision avoidance enabling complex shapes
and functionalities otherwise impossible.\r\nBoth of these methods include inverse
design tools keeping the user in the design loop."
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
acknowledgement: "During the work on this thesis, I received substantial support from
IST Austria’s scientific service units. A big thank you to Todor Asenov and other
Miba Machine Shop team members for their help with fabrication of experimental prototypes.
In addition, I would like to thank Scientific Computing team for the support with
high performance computing.\r\nFinancial support was provided by the European Research
Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented
Computational Design and Modeling, which I gratefully acknowledge."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
citation:
ama: 'Guseinov R. Computational design of curved thin shells: From glass façades
to programmable matter. 2020. doi:10.15479/AT:ISTA:8366'
apa: 'Guseinov, R. (2020). Computational design of curved thin shells: From glass
façades to programmable matter. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:8366'
chicago: 'Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass
Façades to Programmable Matter.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:8366.'
ieee: 'R. Guseinov, “Computational design of curved thin shells: From glass façades
to programmable matter,” Institute of Science and Technology Austria, 2020.'
ista: 'Guseinov R. 2020. Computational design of curved thin shells: From glass
façades to programmable matter. Institute of Science and Technology Austria.'
mla: 'Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass
Façades to Programmable Matter. Institute of Science and Technology Austria,
2020, doi:10.15479/AT:ISTA:8366.'
short: 'R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades
to Programmable Matter, Institute of Science and Technology Austria, 2020.'
date_created: 2020-09-10T16:19:55Z
date_published: 2020-09-21T00:00:00Z
date_updated: 2024-02-21T12:44:29Z
day: '21'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: BeBi
doi: 10.15479/AT:ISTA:8366
ec_funded: 1
file:
- access_level: open_access
checksum: f8da89553da36037296b0a80f14ebf50
content_type: application/pdf
creator: rguseino
date_created: 2020-09-10T16:11:49Z
date_updated: 2020-09-10T16:11:49Z
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file_size: 70950442
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success: 1
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checksum: e8fd944c960c20e0e27e6548af69121d
content_type: application/x-zip-compressed
creator: rguseino
date_created: 2020-09-11T09:39:48Z
date_updated: 2020-09-16T15:11:01Z
file_id: '8374'
file_name: thesis_source.zip
file_size: 76207597
relation: source_file
file_date_updated: 2020-09-16T15:11:01Z
has_accepted_license: '1'
keyword:
- computer-aided design
- shape modeling
- self-morphing
- mechanical engineering
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '118'
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
isbn:
- 978-3-99078-010-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7151'
relation: research_data
status: deleted
- id: '7262'
relation: part_of_dissertation
status: public
- id: '8562'
relation: part_of_dissertation
status: public
- id: '1001'
relation: part_of_dissertation
status: public
- id: '8375'
relation: research_data
status: public
status: public
supervisor:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
title: 'Computational design of curved thin shells: From glass façades to programmable
matter'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7525'
abstract:
- lang: eng
text: "The medial habenula (MHb) is an evolutionary conserved epithalamic structure
important for the modulation of emotional memory. It is involved in regulation
of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and
feeding behavior. MHb receives inputs from septal regions and projects exclusively
to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project
to different subnuclei of MHb: the bed nucleus of anterior commissure projects
to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore,
the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively.
Importantly, these projections have unique features of prominent co-release of
different neurotransmitters and requirement of a peculiar type of calcium channel
for release. In general, synaptic neurotransmission requires an activity-dependent
influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels.
The calcium channel family most commonly involved in neurotransmitter release
comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits,
respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or
Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of
the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements.
This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique
mechanisms of glutamate release in this pathway. One potential example of such
uniqueness is the facilitation of release by GABAB receptor (GBR) activation.
Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting
presynaptic calcium channels. MHb shows the highest expression levels of GBR in
the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are
associated with auxiliary subunits, called potassium channel tetramerization domain
containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b
is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression
in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b
may be involved in the unique mechanisms of neurotransmitter release mediated
by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we
first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways
is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482.
We next found that baclofen, a GBR agonist, has facilitatory effects on release
from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on
release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed
exclusively in ventral MHb may have a role in the facilitatory effects of GBR
activation. In a heterologous expression system using HEK cells, we found that
KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold
electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely
in presynaptic active zone in IPN with KCTD12b being present only in rostral/central
but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely
in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements
and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3,
KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating
that they may form complexes regulating vesicle release in rostral IPN. \r\nOn
electrophysiological studies of wild type (WT) mice, we found that paired-pulse
ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT
and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release
probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8
KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO
mice, the mean variance analysis revealed significantly lower release probability
in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional
regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation
in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8
and KCTD12b KO mice, and found the facilitation of release remained in both KO
mice, indicating that the peculiar effects of the GBR activation in this pathway
do not depend on the selective expression of these KCTD subunits in ventral MHb.
However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen
falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and
KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained
potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in
its termination in the absence of KCTD12b. Consistent with these functional findings,
replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or
GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT
mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the
release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn
summary, our study provided new insights into the physiological roles of presynaptic
Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal
circuit. Future studies will be required to identify the exact molecular mechanism
underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals.
