@article{12280,
  abstract     = {In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate.},
  author       = {Schmid, Laura and Hilbe, Christian and Chatterjee, Krishnendu and Nowak, Martin},
  issn         = {1553-7358},
  journal      = {PLOS Computational Biology},
  keywords     = {Computational Theory and Mathematics, Cellular and Molecular Neuroscience, Genetics, Molecular Biology, Ecology, Modeling and Simulation, Ecology, Evolution, Behavior and Systematics},
  number       = {6},
  publisher    = {Public Library of Science},
  title        = {{Direct reciprocity between individuals that use different strategy spaces}},
  doi          = {10.1371/journal.pcbi.1010149},
  volume       = {18},
  year         = {2022},
}

@article{12281,
  abstract     = {We study the hydrodynamic and hydrostatic limits of the one-dimensional open symmetric inclusion process with slow boundary. Depending on the value of the parameter tuning the interaction rate of the bulk of the system with the boundary, we obtain a linear heat equation with either Dirichlet, Robin or Neumann boundary conditions as hydrodynamic equation. In our approach, we combine duality and first-second class particle techniques to reduce the scaling limit of the inclusion process to the limiting behavior of a single, non-interacting, particle.},
  author       = {Franceschini, Chiara and Gonçalves, Patrícia and Sau, Federico},
  issn         = {1350-7265},
  journal      = {Bernoulli},
  keywords     = {Statistics and Probability},
  number       = {2},
  pages        = {1340--1381},
  publisher    = {Bernoulli Society for Mathematical Statistics and Probability},
  title        = {{Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics}},
  doi          = {10.3150/21-bej1390},
  volume       = {28},
  year         = {2022},
}

@article{12282,
  abstract     = {From a simple thought to a multicellular movement},
  author       = {Amberg, Nicole and Stouffer, Melissa A and Vercellino, Irene},
  issn         = {1477-9137},
  journal      = {Journal of Cell Science},
  number       = {8},
  publisher    = {The Company of Biologists},
  title        = {{Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole}},
  doi          = {10.1242/jcs.260017},
  volume       = {135},
  year         = {2022},
}

@article{12283,
  abstract     = {Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration.},
  author       = {Atherton, Joseph and Stouffer, Melissa A and Francis, Fiona and Moores, Carolyn A.},
  issn         = {1477-9137},
  journal      = {Journal of Cell Science},
  keywords     = {Cell Biology},
  number       = {7},
  publisher    = {The Company of Biologists},
  title        = {{Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography}},
  doi          = {10.1242/jcs.259234},
  volume       = {135},
  year         = {2022},
}

@article{12288,
  abstract     = {To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo.},
  author       = {Sumser, Anton L and Jösch, Maximilian A and Jonas, Peter M and Ben Simon, Yoav},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling}},
  doi          = {10.7554/elife.79848},
  volume       = {11},
  year         = {2022},
}

@article{12290,
  abstract     = {We prove local laws, i.e. optimal concentration estimates for arbitrary products of resolvents of a Wigner random matrix with deterministic matrices in between. We find that the size of such products heavily depends on whether some of the deterministic matrices are traceless. Our estimates correctly account for this dependence and they hold optimally down to the smallest possible spectral scale.},
  author       = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J},
  issn         = {1083-6489},
  journal      = {Electronic Journal of Probability},
  keywords     = {Statistics, Probability and Uncertainty, Statistics and Probability},
  pages        = {1--38},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Optimal multi-resolvent local laws for Wigner matrices}},
  doi          = {10.1214/22-ejp838},
  volume       = {27},
  year         = {2022},
}

