@article{17111,
abstract = {Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets.},
author = {Kamatar, Advika and Bravo, Jack Peter Kelly and Yuan, Feng and Wang, Liping and Lafer, Eileen M. and Taylor, David W. and Stachowiak, Jeanne C. and Parekh, Sapun H.},
issn = {0006-3495},
journal = {Biophysical Journal},
number = {11},
pages = {1494--1507},
publisher = {Elsevier},
title = {{Lipid droplets as substrates for protein phase separation}},
doi = {10.1016/j.bpj.2024.03.015},
volume = {123},
year = {2024},
}
@article{17112,
abstract = {The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide–based antiphage signaling system (CBASS). Cyclic tri–adenosine monophosphate (AMP)–induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas–based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities.},
author = {Steens, Jurre A. and Bravo, Jack Peter Kelly and Salazar, Carl Raymund P. and Yildiz, Caglar and Amieiro, Afonso M. and Köstlbacher, Stephan and Prinsen, Stijn H.P. and Patinios, Constantinos and Bardis, Andreas and Barendregt, Arjan and Scheltema, Richard A. and Ettema, Thijs J.G. and van der Oost, John and Taylor, David W. and Staals, Raymond H.J.},
issn = {1095-9203},
journal = {Science},
number = {6682},
pages = {512--519},
publisher = {American Association for the Advancement of Science},
title = {{Type III-B CRISPR-Cas cascade of proteolytic cleavages}},
doi = {10.1126/science.adk0378},
volume = {383},
year = {2024},
}
@article{17113,
abstract = {CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.},
author = {Hibshman, Grace N. and Bravo, Jack Peter Kelly and Hooper, Matthew M. and Dangerfield, Tyler L. and Zhang, Hongshan and Finkelstein, Ilya J. and Johnson, Kenneth A. and Taylor, David W.},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9}},
doi = {10.1038/s41467-024-47830-3},
volume = {15},
year = {2024},
}
@article{17114,
abstract = {CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction1–5. Target RNA cleavage at regular intervals is characteristic of type III effector complexes6–8. Here, we determine the structures of the Synechocystis type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors9,10, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.},
author = {Schwartz, Evan A. and Bravo, Jack Peter Kelly and Ahsan, Mohd and Macias, Luis A. and McCafferty, Caitlyn L. and Dangerfield, Tyler L. and Walker, Jada N. and Brodbelt, Jennifer S. and Palermo, Giulia and Fineran, Peter C. and Fagerlund, Robert D. and Taylor, David W.},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{RNA targeting and cleavage by the type III-Dv CRISPR effector complex}},
doi = {10.1038/s41467-024-47506-y},
volume = {15},
year = {2024},
}
@article{17122,
abstract = {Background: Motor alterations and lowered physical activity are common in affective disorders. Previous research has indicated a link between depressive symptoms and declining muscle strength primarily focusing on the elderly but not younger individuals. Thus, we aimed to evaluate the relationship between mood and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy. The study was carried out as a prospective observational study at a German psychiatric university hospital between September 2021 and March 2022.
Methods: Employing a standardized strength circuit consisting of computerized strength training devices, we measured the maximal muscle strength (Fmax) using three repetitions maximum across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3) over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood lipid profiling in a clinical setting. For analysis of psychopharmacotherapy, medication was split into activating (AM) and inhibiting (IM) medication and dosages were normalized by the respective WHO defined daily dose.
Results: While we observed a significant decrease of the MADRS score and increase of the relative total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001), we did not reveal a significant bivariate correlation between disease severity (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with longer disease history displayed reduced rTFmax (p = .048). IM was significantly associated with decreased rTFmax (p = .032). Regression models provide a more substantial effect of gender, age, and IM on muscle strength than the depressive episode itself (p < .001).