It remains to be determined whether the prominent presence of presynaptic KCTDs
at active zone could exert similar neuromodulatory functions in different pathways
of the brain.\r\n"
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
citation:
ama: Bhandari P. Localization and functional role of Cav2.3 in the medial habenula
to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525
apa: Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial
habenula to interpeduncular nucleus pathway. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:7525
chicago: Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial
Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.
ieee: P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula
to interpeduncular nucleus pathway,” Institute of Science and Technology Austria,
2020.
ista: Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial
habenula to interpeduncular nucleus pathway. Institute of Science and Technology
Austria.
mla: Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial
Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology
Austria, 2020, doi:10.15479/AT:ISTA:7525.
short: P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula
to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria,
2020.
date_created: 2020-02-26T10:56:37Z
date_published: 2020-02-28T00:00:00Z
date_updated: 2023-09-07T13:20:03Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: RySh
doi: 10.15479/AT:ISTA:7525
file:
- access_level: open_access
checksum: 4589234fdb12b4ad72273b311723a7b4
content_type: application/pdf
creator: pbhandari
date_created: 2020-02-28T08:37:53Z
date_updated: 2021-03-01T23:30:04Z
embargo: 2021-02-28
file_id: '7538'
file_name: Pradeep Bhandari Thesis.pdf
file_size: 9646346
relation: main_file
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
- access_level: closed
checksum: aa79490553ca0a5c9b6fbcd152e93928
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: pbhandari
date_created: 2020-02-28T08:47:14Z
date_updated: 2021-03-01T23:30:04Z
embargo_to: open_access
file_id: '7539'
file_name: Pradeep Bhandari Thesis.docx
file_size: 35252164
relation: source_file
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
file_date_updated: 2021-03-01T23:30:04Z
has_accepted_license: '1'
keyword:
- Cav2.3
- medial habenula (MHb)
- interpeduncular nucleus (IPN)
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '79'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8657'
abstract:
- lang: eng
text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative
studies anchor translation into the context of bacterial physiology and reveal
several mathematical relationships, called “growth laws,” which capture physiological
feedbacks between protein synthesis and cell growth. Growth laws describe the
dependency of the ribosome abundance as a function of growth rate, which can change
depending on the growth conditions. Perturbations of translation reveal that bacteria
employ a compensatory strategy in which the reduced translation capability results
in increased expression of the translation machinery.\r\nPerturbations of translation
are achieved in various ways; clinically interesting is the application of translation-targeting
antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology
are often poorly understood. Bacterial responses to two or more simultaneously
applied antibiotics are even more puzzling. The combined antibiotic effect determines
the type of drug interaction, which ranges from synergy (the effect is stronger
than expected) to antagonism (the effect is weaker) and suppression (one of the
drugs loses its potency).\r\nIn the first part of this work, we systematically
measure the pairwise interaction network for translation inhibitors that interfere
with different steps in translation. We find that the interactions are surprisingly
diverse and tend to be more antagonistic. To explore the underlying mechanisms,
we begin with a minimal biophysical model of combined antibiotic action. We base
this model on the kinetics of antibiotic uptake and binding together with the
physiological response described by the growth laws. The biophysical model explains
some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn
the second part of this work, we hypothesize that elusive suppressive drug interactions
result from the interplay between ribosomes halted in different stages of translation.
To elucidate this putative mechanism of drug interactions between translation
inhibitors, we generate translation bottlenecks genetically using in- ducible
control of translation factors that regulate well-defined translation cycle steps.
These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks partially causes
these interactions.\r\nWe extend this approach by varying two translation bottlenecks
simultaneously. This approach reveals the suppression of translocation inhibition
by inhibited translation. We rationalize this effect by modeling dense traffic
of ribosomes that move on transcripts in a translation factor-mediated manner.
This model predicts a dissolution of traffic jams caused by inhibited translocation
when the density of ribosome traffic is reduced by lowered initiation. We base
this model on the growth laws and quantitative relationships between different
translation and growth parameters.\r\nIn the final part of this work, we describe
a set of tools aimed at quantification of physiological and translation parameters.
We further develop a simple model that directly connects the abundance of a translation
factor with the growth rate, which allows us to extract physiological parameters
describing initiation. We demonstrate the development of tools for measuring translation
rate.\r\nThis thesis showcases how a combination of high-throughput growth rate
mea- surements, genetics, and modeling can reveal mechanisms of drug interactions.
Furthermore, by a gradual transition from combinations of antibiotics to precise
genetic interventions, we demonstrated the equivalency between genetic and chemi-
cal perturbations of translation. These findings tile the path for quantitative
studies of antibiotic combinations and illustrate future approaches towards the
quantitative description of translation."
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
acknowledgement: I thank Life Science Facilities for their continuous support with
providing top-notch laboratory materials, keeping the devices humming, and coordinating
the repairs and building of custom-designed laboratory equipment with the MIBA Machine
shop.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. 2020. doi:10.15479/AT:ISTA:8657'
apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics
to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657'
chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to
Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.'
ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics
and physiology,” Institute of Science and Technology Austria, 2020.'
ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. Institute of Science and Technology Austria.'
mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.'
short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology, Institute of Science and Technology Austria, 2020.'
date_created: 2020-10-13T16:46:14Z
date_published: 2020-10-14T00:00:00Z
date_updated: 2023-09-07T13:20:48Z
day: '14'
ddc:
- '571'
- '530'
- '570'
degree_awarded: PhD
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8657
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date_updated: 2021-10-07T22:30:03Z
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file_size: 52636162
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date_updated: 2021-10-07T22:30:03Z
embargo_to: open_access
file_id: '8664'
file_name: 2020b.zip
file_size: 321681247
relation: source_file
file_date_updated: 2021-10-07T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '271'
publication_identifier:
isbn:
- 978-3-99078-011-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7673'
relation: part_of_dissertation
status: public
- id: '8250'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7680'
abstract:
- lang: eng
text: "Proteins and their complex dynamic interactions regulate cellular mechanisms
from sensing and transducing extracellular signals, to mediating genetic responses,
and sustaining or changing cell morphology. To manipulate these protein-protein
interactions (PPIs) that govern the behavior and fate of cells, synthetically
constructed, genetically encoded tools provide the means to precisely target proteins
of interest (POIs), and control their subcellular localization and activity in
vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger
that does not activate any other endogenous process, thereby allowing manipulation
of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain
from plants, algae and bacteria are re-purposed and genetically fused to POIs.