@inbook{12294,
  abstract     = {Brassicaceae are blessed with specialized metabolites called glucosinolates (GSLs), which along with their degradation products, are beneficial in agriculture and human health. To date, more than 130 GSL structures have been identified, mostly derived from the amino acid methionine. The biosynthesis of methionine-derived aliphatic GSLs starts with a side-chain elongation step involving a recursive three-step cyclic process that incorporates a new methylene group into the 2-oxo acid to form a series of elongated 2-oxo acids. Methylthioalkylmalate synthase (MAMS) catalyzes the first committed step in the side-chain elongation of methionine-derived GSLs. The substrate specificity of MAMS with different 2-oxo acids determines whether reaction products of a given cycle enter for an additional round of chain elongation or enter into core GSLs structure formation. Multiple MAMS encoding genes are present in the Brassicaceae species and are known to play a central role in shaping the diverse profile of aliphatic GSLs. We recently established a highly sensitive LC-MS/MS-based methodology that quantifies the MAMS activity by estimating the amount of the next intermediate of the pathway, the 2-malate derivatives. Overall, this chapter describes the protocol for the expression, purification, and steady-state kinetic analysis of the recombinant MAMS protein.},
  author       = {Kumar, Roshan and Reichelt, Michael and Bisht, Naveen C.},
  booktitle    = {Biochemical Pathways and Environmental Responses in Plants: Part A},
  editor       = {Jez, Joseph},
  isbn         = {9780323955614},
  issn         = {0076-6879},
  pages        = {49--69},
  publisher    = {Elsevier},
  title        = {{An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis}},
  doi          = {10.1016/bs.mie.2022.07.019},
  volume       = {676},
  year         = {2022},
}

@inproceedings{12298,
  abstract     = {Existing committee-based Byzantine state machine replication (SMR) protocols, typically deployed in production blockchains, face a clear trade-off: (1) they either achieve linear communication cost in the steady state, but sacrifice liveness during periods of asynchrony, or (2) they are robust (progress with probability one) but pay quadratic communication cost. We believe this trade-off is unwarranted since existing linear protocols still have asymptotic quadratic cost in the worst case. We design Ditto, a Byzantine SMR protocol that enjoys the best of both worlds: optimal communication on and off the steady state (linear and quadratic, respectively) and progress guarantee under asynchrony and DDoS attacks. We achieve this by replacing the view-synchronization of partially synchronous protocols with an asynchronous fallback mechanism at no extra asymptotic cost. Specifically, we start from HotStuff, a state-of-the-art linear protocol, and gradually build Ditto. As a separate contribution and an intermediate step, we design a 2-chain version of HotStuff, Jolteon, which leverages a quadratic view-change mechanism to reduce the latency of the standard 3-chain HotStuff. We implement and experimentally evaluate all our systems to prove that breaking the robustness-efficiency trade-off is in the realm of practicality.},
  author       = {Gelashvili, Rati and Kokoris Kogias, Eleftherios and Sonnino, Alberto and Spiegelman, Alexander and Xiang, Zhuolun},
  booktitle    = {Financial Cryptography and Data Security},
  isbn         = {9783031182822},
  issn         = {1611-3349},
  location     = {Radisson Grenada Beach Resort, Grenada},
  pages        = {296--315},
  publisher    = {Springer Nature},
  title        = {{Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback}},
  doi          = {10.1007/978-3-031-18283-9_14},
  volume       = {13411},
  year         = {2022},
}

@inproceedings{12302,
  abstract     = {We propose a novel algorithm to decide the language inclusion between (nondeterministic) Büchi automata, a PSPACE-complete problem. Our approach, like others before, leverage a notion of quasiorder to prune the search for a counterexample by discarding candidates which are subsumed by others for the quasiorder. Discarded candidates are guaranteed to not compromise the completeness of the algorithm. The novelty of our work lies in the quasiorder used to discard candidates. We introduce FORQs (family of right quasiorders) that we obtain by adapting the notion of family of right congruences put forward by Maler and Staiger in 1993. We define a FORQ-based inclusion algorithm which we prove correct and instantiate it for a specific FORQ, called the structural FORQ, induced by the Büchi automaton to the right of the inclusion sign. The resulting implementation, called FORKLIFT, scales up better than the state-of-the-art on a variety of benchmarks including benchmarks from program verification and theorem proving for word combinatorics. Artifact: https://doi.org/10.5281/zenodo.6552870},
  author       = {Doveri, Kyveli and Ganty, Pierre and Mazzocchi, Nicolas Adrien},
  booktitle    = {Computer Aided Verification},
  isbn         = {9783031131875},
  issn         = {1611-3349},
  location     = {Haifa, Israel},
  pages        = {109--129},
  publisher    = {Springer Nature},
  title        = {{FORQ-based language inclusion formal testing}},
  doi          = {10.1007/978-3-031-13188-2_6},
  volume       = {13372},
  year         = {2022},
}