Conclusions: The results of the study indicate that disease severity and muscle strength are not associated in young to middle-aged inpatients with affective disorders using a strength circuit as observational measurement. Future research will be needed to differentiate the effect of medication, gender, and age on muscle strength and to develop interventions for prevention of muscle weakness, especially in younger patients with chronic affective illnesses.},
author = {Ramming, Hannah and Theuerkauf, Linda and Hoos, Olaf and Lichter, Katharina and Kittel-Schneider, Sarah},
issn = {1471-244X},
journal = {BMC Psychiatry},
publisher = {Springer Nature},
title = {{The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study}},
doi = {10.1186/s12888-024-05849-2},
volume = {24},
year = {2024},
}
@article{17123,
abstract = {A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes.},
author = {Brückner, David and Tkačik, Gašper},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {23},
publisher = {National Academy of Sciences},
title = {{Information content and optimization of self-organized developmental systems}},
doi = {10.1073/pnas.2322326121},
volume = {121},
year = {2024},
}
@article{17125,
abstract = {We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.},
author = {Bassani, Carlos L. and Van Anders, Greg and Banin, Uri and Baranov, Dmitry and Chen, Qian and Dijkstra, Marjolein and Dimitriyev, Michael S. and Efrati, Efi and Faraudo, Jordi and Gang, Oleg and Gaston, Nicola and Golestanian, Ramin and Guerrero-Garcia, G. Ivan and Gruenwald, Michael and Haji-Akbari, Amir and Ibáñez, Maria and Karg, Matthias and Kraus, Tobias and Lee, Byeongdu and Van Lehn, Reid C. and Macfarlane, Robert J. and Mognetti, Bortolo M. and Nikoubashman, Arash and Osat, Saeed and Prezhdo, Oleg V. and Rotskoff, Grant M. and Saiz, Leonor and Shi, An Chang and Skrabalak, Sara and Smalyukh, Ivan I. and Tagliazucchi, Mario and Talapin, Dmitri V. and Tkachenko, Alexei V. and Tretiak, Sergei and Vaknin, David and Widmer-Cooper, Asaph and Wong, Gerard C.L. and Ye, Xingchen and Zhou, Shan and Rabani, Eran and Engel, Michael and Travesset, Alex},
issn = {1936-086X},
journal = {ACS Nano},
number = {23},
pages = {14791--14840},
publisher = {American Chemical Society},
title = {{Nanocrystal assemblies: Current advances and open problems}},
doi = {10.1021/acsnano.3c10201},
volume = {18},
year = {2024},
}
@inproceedings{17126,
abstract = {Functional encryption (FE) is a primitive where the holder of a master secret key can control which functions a user can evaluate on encrypted data. It is a powerful primitive that even implies indistinguishability obfuscation (iO), given sufficiently compact ciphertexts (Ananth-Jain, CRYPTO’15 and Bitansky-Vaikuntanathan, FOCS’15). However, despite being extensively studied, there are FE schemes, such as function-hiding inner-product FE (Bishop-Jain-Kowalczyk, AC’15, Abdalla-Catalano-Fiore-Gay-Ursu, CRYPTO’18) and compact quadratic FE (Baltico-Catalano-Fiore-Gay, Lin, CRYPTO’17), that can be only realized using pairings. This raises the question if there are some mathematical barriers that hinder us from realizing these FE schemes from other assumptions.
In this paper, we study the difficulty of constructing lattice-based compact FE. We generalize the impossibility results of Ünal (EC’20) for lattice-based function-hiding FE, and extend it to the case of compact FE. Concretely, we prove lower bounds for lattice-based compact FE schemes which meet some (natural) algebraic restrictions at encryption and decryption, and have ciphertexts of linear size and secret keys of minimal degree. We see our results as important indications of why it is hard to construct lattice-based FE schemes for new functionalities, and which mathematical barriers have to be overcome.},
author = {Tairi, Erkan and Ünal, Akin},
booktitle = {Advances in Cryptology – EUROCRYPT 2024},
isbn = {9783031587221},
issn = {1611-3349},
location = {Zurich, Switzerland},
pages = {249--279},
publisher = {Springer Nature},
title = {{Lower bounds for lattice-based compact functional encryption}},
doi = {10.1007/978-3-031-58723-8_9},
volume = {14652},
year = {2024},
}
@article{17128,
abstract = {The onset of turbulence in pipe flow has defied detailed understanding ever since the first observations of the spatially heterogeneous nature of the transition. Recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed-percolation non-equilibrium phase transition, but whether these findings are generic and also apply to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behaviour virtually impossible. Here we find a technical solution to that limitation and show that the universality class of the transition is directed percolation, from which a jammed phase of puffs emerges above the critical point. Our method is to experimentally characterize all pairwise interactions between localized patches of turbulence puffs and use these interactions as input for renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. The strong interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed-percolation scaling applies beyond simple closed shear flows and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases.},
author = {Lemoult, Grégoire M and Vasudevan, Mukund and Shih, Hong Yan and Linga, Gaute and Mathiesen, Joachim and Goldenfeld, Nigel and Hof, Björn},
issn = {1745-2481},
journal = {Nature Physics},
pages = {1339--1345},
publisher = {Springer Nature},
title = {{Directed percolation and puff jamming near the transition to pipe turbulence}},
doi = {10.1038/s41567-024-02513-0},
volume = {20},
year = {2024},
}
@phdthesis{17133,
abstract = {An ideal quantum computer relies on qubits capable of performing fast gate operations and
maintaining strong interconnections while preserving their quantum coherence. Since the
inception of experimental eforts toward building a quantum computer, the community has
faced challenges in engineering such a system. Among the various methods of implementing a
quantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,
with the state-of-the-art reaching a coherence of a few milliseconds. However, achieving
simultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits
with high coherence require isolation from the environment, while fast operation necessitates
strong coupling of the qubit. This thesis approaches this issue by proposing the idea of
engineering superconducting qubits capable of transitioning between operating in a protected
regime, where the qubit is completely isolated from the environment, and coupling to the
communication channels as needed. In this direction, we use the geometric superinductor to
scan the parameter space of rf-SQUID devices, searching for a regime where we can take the
qubit protection to its extreme.
This leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1
and EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier
separating the local ground states of each quantum well. In this regime, although it is
anticipated that the two quantum wells would be isolated from each other, we observe single
fuxon tunneling between them. The interplay of the cavity photons and the fuxon transition
forms a rich physical system, containing resonance conditions that allow the preparation of the
fuxon ground or excited states. This enables us to study the relaxation rate of such transition
and show that it can be as large as 3.6 hours. Dynamically controlling the barrier height
between the two quantum wells allows for controllable coupling, which scales exponentially,
for a qubit encoded in two fuxon states.
The 0-π qubit is one of the very few known superconducting circuit types that ofers exponential
protection from both relaxation and dephasing simultaneously. However, this qubit is not
exempt from the fact that such protection comes at the expense of complex readout and
control. In this thesis, we propose a way to controllably break the circuit symmetry, the
key reason for the protection, to momentarily restore the ability to control and manipulate
the qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental
since they lead to coupling of the protected state to the thermally occupied parasitic mode
of the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies
and show that this can be used as a tunable coupler between the protected states. In the
future, this should allow to perform gate operations by dynamically controlling the asymmetry
instead of driving the protected transition with microwave pulses. Therefore, we believe that
the proposed method can make the use of protected qubits more practical in experimental
realizations of quantum computing.},
author = {Hassani, Farid},
isbn = {978-3-99078-040-4},
issn = {2663-337X},
keywords = {Quantum information, Qubits, Superconducting devices},
pages = {161},
publisher = {Institute of Science and Technology Austria},
title = {{Superconducting qubits capable of dynamic switching between protected and high-speed control regimes}},
doi = {10.15479/at:ista:17133},
year = {2024},
}
@unpublished{17136,
abstract = {This paper focuses on Majority Dynamics in sparse graphs, in particular, as a
tool to study internal cuts. It is known that, in Majority Dynamics on a finite
graph, each vertex eventually either comes to a fixed state, or oscillates with
period two. The empirical evidence acquired by simulations suggests that for
random odd-regular graphs, approximately half of the vertices end up
oscillating with high probability. We notice a local symmetry between
oscillating and non-oscillating vertices, that potentially can explain why the
fraction of the oscillating vertices is concentrated around $\frac{1}{2}$. In
our simulations, we observe that the parts of random odd-regular graph under
Majority Dynamics with high probability do not contain $\lceil \frac{d}{2}
\rceil$-cores at any timestep, and thus, one cannot use Majority Dynamics to
prove that internal cuts exist in odd-regular graphs almost surely. However, we
suggest a modification of Majority Dynamics, that yields parts with desired
cores with high probability.},
author = {Arkhipov, Pavel},
booktitle = {arXiv},
title = {{Majority dynamics and internal partitions of random regular graphs: Experimental results}},
doi = {10.48550/arXiv.2406.07026},
year = {2024},
}
@inproceedings{17139,
author = {Schlögl, Alois and Khalid, Waleed and Elefante, Stefano and Stadlbauer, Stephan},
booktitle = {ASHPC24 - Austrian-Slovenian HPC Meeting 2024},
isbn = {9783200096455},
location = {Grundlsee, Austria},
pages = {46},
publisher = {EuroCC Austria},
title = {{How much memory per CPU core is requested?}},
doi = {10.25365/phaidra.463},
year = {2024},
}
@article{17141,
abstract = {The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted to (de)active transcriptional regulation, thus controlling auxin-associated developmental processes. However, the theme of a rapid auxin response has emerged since the 2018 Auxins and Cytokinin in Plant Development conference. To date, a few signaling components have been identified to mediate both slow and rapid auxin responses, which unveils the complexity of auxin signaling.},
author = {Zhang, Zilin and Chen, Huihuang and Peng, Shuaiying and Han, Huibin},
issn = {0022-0957},
journal = {Journal of Experimental Botany},
number = {18},
publisher = {Oxford University Press},
title = {{Slow and rapid auxin responses in Arabidopsis}},
doi = {10.1093/jxb/erae246},
volume = {75},
year = {2024},
}
@article{17142,
abstract = {Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments—a nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment and define a nondevelopmental source of such deficits in ASD.},
author = {Burnett, Laura and Koppensteiner, Peter and Symonova, Olga and Masson, Tomas and Vega Zuniga, Tomas A and Contreras, Ximena and Rülicke, Thomas and Shigemoto, Ryuichi and Novarino, Gaia and Jösch, Maximilian A},