Illumination with light of a specific wavelength triggers a conformational change
that can mediate PPIs, such as dimerization or oligomerization. By using light
as a trigger, these tools can be activated with high spatial and temporal precision,
on subcellular and millisecond scales. Chemogenetic tools consist of protein domains
that recognize and bind small molecules. By genetic fusion to POIs, these domains
can mediate PPIs upon addition of their specific ligands, which are often synthetically
designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost
optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding
to red, blue or near-UV light, leaving a striking gap in the green band of the
visible light spectrum. Among both optogenetic and chemogenetic tools, there is
an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination,
rely on covalent linkage and subsequent enzymatic cleavage or initially result
in protein clustering of unknown stoichiometry.\r\nThis work describes how the
recently structurally and photochemically characterized green-light responsive
cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed
to function as a green-light responsive optogenetic tool. In contrast to previously
engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI
already upon expression, which can be rapidly disrupted by illumination. This
was employed to mimic inhibition of constitutive activity of a growth factor receptor,
and successfully implement for cell signalling in mammalian cells and in vivo
to rescue development in zebrafish. This work further describes the development
and application of a chemically induced de-dimerizer (CDD) based on a recently
identified and structurally described bacterial oxyreductase. CDD forms a dimer
upon expression in absence of its cofactor, the flavin derivative F420. Safety
and of domain expression and ligand exposure are demonstrated in vitro and in
vivo in zebrafish. The system is further applied to inhibit cell signalling output
from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire
of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing
previously not utilized cues. In the future, they can readily be combined with
existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
citation:
ama: Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of
cellular signals. 2020. doi:10.15479/AT:ISTA:7680
apa: Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680
chicago: Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic
Inhibition of Cellular Signals.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:7680.
ieee: S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals,” Institute of Science and Technology Austria, 2020.
ista: Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria.
mla: Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.
short: S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals, Institute of Science and Technology Austria, 2020.
date_created: 2020-04-24T16:00:51Z
date_published: 2020-04-24T00:00:00Z
date_updated: 2023-09-22T09:20:10Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7680
file:
- access_level: open_access
checksum: fb9a4468eb27be92690728e35c823796
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date_created: 2020-04-28T11:19:21Z
date_updated: 2021-10-31T23:30:05Z
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file_size: 3268017
relation: main_file
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creator: stgingl
date_created: 2020-04-28T11:19:24Z
date_updated: 2021-10-31T23:30:05Z
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file_id: '7693'
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file_size: 5167703
relation: source_file
file_date_updated: 2021-10-31T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: None
page: '98'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1028'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8620'
abstract:
- lang: eng
text: "The development of the human brain occurs through a tightly regulated series
of dynamic and adaptive processes during prenatal and postnatal life. A disruption
of this strictly orchestrated series of events can lead to a number of neurodevelopmental
conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common,
etiologically and phenotypically heterogeneous group of disorders sharing the
core symptoms of social interaction and communication deficits and restrictive
and repetitive interests and behaviors. They are estimated to affect one in 59
individuals in the U.S. and, over the last three decades, mutations in more than
a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet,
for the vast majority of these ASD-risk genes their role during brain development
and precise molecular function still remain elusive.\r\nDe novo loss of function
mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In
the study described here, we used Cul3 mouse models to evaluate the consequences
of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice
exhibit deficits in motor coordination as well as ASD-relevant social and cognitive
impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display
cortical lamination abnormalities due to defective migration of post-mitotic excitatory
neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line
with the observed abnormal cortical organization, Cul3 heterozygous deletion is
associated with decreased spontaneous excitatory and inhibitory activity in the
cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion
protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal
proteins in Cul3 mutant neural cells results in atypical organization of the actin
mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult
mice does not induce the majority of the behavioral defects observed in constitutive
Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn
conclusion, our data indicate that Cul3 plays a critical role in the regulation
of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral
abnormalities are primarily due to dosage sensitive Cul3 functions at early brain
developmental stages."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: I would like to especially thank Armel Nicolas from the Proteomics
and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to
thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka,
Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line
maintenance and their great support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
citation:
ama: Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis.
2020. doi:10.15479/AT:ISTA:8620
apa: Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620
chicago: Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.
ieee: J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,”
Institute of Science and Technology Austria, 2020.
ista: Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria.
mla: Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.
short: J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis,
Institute of Science and Technology Austria, 2020.
date_created: 2020-10-07T14:53:13Z
date_published: 2020-10-12T00:00:00Z
date_updated: 2023-09-07T13:22:14Z
day: '12'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:8620
file:
- access_level: open_access
checksum: 7ee83e42de3e5ce2fedb44dff472f75f
content_type: application/pdf
creator: jmorande
date_created: 2020-10-07T14:41:49Z
date_updated: 2021-10-16T22:30:04Z
embargo: 2021-10-15
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date_created: 2020-10-07T14:45:07Z
date_updated: 2021-10-16T22:30:04Z
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file_id: '8622'
file_name: Jasmin_Morandell_Thesis-2020_final.zip
file_size: 24344152
relation: source_file
file_date_updated: 2021-10-16T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
grant_number: F07807
name: Neural stem cells in autism and epilepsy
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7800'
relation: part_of_dissertation
status: public
- id: '8131'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: Illuminating the role of Cul3 in autism spectrum disorder pathogenesis
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8340'
abstract:
- lang: eng
text: Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative
phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven
proton pumping machines which establish a proton motive force across the inner
mitochondrial membrane. This electrochemical proton gradient is used to drive
ATP synthesis, which powers the majority of cellular processes such as protein
synthesis, locomotion and signalling. In this thesis I investigate the structures
and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory
complex I and transhydrogenase. I present the first high-resolution structure
of the full transhydrogenase from any species, and a significantly improved structure
of complex I. Improving the resolution from 3.3 Å available previously to up to
2.3 Å in this thesis allowed us to model bound water molecules, crucial in the
proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different
substrates and inhibitors bound were solved to delineate the catalytic cycle and
understand the proton pumping mechanism. In transhydrogenase, the proton channel
is gated by reversible detachment of the NADP(H)-binding domain which opens the
proton channel to the opposite sites of the membrane. In complex I, the proton
channels are gated by reversible protonation of key glutamate and lysine residues
and breaking of the water wire connecting the proton pumps with the quinone reduction
site. The tight coupling between the redox and the proton pumping reactions in
transhydrogenase is achieved by controlling the NADP(H) exchange which can only
happen when the NADP(H)-binding domain interacts with the membrane domain. In
complex I, coupling is achieved by cycling of the whole complex between the closed
state, in which quinone can get reduced, and the open state, in which NADH can
induce quinol ejection from the binding pocket. On the basis of these results
I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex
I that are consistent with a large amount of previous work. In both enzymes, conformational
and electrostatic mechanisms contribute to the overall catalytic process. Results
presented here could be used for better understanding of the human pathologies
arising from deficiencies of complex I or transhydrogenase and could be used to
develop novel therapies.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'I acknowledge the support of IST facilities, especially the Electron
Miscroscopy facility for providing training and resources. Special thanks also go
to cryo-EM specialists who helped me to collect the data present here: Dr Valentin
Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni.
of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT,
project number 653706, funded by the Horizon 2020 programme of the European Union.