@inbook{12303,
  abstract     = {We construct for each choice of a quiver Q, a cohomology theory A, and a poset P a “loop Grassmannian” GP(Q,A). This generalizes loop Grassmannians of semisimple groups and the loop Grassmannians of based quadratic forms. The addition of a “dilation” torus D⊆G2m gives a quantization GPD(Q,A). This construction is motivated by the program of introducing an inner cohomology theory in algebraic geometry adequate for the Geometric Langlands program (Mirković, Some extensions of the notion of loop Grassmannians. Rad Hrvat. Akad. Znan. Umjet. Mat. Znan., the Mardešić issue. No. 532, 53–74, 2017) and on the construction of affine quantum groups from generalized cohomology theories (Yang and Zhao, Quiver varieties and elliptic quantum groups, preprint. arxiv1708.01418).},
  author       = {Mirković, Ivan and Yang, Yaping and Zhao, Gufang},
  booktitle    = {Representation Theory and Algebraic Geometry},
  editor       = {Baranovskky, Vladimir and Guay, Nicolas and Schedler, Travis},
  isbn         = {9783030820060},
  issn         = {2297-024X},
  pages        = {347--392},
  publisher    = {Springer Nature; Birkhäuser},
  title        = {{Loop Grassmannians of Quivers and Affine Quantum Groups}},
  doi          = {10.1007/978-3-030-82007-7_8},
  year         = {2022},
}

@article{12304,
  abstract     = {We establish sharp criteria for the instantaneous propagation of free boundaries in solutions to the thin-film equation. The criteria are formulated in terms of the initial distribution of mass (as opposed to previous almost-optimal results), reflecting the fact that mass is a locally conserved quantity for the thin-film equation. In the regime of weak slippage, our criteria are at the same time necessary and sufficient. The proof of our upper bounds on free boundary propagation is based on a strategy of “propagation of degeneracy” down to arbitrarily small spatial scales: We combine estimates on the local mass and estimates on energies to show that “degeneracy” on a certain space-time cylinder entails “degeneracy” on a spatially smaller space-time cylinder with the same time horizon. The derivation of our lower bounds on free boundary propagation is based on a combination of a monotone quantity and almost optimal estimates established previously by the second author with a new estimate connecting motion of mass to entropy production.},
  author       = {De Nitti, Nicola and Fischer, Julian L},
  issn         = {1532-4133},
  journal      = {Communications in Partial Differential Equations},
  keywords     = {Applied Mathematics, Analysis},
  number       = {7},
  pages        = {1394--1434},
  publisher    = {Taylor & Francis},
  title        = {{Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation}},
  doi          = {10.1080/03605302.2022.2056702},
  volume       = {47},
  year         = {2022},
}

@article{12305,
  abstract     = {This paper is concerned with the sharp interface limit for the Allen--Cahn equation with a nonlinear Robin boundary condition in a bounded smooth domain Ω⊂\R2. We assume that a diffuse interface already has developed and that it is in contact with the boundary ∂Ω. The boundary condition is designed in such a way that the limit problem is given by the mean curvature flow with constant α-contact angle. For α close to 90° we prove a local in time convergence result for well-prepared initial data for times when a smooth solution to the limit problem exists. Based on the latter we construct a suitable curvilinear coordinate system and carry out a rigorous asymptotic expansion for the Allen--Cahn equation with the nonlinear Robin boundary condition. Moreover, we show a spectral estimate for the corresponding linearized Allen--Cahn operator and with its aid we derive strong norm estimates for the difference of the exact and approximate solutions using a Gronwall-type argument.},
  author       = {Abels, Helmut and Moser, Maximilian},
  issn         = {1095-7154},
  journal      = {SIAM Journal on Mathematical Analysis},
  keywords     = {Applied Mathematics, Computational Mathematics, Analysis},
  number       = {1},
  pages        = {114--172},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°}},
  doi          = {10.1137/21m1424925},
  volume       = {54},
  year         = {2022},
}