issn = {1545-7885},
journal = {PLoS Biology},
publisher = {Public Library of Science},
title = {{Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice}},
doi = {10.1371/journal.pbio.3002668},
volume = {22},
year = {2024},
}
@article{17143,
abstract = {This paper deals with local criteria for the convergence to a global minimiser for gradient flow trajectories and their discretisations. To obtain quantitative estimates on the speed of convergence, we consider variations on the classical Kurdyka–Łojasiewicz inequality for a large class of parameter functions. Our assumptions are given in terms of the initial data, without any reference to an equilibrium point. The main results are convergence statements for gradient flow curves and proximal point sequences to a global minimiser, together with sharp quantitative estimates on the speed of convergence. These convergence results apply in the general setting of lower semicontinuous functionals on complete metric spaces, generalising recent results for smooth functionals on Rn. While the non-smooth setting covers very general spaces, it is also useful for (non)-smooth functionals on Rn.
.},
author = {Dello Schiavo, Lorenzo and Maas, Jan and Pedrotti, Francesco},
issn = {1088-6850},
journal = {Transactions of the American Mathematical Society},
number = {6},
pages = {3779--3804},
publisher = {American Mathematical Society},
title = {{Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces}},
doi = {10.1090/tran/9156},
volume = {377},
year = {2024},
}
@inproceedings{17144,
abstract = {We prove that the medial axis of closed sets is Hausdorff stable in the following sense: Let 𝒮 ⊆ ℝ^d be a fixed closed set that contains a bounding sphere. That is, the bounding sphere is part of the set 𝒮. Consider the space of C^{1,1} diffeomorphisms of ℝ^d to itself, which keep the bounding sphere invariant. The map from this space of diffeomorphisms (endowed with a Banach norm) to the space of closed subsets of ℝ^d (endowed with the Hausdorff distance), mapping a diffeomorphism F to the closure of the medial axis of F(𝒮), is Lipschitz. This extends a previous stability result of Chazal and Soufflet on the stability of the medial axis of C² manifolds under C² ambient diffeomorphisms.},
author = {Kourimska, Hana and Lieutier, André and Wintraecken, Mathijs},
booktitle = {40th International Symposium on Computational Geometry},
isbn = {9783959773164},
issn = {1868-8969},
location = {Athens, Greece},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms}},
doi = {10.4230/LIPIcs.SoCG.2024.69},
volume = {293},
year = {2024},
}
@inproceedings{17145,
abstract = {Grid peeling is the process of repeatedly removing the convex hull vertices of the grid points that lie inside a given convex curve. It has been conjectured that, for a more and more refined grid, grid peeling converges to a continuous process, the affine curve-shortening flow, which deforms the curve based on the curvature. We prove this conjecture for one class of curves, parabolas with a vertical axis, and we determine the value of the constant factor in the formula that relates the two processes.},
author = {Rote, Günter and Rüber, Moritz and Saghafian, Morteza},
booktitle = {40th International Symposium on Computational Geometry},
isbn = {9783959773164},
issn = {1868-8969},
location = {Athens, Greece},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Grid peeling of parabolas}},
doi = {10.4230/LIPIcs.SoCG.2024.76},
volume = {293},
year = {2024},
}
@article{17154,
abstract = {We compute the deterministic approximation for mixed fluctuation moments of products of deterministic matrices and general Sobolev functions of Wigner matrices. Restricting to polynomials, our formulas reproduce recent results of Male et al. (Random Matrices Theory Appl. 11(2):2250015, 2022), showing that the underlying combinatorics of non-crossing partitions and annular non-crossing permutations continue to stay valid beyond the setting of second-order free probability theory. The formulas obtained further characterize the variance in the functional central limit theorem given in the recent companion paper (Reker in Preprint, arXiv:2204.03419, 2023). and thus allow identifying the fluctuation around the thermal value in certain thermalization problems.},
author = {Reker, Jana},
issn = {1572-9656},
journal = {Mathematical Physics, Analysis and Geometry},
number = {3},
publisher = {Springer Nature},
title = {{Fluctuation moments for regular functions of Wigner Matrices}},
doi = {10.1007/s11040-024-09483-y},
volume = {27},
year = {2024},
}
@phdthesis{17156,
abstract = {This dissertation is the summary of the author’s work, concerning the relations between
cohomology rings of algebraic varieties and rings of functions on zero schemes and fixed
point schemes. For most of the thesis, the focus is on smooth complex varieties with
an action of a principally paired group, e.g. a parabolic subgroup of a reductive group.