This project has received funding from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
citation:
ama: Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping
enzymes. 2020. doi:10.15479/AT:ISTA:8340
apa: Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled
proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340
chicago: Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340.
ieee: D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping
enzymes,” Institute of Science and Technology Austria, 2020.
ista: Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton
pumping enzymes. Institute of Science and Technology Austria.
mla: Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.
short: D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping
Enzymes, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-07T18:42:23Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2023-09-07T13:26:17Z
day: '09'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: LeSa
doi: 10.15479/AT:ISTA:8340
ec_funded: 1
file:
- access_level: closed
checksum: dd270baf82121eb4472ad19d77bf227c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dkampjut
date_created: 2020-09-08T13:32:06Z
date_updated: 2021-09-11T22:30:04Z
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file_name: ThesisFull20200908.docx
file_size: 166146359
relation: source_file
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content_type: application/pdf
creator: dernst
date_created: 2020-09-14T15:02:20Z
date_updated: 2021-09-11T22:30:04Z
embargo: 2021-09-10
file_id: '8393'
file_name: 2020_Thesis_Kampjut.pdf
file_size: 13873769
relation: main_file
file_date_updated: 2021-09-11T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: None
page: '242'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-008-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6848'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
title: Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8983'
abstract:
- lang: eng
text: Metabolic adaptation is a critical feature of migrating cells. It tunes the
metabolic programs of migrating cells to allow them to efficiently exert their
crucial roles in development, inflammatory responses and tumor metastasis. Cell
migration through physically challenging contexts requires energy. However, how
the metabolic reprogramming that underlies in vivo cell invasion is controlled
is still unanswered. In my PhD project, I identify a novel conserved metabolic
shift in Drosophila melanogaster immune cells that by modulating their bioenergetic
potential controls developmentally programmed tissue invasion. We show that this
regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances
the transcription of a set of proteins, including an RNA helicase Porthos and
two metabolic enzymes, each of which increases the tissue invasion of leading
Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively
regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR
cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related
proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS)
components III and V and other metabolic-related proteins. Porthos powers up mitochondrial
OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion
of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion
defect. In my PhD project, I elucidate that Atossa displays a conserved developmental
metabolic control to modulate metabolic capacities and the cellular energy state,
through altered transcription and translation, to aid the tissue infiltration
of leading cells into energy demanding barriers.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: CampIT
acknowledgement: Also, I would like to express my appreciation and thanks to the Bioimaging
facility, LSF, GSO, library, and IT people at IST Austria.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
citation:
ama: Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion.
2020. doi:10.15479/AT:ISTA:8983
apa: Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue
invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983
chicago: Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue
Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983.
ieee: S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,”
Institute of Science and Technology Austria, 2020.
ista: Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion.
Institute of Science and Technology Austria.
mla: Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.
short: S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion,
Institute of Science and Technology Austria, 2020.
date_created: 2020-12-30T15:41:26Z
date_published: 2020-12-30T00:00:00Z
date_updated: 2023-09-07T13:24:17Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: DaSi
doi: 10.15479/AT:ISTA:8983
file:
- access_level: open_access
checksum: ec2797ab7a6f253b35df0572b36d1b43
content_type: application/pdf
creator: semtenan
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publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8557'
relation: part_of_dissertation
status: public
- id: '6187'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: Metabolic regulation of Drosophila macrophage tissue invasion
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7258'
abstract:
- lang: eng
text: Many flows encountered in nature and applications are characterized by a chaotic
motion known as turbulence. Turbulent flows generate intense friction with pipe
walls and are responsible for considerable amounts of energy losses at world scale.
The nature of turbulent friction and techniques aimed at reducing it have been
subject of extensive research over the last century, but no definite answer has
been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds
numbers friction is better described by the power law first introduced by Blasius
and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale
motions gradually become more important in the flow and can be related to the
change in scaling of friction. Next, we present a series of new techniques that
can relaminarize turbulence by suppressing a key mechanism that regenerates it
at walls, the lift–up effect. In addition, we investigate the process of turbulence
decay in several experiments and discuss the drag reduction potential. Finally,
we examine the behavior of friction under pulsating conditions inspired by the
human heart cycle and we show that under such circumstances turbulent friction
can be reduced to produce energy savings.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
citation:
ama: Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020.
doi:10.15479/AT:ISTA:7258
apa: Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe
flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258
chicago: Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe
Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258.
ieee: D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,”
Institute of Science and Technology Austria, 2020.
ista: Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow.
Institute of Science and Technology Austria.
mla: Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258.
short: D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute
of Science and Technology Austria, 2020.
date_created: 2020-01-12T16:07:26Z
date_published: 2020-01-13T00:00:00Z
date_updated: 2023-09-15T12:20:08Z
day: '13'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: BjHo
doi: 10.15479/AT:ISTA:7258
ec_funded: 1
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month: '01'
oa: 1
oa_version: None
page: '174'
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 25104D44-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '737549'
name: Eliminating turbulence in oil pipelines
- _id: 25136C54-B435-11E9-9278-68D0E5697425
grant_number: HO 4393/1-2
name: Experimental studies of the turbulence transition and transport processes
in turbulent Taylor-Couette currents
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6228'
relation: part_of_dissertation
status: public
- id: '6486'
relation: part_of_dissertation
status: public
- id: '461'
relation: part_of_dissertation
status: public
- id: '422'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: New approaches to reduce friction in turbulent pipe flow
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8653'
abstract:
- lang: eng
text: "Mutations are the raw material of evolution and come in many different flavors.