@article{12307,
  abstract     = {Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences.},
  author       = {Shipman, Barbara A. and Stephenson, Elizabeth R},
  issn         = {1935-4053},
  journal      = {PRIMUS},
  keywords     = {Education, General Mathematics},
  number       = {5},
  pages        = {593--609},
  publisher    = {Taylor & Francis},
  title        = {{Tangible topology through the lens of limits}},
  doi          = {10.1080/10511970.2021.1872750},
  volume       = {32},
  year         = {2022},
}

@article{12332,
  abstract     = {Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments.},
  author       = {Mlynarski, Wiktor F and Tkačik, Gašper},
  issn         = {1545-7885},
  journal      = {PLoS Biology},
  number       = {12},
  pages        = {e3001889},
  publisher    = {Public Library of Science},
  title        = {{Efficient coding theory of dynamic attentional modulation}},
  doi          = {10.1371/journal.pbio.3001889},
  volume       = {20},
  year         = {2022},
}

@article{12333,
  abstract     = {Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli. We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales.},
  author       = {Tomanek, Isabella and Guet, Calin C},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Adaptation dynamics between copynumber and point mutations}},
  doi          = {10.7554/ELIFE.82240},
  volume       = {11},
  year         = {2022},
}

@misc{12339,
  abstract     = {Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales.},
  author       = {Tomanek, Isabella and Guet, Calin C},
  publisher    = {Dryad},
  title        = {{Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose}},
  doi          = {10.5061/dryad.rfj6q57ds},
  year         = {2022},
}

@phdthesis{12358,
  abstract     = {The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and
visual complexity. The small-scale interactions of yarns colliding with and pulling on each
other result in drastically different large-scale stretching and bending behavior, introducing
anisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this
complexity and match the quality of real fabric, it may be too computationally expensive for
large fabrics. On the other hand, continuum-based approaches do not need to discretize the
cloth at a stitch-level, but it is non-trivial to find a material model that would replicate the
large-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,
we discuss three methods to try and bridge the gap between small-scale and large-scale yarn
mechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively
fitting yarn parameters to physical measurements of real fabric.
To start, we present a method for animating yarn-level cloth effects using a thin-shell solver.
We first use a large number of periodic yarn-level simulations to build a model of the potential
energy density of the cloth, and then use it to compute forces in a thin-shell simulator. The
resulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics
and the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of
full yarn-level simulation.
While our thin-shell simulations are able to capture large-scale yarn mechanics, they lack
the rich visual detail of yarn-level simulations. Therefore, we propose a method to animate
yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware
fashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are
able to reproduce effects such as knit loops tightening under stretching at negligible cost.
Finally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,
based on the mechanical response of fabrics in the real world. We compile a database from
physical tests of several knitted fabrics used in the textile industry spanning diverse physical
properties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized
shell models to speed up computation and adding some small-but-necessary extensions to
yarn-level models used in computer graphics.
},
  author       = {Sperl, Georg},
  isbn         = {978-3-99078-020-6},
  issn         = {2663-337X},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting}},
  doi          = {10.15479/at:ista:12103},
  year         = {2022},
}

@phdthesis{12368,
  abstract     = {Metazoan development relies on the formation and remodeling of cell-cell contacts. The 
binding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell 
interaction sites have been implicated in cell-cell contact formation. Yet, how these two 
processes functionally interact to drive cell-cell contact expansion and strengthening 
remains unclear. Here, we study how primary germ layer progenitor cells from zebrafish 
bind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an 
assay system for monitoring cell-cell contact formation at high spatiotemporal resolution. 
We show that cell-cell contact formation represents a two-tiered process: E-cadherinmediated downregulation of the small GTPase RhoA at the forming contact leads to both 
depletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin 
network flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the 
contact zone, with Myosin-2 displaying higher cortical localization outside than inside of 
the contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin 
network at the contact disc, but also lead to an accumulation of both F-actin and Ecadherin at the contact rim. Eventually, this combination of actomyosin downregulation 
and flows at the contact contribute to the characteristic molecular organization implicated 
in contact formation and maintenance: depletion of cortical actomyosin at the contact disc, 
driving contact expansion by lowering interfacial tension at the contact, and accumulation 
of both E-cadherin and F-actin at the contact rim, mechanically linking the contractile 
cortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how 
adhesion signaling and cell mechanics function together to modulate the spatial 
organization of cell-cell contacts.},
  author       = {Arslan, Feyza N},
  isbn         = {978-3-99078-025-1 },
  issn         = {2663-337X},
  pages        = {113},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Remodeling of E-cadherin-mediated contacts via cortical  flows}},
  doi          = {10.15479/at:ista:12153},
  year         = {2022},
}