The fundamental theorem 5.2.11 from co-authored article [66] says that if the principal
nilpotent has a unique zero, then the zero scheme over the Kostant section is isomorphic
to the spectrum of the equivariant cohomology ring, remembering the grading in terms of
a C^* action. A similar statement is proved also for the G-invariant functions on the total
zero scheme over the whole Lie algebra. Additionally, we are able to prove an analogous
result for the GKM spaces, which poses the question on a joint generalisation.
We also tackle the situation of a singular variety. As long as it is embedded in a smooth
variety with regular action, we are able to study its cohomology as well by means of
the zero scheme. In case of e.g. Schubert varieties this determines the cohomology ring
completely. In largest generality, this allows us to see a significant part of the cohomology
ring.
We also show (Theorem 6.2.1) that the cohomology ring of spherical varieties appears as
the ring of functions on the zero scheme. The computational aspect is not easy, but one
can hope that this can bring some concrete information about such cohomology rings.
Lastly, the K-theory conjecture 6.3.1 is studied, with some results attained for GKM
spaces.
The thesis includes also an introduction to group actions on algebraic varieties. In
particular, the vector fields associated to the actions are extensively studied. We also
provide a version of the Kostant section for arbitrary principally paired group, which
parametrises the regular orbits in the Lie algebra of an algebraic group. Before proving
the main theorem, we also include a historical overview of the field. In particular we bring
together the results of Akyildiz, Carrell and Lieberman on non-equivariant cohomology
rings.},
author = {Rychlewicz, Kamil P},
issn = {2663-337X},
keywords = {equivariant cohomology, zero schemes, algebraic groups, Lie algebras},
pages = {117},
publisher = {Institute of Science and Technology Austria},
title = {{Equivariant cohomology and rings of functions}},
doi = {10.15479/at:ista:17156},
year = {2024},
}
@article{17162,
abstract = {Cost analysis, also known as resource usage analysis, is the task of finding bounds on the total cost of a program and is a well-studied problem in static analysis. In this work, we consider two classical quantitative problems in cost analysis for probabilistic programs. The first problem is to find a bound on the expected total cost of the program. This is a natural measure for the resource usage of the program and can also be directly applied to average-case runtime analysis. The second problem asks for a tail bound, i.e. given a threshold t the goal is to find a probability bound p such that ℙ[total cost ≥ t] ≤ p. Intuitively, given a threshold t on the resource, the problem is to find the likelihood that the total cost exceeds this threshold.
First, for expectation bounds, a major obstacle in previous works on cost analysis is that they can handle only non-negative costs or bounded variable updates. In contrast, we provide a new variant of the standard notion of cost martingales, that allows us to find expectation bounds for a class of programs with general positive or negative costs and no restriction on the variable updates. More specifically, our approach is applicable as long as there is a lower bound on the total cost incurred along every path.
Second, for tail bounds, all previous methods are limited to programs in which the expected total cost is finite. In contrast, we present a novel approach, based on a combination of our martingale-based method for expectation bounds with a quantitative safety analysis, to obtain a solution to the tail bound problem that is applicable even to programs with infinite expected cost. Specifically, this allows us to obtain runtime tail bounds for programs that do not terminate almost-surely.
In summary, we provide a novel combination of martingale-based cost analysis and quantitative safety analysis that is able to find expectation and tail cost bounds for probabilistic programs, without the restrictions of non-negative costs, bounded updates, or finiteness of the expected total cost. Finally, we provide experimental results showcasing that our approach can solve instances that were beyond the reach of previous methods.},
author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Meggendorfer, Tobias and Zikelic, Dorde},
issn = {2475-1421},
journal = {Proceedings of the ACM on Programming Languages},
number = {OOPSLA1},
publisher = {Association for Computing Machinery},
title = {{Quantitative bounds on resource usage of probabilistic programs}},
doi = {10.1145/3649824},
volume = {8},
year = {2024},
}