Point mutations change a single letter in the DNA sequence, while copy number
mutations like duplications or deletions add or remove many letters of the DNA
sequence simultaneously. Each type of mutation exhibits specific properties like
its rate of formation and reversal. \r\nGene expression is a fundamental phenotype
that can be altered by both, point and copy number mutations. The following thesis
is concerned with the dynamics of gene expression evolution and how it is affected
by the properties exhibited by point and copy number mutations. Specifically,
we are considering i) copy number mutations during adaptation to fluctuating environments
and ii) the interaction of copy number and point mutations during adaptation to
constant environments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. The evolution of gene expression by copy number and point mutations.
2020. doi:10.15479/AT:ISTA:8653
apa: Tomanek, I. (2020). The evolution of gene expression by copy number and
point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653
chicago: Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and
Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.
ieee: I. Tomanek, “The evolution of gene expression by copy number and point mutations,”
Institute of Science and Technology Austria, 2020.
ista: Tomanek I. 2020. The evolution of gene expression by copy number and point
mutations. Institute of Science and Technology Austria.
mla: Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point
Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.
short: I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations,
Institute of Science and Technology Austria, 2020.
date_created: 2020-10-13T13:02:33Z
date_published: 2020-10-13T00:00:00Z
date_updated: 2023-09-07T13:22:42Z
day: '13'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:8653
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file_date_updated: 2021-10-20T22:30:03Z
has_accepted_license: '1'
keyword:
- duplication
- amplification
- promoter
- CNV
- AMGET
- experimental evolution
- Escherichia coli
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '117'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7652'
relation: research_data
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: The evolution of gene expression by copy number and point mutations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8822'
abstract:
- lang: eng
text: "Self-organization is a hallmark of plant development manifested e.g. by intricate
leaf vein patterns, flexible formation of vasculature during organogenesis or
its regeneration following wounding. Spontaneously arising channels transporting
the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED
1 (PIN1) auxin exporter, provide positional cues for these as well as other plant
patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB
auxin signaling pathway essential for PIN1 coordinated polarization during auxin
canalization, we performed microarray experiments. Besides the known components
of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified
and characterized a new regulator of auxin canalization, the transcription factor
WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray
experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23
involved in the regulation of auxin-mediated PIN repolarization. We identified
a novel and crucial part of the molecular machinery underlying auxin canalization.
The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated
leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate
PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular
trafficking and auxin-mediated repolarization leading to defects in auxin transport,
ultimately to leaf venation and vasculature regeneration defects. Our results
describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back
on its own transport and thus for coordinated tissue polarization during auxin
canalization."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
citation:
ama: Hajny J. Identification and characterization of the molecular machinery of
auxin-dependent canalization during vasculature formation and regeneration. 2020.
doi:10.15479/AT:ISTA:8822
apa: Hajny, J. (2020). Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822
chicago: Hajny, Jakub. “Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.
ieee: J. Hajny, “Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration,”
Institute of Science and Technology Austria, 2020.
ista: Hajny J. 2020. Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration.
Institute of Science and Technology Austria.
mla: Hajny, Jakub. Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.
short: J. Hajny, Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration,
Institute of Science and Technology Austria, 2020.
date_created: 2020-12-01T12:38:18Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2023-09-19T10:39:33Z
day: '01'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/AT:ISTA:8822
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date_created: 2020-12-04T07:27:52Z
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date_updated: 2021-12-08T23:30:03Z
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language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '249'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7427'
relation: part_of_dissertation
status: public
- id: '6260'
relation: part_of_dissertation
status: public
- id: '7500'
relation: part_of_dissertation
status: public
- id: '191'
relation: part_of_dissertation
status: public
- id: '449'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Identification and characterization of the molecular machinery of auxin-dependent
canalization during vasculature formation and regeneration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8350'
abstract:
- lang: eng
text: "Cytoplasm is a gel-like crowded environment composed of tens of thousands
of macromolecules, organelles, cytoskeletal networks and cytosol. The structure
of the cytoplasm is thought to be highly organized and heterogeneous due to the
crowding of its constituents and their effective compartmentalization. In such
an environment, the diffusive dynamics of the molecules is very restricted, an
effect that is further amplified by clustering and anchoring of molecules. Despite
the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization
of cytoplasm is essential for important cellular functions, such as nuclear positioning
and cell division. How such mesoscale reorganization of the cytoplasm is achieved,
especially for very large cells such as oocytes or syncytial tissues that can
span hundreds of micrometers in size, has only begun to be understood.\r\nIn this
thesis, I focus on the recent advances in elucidating the molecular, cellular
and biophysical principles underlying cytoplasmic organization across different
scales, structures and species. First, I outline which of these principles have
been identified by reductionist approaches, such as in vitro reconstitution assays,
where boundary conditions and components can be modulated at ease. I then describe
how the theoretical and experimental framework established in these reduced systems
have been applied to their more complex in vivo counterparts, in particular oocytes
and embryonic syncytial structures, and discuss how such complex biological systems
can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine
an example of large-scale reorganizations taking place in zebrafish embryos, where
extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk
granules along the animal-vegetal axis of the embryo. Using biophysical experimentation
and theory, I investigate the forces underlying this process, to show that this
process does not rely on cortical actin reorganization, as previously thought,
but instead on a cell-cycle-dependent bulk actin polymerization wave traveling
from the animal to the vegetal pole of the embryo. This wave functions in segregation
by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm
pulling is mediated by bulk actin network flows exerting friction forces on the
cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling
actin comet formation on yolk granules. This study defines a novel role of bulk
actin polymerization waves in embryo polarization via cytoplasmic segregation.
Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish
oocyte maturation, where the initial segregation of the cytoplasm and yolk granules
occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster
formation, traveling the oocyte along the animal-vegetal axis. Further research
is required to determine the role of such microtubule structures in cytoplasmic
reorganizations therein.\r\nCollectively, these studies provide further evidence
for the coupling between cell cytoskeleton and cell cycle machinery, which can
underlie a core self-organizing mechanism for orchestrating large-scale reorganizations
in a cell-cycle-tunable manner, where the modulations of the force-generating
machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: EM-Fac
acknowledgement: "I would have had no fish and hence no results without our wonderful
fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak.
Special thanks to Verena for being always happy to help and dealing with our chaotic
schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch
zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and
EM facilities at IST Austria for supporting us every day. Very special thanks would
go to Robert Hauschild for his continuous support on data analysis and also to Jack
Merrin for designing and building microfabricated chambers for the project and for
the various discussions on making zebrafish extracts."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
citation:
ama: Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes
. 2020. doi:10.15479/AT:ISTA:8350
apa: Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish
oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350
chicago: Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.
ieee: S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes
,” Institute of Science and Technology Austria, 2020.
ista: Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish
oocytes . Institute of Science and Technology Austria.
mla: Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.
short: S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes
, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-09T11:12:10Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2023-09-27T14:16:45Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: BjHo
- _id: CaHe
doi: 10.15479/AT:ISTA:8350
file:
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checksum: 6e47871c74f85008b9876112eb3fcfa1
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creator: sshamip
date_created: 2020-09-09T11:06:27Z
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date_created: 2020-09-09T11:06:13Z
date_updated: 2021-09-11T22:30:05Z
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language:
- iso: eng
month: '09'
oa: 1
oa_version: None
page: '107'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '661'
relation: part_of_dissertation
status: public
- id: '6508'
relation: part_of_dissertation
status: public
- id: '7001'
relation: part_of_dissertation
status: public
- id: '735'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: 'Bulk actin dynamics drive phase segregation in zebrafish oocytes '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7902'
abstract:
- lang: eng
text: "Mosaic genetic analysis has been widely used in different model organisms
such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific
fashion. More recently, and less easily conducted, mosaic genetic analysis in
mice has also been enabled with the ambition to shed light on human gene function
and disease. These genetic tools are of particular interest, but not restricted
to, the study of the brain. Notably, the MADM technology offers a genetic approach
in mice to visualize and concomitantly manipulate small subsets of genetically
defined cells at a clonal level and single cell resolution. MADM-based analysis
has already advanced the study of genetic mechanisms regulating brain development
and is expected that further MADM-based analysis of genetic alterations will continue
to reveal important insights on the fundamental principles of development and
disease to potentially assist in the development of new therapies or treatments.\r\nIn
summary, this work completed and characterized the necessary genome-wide genetic
tools to perform MADM-based analysis at single cell level of the vast majority
of mouse genes in virtually any cell type and provided a protocol to perform lineage
tracing using the novel MADM resource. Importantly, this work also explored and
revealed novel aspects of biologically relevant events in an in vivo context,
such as the chromosome-specific bias of chromatid sister segregation pattern,
the generation of cell-type diversity in the cerebral cortex and in the cerebellum
and finally, the relevance of the interplay between the cell-autonomous gene function
and cell-non-autonomous (community) effects in radial glial progenitor lineage
progression.\r\nThis work provides a foundation and opens the door to further
elucidating the molecular mechanisms underlying neuronal diversity and astrocyte
generation."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
citation:
ama: Contreras X. Genetic dissection of neural development in health and disease
at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902
apa: Contreras, X. (2020). Genetic dissection of neural development in health
and disease at single cell resolution. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:7902
chicago: Contreras, Ximena. “Genetic Dissection of Neural Development in Health
and Disease at Single Cell Resolution.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:7902.
ieee: X. Contreras, “Genetic dissection of neural development in health and disease
at single cell resolution,” Institute of Science and Technology Austria, 2020.
ista: Contreras X. 2020. Genetic dissection of neural development in health and
disease at single cell resolution. Institute of Science and Technology Austria.
mla: Contreras, Ximena. Genetic Dissection of Neural Development in Health and
Disease at Single Cell Resolution. Institute of Science and Technology Austria,
2020, doi:10.15479/AT:ISTA:7902.
short: X. Contreras, Genetic Dissection of Neural Development in Health and Disease
at Single Cell Resolution, Institute of Science and Technology Austria, 2020.
date_created: 2020-05-29T08:27:32Z
date_published: 2020-06-05T00:00:00Z
date_updated: 2023-10-18T08:45:16Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: SiHi
doi: 10.15479/AT:ISTA:7902
ec_funded: 1
file:
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checksum: 43c172bf006c95b65992d473c7240d13
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creator: xcontreras
date_created: 2020-06-05T08:18:08Z
date_updated: 2021-06-07T22:30:03Z
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file_id: '7927'
file_name: PhDThesis_Contreras.docx
file_size: 53134142
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checksum: addfed9128271be05cae3608e03a6ec0
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creator: xcontreras
date_created: 2020-06-05T08:18:07Z
date_updated: 2021-06-07T22:30:03Z
embargo: 2021-06-06
file_id: '7928'
file_name: PhDThesis_Contreras.pdf
file_size: 35117191
relation: main_file
file_date_updated: 2021-06-07T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '214'
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6830'
relation: dissertation_contains
status: public
- id: '28'
relation: dissertation_contains
status: public
- id: '7815'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Genetic dissection of neural development in health and disease at single cell
resolution
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '6957'
abstract:
- lang: eng
text: "In many shear flows like pipe flow, plane Couette flow, plane Poiseuille
flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough
perturbations, the flow becomes turbulent in spite of the laminar base flow being
linearly stable. The nature of this instability has puzzled the scientific community
for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally
intermittent. In pipe flow the localized turbulent structures are referred to
as puffs and in planar flows like plane Couette and channel flow, patches arise
in the form of localized oblique bands. In this thesis, we study the onset of
turbulence in channel flow in direct numerical simulations from a dynamical system
theory perspective, as well as by performing experiments in a large aspect ratio
channel.\r\n\r\nThe aim of the experimental work is to determine the critical
Reynolds number where turbulence first becomes sustained. Recently, the onset
of turbulence has been described in analogy to absorbing state phase transition
(i.e. directed percolation). In particular, it has been shown that the critical
point can be estimated from the competition between spreading and decay processes.