@phdthesis{12390,
  abstract     = {The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that
is broken on the level of the corresponding effective theory. In particular we are going to
investigate translation-invariant Bose gases in the mean field limit, effectively described by
the Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively
described by the Pekar functional. The latter is a model describing the interaction between a
charged particle and the optical modes of a polar crystal. Regarding the former, we assume in
addition that the particles in the gas are unconfined, and typically we will consider particles
that are subject to an attractive interaction. In both cases the ground state energy of the
Hamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on
the contrary there exists a whole invariant orbit of minimizers for the corresponding effective
functionals. Both, the absence of proper eigenstates and the broken symmetry of the effective
theory, make the study significantly more involved and it is the content of this thesis to
develop a frameworks which allows for a systematic way to circumvent these issues.
It is a well-established result that the ground state energy of Bose gases in the mean field limit,
as well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is
to leading order given by the minimal energy of the corresponding effective theory. As part
of this thesis we identify the sub-leading term in the expansion of the ground state energy,
which can be interpreted as the quantum correction to the classical energy, since the effective
theories under consideration can be seen as classical counterparts.
We are further going to establish an asymptotic expression for the energy-momentum relation
of the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,
this asymptotic expression agrees with the energy-momentum relation of a free particle having
an effectively increased mass, and we find that this effectively increased mass agrees with the
conjectured value in the physics literature.
In addition we will discuss two unrelated papers written by the author during his stay at ISTA
in the appendix. The first one concerns the realization of anyons, which are quasi-particles
acquiring a non-trivial phase under the exchange of two particles, as molecular impurities.
The second one provides a classification of those vector fields defined on a given manifold
that can be written as the gradient of a given functional with respect to a suitable metric,
provided that some mild smoothness assumptions hold. This classification is subsequently
used to identify those quantum Markov semigroups that can be written as a gradient flow of
the relative entropy.
},
  author       = {Brooks, Morris},
  issn         = {2663-337X},
  pages        = {196},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Translation-invariant quantum systems with effectively broken symmetry}},
  doi          = {10.15479/at:ista:12390},
  year         = {2022},
}

@article{12431,
  abstract     = {This paper presents a new representation of curve dynamics, with applications to vortex filaments in fluid dynamics. Instead of representing these filaments with explicit curve geometry and Lagrangian equations of motion, we represent curves implicitly with a new co-dimensional 2 level set description. Our implicit representation admits several redundant mathematical degrees of freedom in both the configuration and the dynamics of the curves, which can be tailored specifically to improve numerical robustness, in contrast to naive approaches for implicit curve dynamics that suffer from overwhelming numerical stability problems. Furthermore, we note how these hidden degrees of freedom perfectly map to a Clebsch representation in fluid dynamics. Motivated by these observations, we introduce untwisted level set functions and non-swirling dynamics which successfully regularize sources of numerical instability, particularly in the twisting modes around curve filaments. A consequence is a novel simulation method which produces stable dynamics for large numbers of interacting vortex filaments and effortlessly handles topological changes and re-connection events.},
  author       = {Ishida, Sadashige and Wojtan, Christopher J and Chern, Albert},
  issn         = {1557-7368},
  journal      = {ACM Transactions on Graphics},
  number       = {6},
  publisher    = {Association for Computing Machinery},
  title        = {{Hidden degrees of freedom in implicit vortex filaments}},
  doi          = {10.1145/3550454.3555459},
  volume       = {41},
  year         = {2022},
}