Here, by performing experiments, we identify the mechanisms underlying turbulence
proliferation in channel flow and find the critical Reynolds number, above which
turbulence becomes sustained. Above the critical point, the continuous growth
at the tip of the stripes outweighs the stochastic shedding of turbulent patches
at the tail and the stripes expand. For growing stripes, the probability to decay
decreases while the probability of stripe splitting increases. Consequently, and
unlike for the puffs in pipe flow, neither of these two processes is time-independent
i.e. memoryless. Coupling between stripe expansion and creation of new stripes
via splitting leads to a significantly lower critical point ($Re_c=670+/-10$)
than most earlier studies suggest. \r\n\r\nWhile the above approach sheds light
on how turbulence first becomes sustained, it provides no insight into the origin
of the stripes themselves. In the numerical part of the thesis we investigate
how turbulent stripes form from invariant solutions of the Navier-Stokes equations.
The origin of these turbulent stripes can be identified by applying concepts from
the dynamical system theory. In doing so, we identify the exact coherent structures
underlying stripes and their bifurcations and how they give rise to the turbulent
attractor in phase space. We first report a family of localized nonlinear traveling
wave solutions of the Navier-Stokes equations in channel flow. These solutions
show structural similarities with turbulent stripes in experiments like obliqueness,
quasi-streamwise streaks and vortices, etc. A parametric study of these traveling
wave solution is performed, with parameters like Reynolds number, stripe tilt
angle and domain size, including the stability of the solutions. These solutions
emerge through saddle-node bifurcations and form a phase space skeleton for the
turbulent stripes observed in the experiments. The lower branches of these TW
solutions at different tilt angles undergo Hopf bifurcation and new solutions
branches of relative periodic orbits emerge. These RPO solutions do not belong
to the same family and therefore the routes to chaos for different angles are
different. \r\n\r\nIn shear flows, turbulence at onset is transient in nature.
\ Consequently,turbulence can not be tracked to lower Reynolds numbers, where
the dynamics may simplify. Before this happens, turbulence becomes short-lived
and laminarizes. In the last part of the thesis, we show that using numerical
simulations we can continue turbulent stripes in channel flow past the 'relaminarization
barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies
and the fluctuations are no longer stochastic and the stripe settles down to a
relative periodic orbit. This relative periodic orbit originates from the aforementioned
traveling wave solutions. Starting from the relative periodic orbit, a small increase
in speed i.e. Reynolds number gives rise to chaos and the attractor dimension
sharply increases in contrast to the classical transition scenario where the instabilities
affect the flow globally and give rise to much more gradual route to turbulence."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Chaitanya S
full_name: Paranjape, Chaitanya S
id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87
last_name: Paranjape
citation:
ama: Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:10.15479/AT:ISTA:6957
apa: Paranjape, C. S. (2019). Onset of turbulence in plane Poiseuille flow.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6957
chicago: Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6957.
ieee: C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute
of Science and Technology Austria, 2019.
ista: Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute
of Science and Technology Austria.
mla: Paranjape, Chaitanya S. Onset of Turbulence in Plane Poiseuille Flow.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6957.
short: C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of
Science and Technology Austria, 2019.
date_created: 2019-10-22T12:08:43Z
date_published: 2019-10-24T00:00:00Z
date_updated: 2023-09-07T12:53:25Z
day: '24'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: BjHo
doi: 10.15479/AT:ISTA:6957
file:
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checksum: 7ba298ba0ce7e1d11691af6b8eaf0a0a
content_type: application/zip
creator: cparanjape
date_created: 2019-10-23T09:54:43Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6962'
file_name: Chaitanya_Paranjape_source_files_tex_figures.zip
file_size: 45828099
relation: source_file
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checksum: 642697618314e31ac31392da7909c2d9
content_type: application/pdf
creator: cparanjape
date_created: 2019-10-23T10:37:09Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6963'
file_name: Chaitanya_Paranjape_Thesis.pdf
file_size: 19504197
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
keyword:
- Instabilities
- Turbulence
- Nonlinear dynamics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '138'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Onset of turbulence in plane Poiseuille flow
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7186'
abstract:
- lang: eng
text: "Tissue morphogenesis in developmental or physiological processes is regulated
by molecular\r\nand mechanical signals. While the molecular signaling cascades
are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape
changes have only recently been\r\nstudied in greater detail. To gain more insight
into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process
(epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation
and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial
cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe
cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the
end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing
within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction
motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely
transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature
and formation of the junctional structure\r\nmediating this process has not been
well described so far. Therefore, our main aim was to\r\ndetermine the nature,
dynamics and potential function of the EVL-YSL junction during this\r\nepithelial
tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive
structure, predominantly made of tight junction (TJ) proteins. The process\r\nof
TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula
Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly,
we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface
of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely
renders the protein\r\nresponsive to flows. These flows are directed towards the
junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching
the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated
through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or
ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive
responses resulting in slower tissue spreading. We could further\r\ndemonstrate
that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring
formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish
epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility
and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale
polarization process mediated through the flow of phase-separated protein\r\nclusters
might have implications for other processes such as immunological synapse\r\nformation,
C. elegans zygote polarization and wound healing."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: EM-Fac
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
citation:
ama: Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation
and flow. 2019. doi:10.15479/AT:ISTA:7186
apa: Schwayer, C. (2019). Mechanosensation of tight junctions depends on ZO-1
phase separation and flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7186
chicago: Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1
Phase Separation and Flow.” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:7186.
ieee: C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation
and flow,” Institute of Science and Technology Austria, 2019.
ista: Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase
separation and flow. Institute of Science and Technology Austria.
mla: Schwayer, Cornelia. Mechanosensation of Tight Junctions Depends on ZO-1
Phase Separation and Flow. Institute of Science and Technology Austria, 2019,
doi:10.15479/AT:ISTA:7186.
short: C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation
and Flow, Institute of Science and Technology Austria, 2019.
date_created: 2019-12-16T14:26:14Z
date_published: 2019-12-16T00:00:00Z
date_updated: 2023-09-07T12:56:42Z
day: '16'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: CaHe
doi: 10.15479/AT:ISTA:7186
file:
- access_level: closed
checksum: 585583c1c875c5d9525703a539668a7c
content_type: application/zip
creator: cschwayer
date_created: 2019-12-19T15:18:11Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7194'
file_name: DocumentSourceFiles.zip
file_size: 19431292
relation: source_file
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checksum: 9b9b24351514948d27cec659e632e2cd
content_type: application/pdf
creator: cschwayer
date_created: 2019-12-19T15:19:21Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7195'
file_name: Thesis_CS_final.pdf
file_size: 19226428
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '107'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1096'
relation: dissertation_contains
status: public
- id: '7001'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6681'
abstract:
- lang: eng
text: "The first part of the thesis considers the computational aspects of the homotopy
groups πd(X) of a topological space X. It is well known that there is no algorithm
to decide whether the fundamental group π1(X) of a given finite simplicial complex
X is trivial. On the other hand, there are several algorithms that, given a finite
simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute
the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms
come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract
finitely generated abelian group given by generators and relations, but they work
with very implicit representations of the elements of πd(X). We present an algorithm
that, given a simply connected space X, computes πd(X) and represents its elements
as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed
d, the algorithm runs in time exponential in size(X), the number of simplices
of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct
a family of simply connected spaces X such that for any simplicial map representing
a generator of πd(X), the size of the triangulation of S d on which the map is
defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove
that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋,
k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable
range: Given a finite simplicial complex K of dimension k, decide whether there
exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of
K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephan Y
full_name: Zhechev, Stephan Y
id: 3AA52972-F248-11E8-B48F-1D18A9856A87
last_name: Zhechev
citation:
ama: Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019.
doi:10.15479/AT:ISTA:6681
apa: Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681
chicago: Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681.
ieee: S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,”
Institute of Science and Technology Austria, 2019.
ista: Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability.
Institute of Science and Technology Austria.
mla: Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681.
short: S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute
of Science and Technology Austria, 2019.
date_created: 2019-07-26T11:14:34Z
date_published: 2019-08-08T00:00:00Z
date_updated: 2023-09-07T13:10:36Z
day: '08'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: UlWa
doi: 10.15479/AT:ISTA:6681
file:
- access_level: open_access
checksum: 3231e7cbfca3b5687366f84f0a57a0c0
content_type: application/pdf
creator: szhechev
date_created: 2019-08-07T13:02:50Z
date_updated: 2020-07-14T12:47:37Z
file_id: '6771'
file_name: Stephan_Zhechev_thesis.pdf
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creator: szhechev
date_created: 2019-08-07T13:03:22Z
date_updated: 2020-07-14T12:47:37Z
file_id: '6772'
file_name: Stephan_Zhechev_thesis.tex
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creator: szhechev
date_created: 2019-08-07T13:03:34Z
date_updated: 2020-07-14T12:47:37Z
file_id: '6773'
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file_size: 1087004
relation: supplementary_material
file_date_updated: 2020-07-14T12:47:37Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '104'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6774'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: Algorithmic aspects of homotopy theory and embeddability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6894'
abstract:
- lang: eng
text: "Hybrid automata combine finite automata and dynamical systems, and model
the interaction of digital with physical systems. Formal analysis that can guarantee
the safety of all behaviors or rigorously witness failures, while unsolvable in
general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking,
assisted theorem proving.\r\nNevertheless, very few methods have addressed the
time-unbounded reachability analysis of hybrid automata and, for current sound
and automatic tools, scalability remains critical. We develop methods for the
polyhedral abstraction of hybrid automata, which construct coarse overapproximations
and tightens them incrementally, in a CEGAR fashion. We use template polyhedra,
i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile,
previously, directions were given by the user, we introduce (1) the first method\r\nfor
computing template directions from spurious counterexamples, so as to generalize
and\r\neliminate them. The method applies naturally to convex hybrid automata,
i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives
only, while for linear\r\nODE requires further abstraction. Specifically, we introduce
(2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate
(possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight
sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time
interpolation, which, combining interval arithmetic\r\nand template refinement,
computes appropriate (possibly non-uniform) time partitioning\r\nand template
directions along spurious trajectories, so as to eliminate them.\r\nWe obtain
sound and automatic methods for the reachability analysis over dense\r\nand unbounded
time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build
prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art
tools, on several benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
citation:
ama: Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems.
2019. doi:10.15479/AT:ISTA:6894
apa: Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid
systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894
chicago: Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid
Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894.
ieee: M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,”
Institute of Science and Technology Austria, 2019.
ista: Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid
systems. Institute of Science and Technology Austria.
mla: Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid
Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894.
short: M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems,
Institute of Science and Technology Austria, 2019.
date_created: 2019-09-22T14:08:44Z
date_published: 2019-09-30T00:00:00Z
date_updated: 2023-09-19T09:30:43Z
day: '30'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:6894
file:
- access_level: open_access
checksum: 773beaf4a85dc2acc2c12b578fbe1965
content_type: application/pdf
creator: mgiacobbe
date_created: 2019-09-27T14:15:05Z
date_updated: 2020-07-14T12:47:43Z
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file_name: giacobbe_thesis.pdf
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creator: mgiacobbe
date_created: 2019-09-27T14:22:04Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6917'
file_name: giacobbe_thesis_src.tar.gz
file_size: 7959732
relation: source_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '132'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '631'
relation: part_of_dissertation
status: public
- id: '647'
relation: part_of_dissertation
status: public
- id: '140'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Automatic time-unbounded reachability analysis of hybrid systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...