@article{8373,
abstract = {It is well known that special Kubo-Ando operator means admit divergence center interpretations, moreover, they are also mean squared error estimators for certain metrics on positive definite operators. In this paper we give a divergence center interpretation for every symmetric Kubo-Ando mean. This characterization of the symmetric means naturally leads to a definition of weighted and multivariate versions of a large class of symmetric Kubo-Ando means. We study elementary properties of these weighted multivariate means, and note in particular that in the special case of the geometric mean we recover the weighted A#H-mean introduced by Kim, Lawson, and Lim.},
author = {Pitrik, József and Virosztek, Daniel},
issn = {0024-3795},
journal = {Linear Algebra and its Applications},
keywords = {Kubo-Ando mean, weighted multivariate mean, barycenter},
pages = {203--217},
publisher = {Elsevier},
title = {{A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means}},
doi = {10.1016/j.laa.2020.09.007},
volume = {609},
year = {2021},
}
@article{8988,
abstract = {The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.},
author = {Düllberg, Christian F and Auer, Albert and Canigova, Nikola and Loibl, Katrin and Loose, Martin},
issn = {10916490},
journal = {PNAS},
number = {1},
publisher = {National Academy of Sciences},
title = {{In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1}},
doi = {10.1073/pnas.2010054118},
volume = {118},
year = {2021},
}
@article{8992,
abstract = {The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.},
author = {Tan, Shutang and Luschnig, Christian and Friml, Jiří},
issn = {17529867},
journal = {Molecular Plant},
number = {1},
pages = {151--165},
publisher = {Elsevier},
title = {{Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling}},
doi = {10.1016/j.molp.2020.11.004},
volume = {14},
year = {2021},
}
@article{8993,
abstract = {N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.},
author = {Abas, Lindy and Kolb, Martina and Stadlmann, Johannes and Janacek, Dorina P. and Lukic, Kristina and Schwechheimer, Claus and Sazanov, Leonid A and Mach, Lukas and Friml, Jiří and Hammes, Ulrich Z.},
issn = {10916490},
journal = {PNAS},
number = {1},
publisher = {National Academy of Sciences},
title = {{Naphthylphthalamic acid associates with and inhibits PIN auxin transporters}},
doi = {10.1073/pnas.2020857118},
volume = {118},
year = {2021},
}
@article{8997,
abstract = {Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.},
author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias},
issn = {1553-7358},
journal = {PLOS Computational Biology},
keywords = {Modelling and Simulation, Genetics, Molecular Biology, Antibiotics, Drug interactions},
number = {1},
publisher = {Public Library of Science},
title = {{Minimal biophysical model of combined antibiotic action}},
doi = {10.1371/journal.pcbi.1008529},
volume = {17},
year = {2021},
}
@article{8999,
abstract = {In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not
arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. },
author = {Avila, Kerstin and Hof, Björn},
issn = {1099-4300},
journal = {Entropy},
number = {1},
publisher = {MDPI},
title = {{Second-order phase transition in counter-rotating taylor-couette flow experiment}},
doi = {10.3390/e23010058},
volume = {23},
year = {2021},
}
@phdthesis{8934,
abstract = {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.
We 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.},
author = {Goharshady, Amir Kafshdar},
issn = {2663-337X},
pages = {278},
publisher = {IST Austria},
title = {{Parameterized and algebro-geometric advances in static program analysis}},
doi = {10.15479/AT:ISTA:8934},
year = {2021},
}
@article{177,
abstract = {We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree.},
author = {Browning, Timothy D and Sawin, Will},
journal = {Annals of Mathematics},
number = {3},
pages = {893--948},
publisher = {Princeton University},
title = {{A geometric version of the circle method}},
doi = {10.4007/annals.2020.191.3.4},
volume = {191},
year = {2020},
}
@article{179,
abstract = {An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.},
author = {Browning, Timothy D and Heath Brown, Roger},
journal = {Duke Mathematical Journal},
number = {16},
pages = {3099--3165},
publisher = {Project Euclid},
title = {{Density of rational points on a quadric bundle in ℙ3×ℙ3}},
doi = {10.1215/00127094-2020-0031},
volume = {169},
year = {2020},
}
@article{5681,
abstract = {We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.},
author = {Hikaru, Ibayashi and Wojtan, Christopher J and Thuerey, Nils and Igarashi, Takeo and Ando, Ryoichi},
issn = {19410506},
journal = {IEEE Transactions on Visualization and Computer Graphics},
number = {6},
pages = {2288--2302},
publisher = {IEEE},
title = {{Simulating liquids on dynamically warping grids}},
doi = {10.1109/TVCG.2018.2883628},
volume = {26},
year = {2020},
}
@article{6185,
abstract = {For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).},
author = {Erdös, László and Krüger, Torben H and Schröder, Dominik J},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
pages = {1203--1278},
publisher = {Springer Nature},
title = {{Cusp universality for random matrices I: Local law and the complex Hermitian case}},
doi = {10.1007/s00220-019-03657-4},
volume = {378},
year = {2020},
}
@article{6184,
abstract = {We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.},
author = {Alt, Johannes and Erdös, László and Krüger, Torben H and Schröder, Dominik J},
journal = {Annals of Probability},
number = {2},
pages = {963--1001},
publisher = {Project Euclid},
title = {{Correlated random matrices: Band rigidity and edge universality}},
volume = {48},
year = {2020},
}
@article{6358,
abstract = {We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras. Our settingcovers arbitrary skew-derivations and it provides a unified framework that simultaneously generalizes recently constructed transport metrics for Markov chains, Lindblad equations, and the Fermi Ornstein–Uhlenbeck semigroup. We develop a non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature bounds, logarithmic Sobolev inequalities, transport-entropy inequalities, andspectral gap estimates.},
author = {Carlen, Eric A. and Maas, Jan},
issn = {15729613},
journal = {Journal of Statistical Physics},
number = {2},
pages = {319--378},
publisher = {Springer Nature},
title = {{Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems}},
doi = {10.1007/s10955-019-02434-w},
volume = {178},
year = {2020},
}
@article{6359,
abstract = {The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.},
author = {Dareiotis, Konstantinos and Gerencser, Mate},
issn = {1083-6489},
journal = {Electronic Journal of Probability},
publisher = { Institute of Mathematical Statistics},
title = {{On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift}},
doi = {10.1214/20-EJP479},
volume = {25},
year = {2020},
}
@article{6488,
abstract = {We prove a central limit theorem for the difference of linear eigenvalue statistics of a sample covariance matrix W˜ and its minor W. We find that the fluctuation of this difference is much smaller than those of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of W˜ and W. Our result identifies the fluctuation of the spatial derivative of the approximate Gaussian field in the recent paper by Dumitru and Paquette. Unlike in a similar result for Wigner matrices, for sample covariance matrices, the fluctuation may entirely vanish.},
author = {Cipolloni, Giorgio and Erdös, László},
issn = {20103271},
journal = {Random Matrices: Theory and Application},
number = {3},
publisher = {World Scientific Publishing},
title = {{Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices}},
doi = {10.1142/S2010326320500069},
volume = {9},
year = {2020},
}
@article{6563,
abstract = {This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋.},
author = {Filakovský, Marek and Vokřínek, Lukas},
issn = {16153383},
journal = {Foundations of Computational Mathematics},
pages = {311--330},
publisher = {Springer Nature},
title = {{Are two given maps homotopic? An algorithmic viewpoint}},
doi = {10.1007/s10208-019-09419-x},
volume = {20},
year = {2020},
}
@article{6593,
abstract = {We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising.},
author = {Shehu, Yekini and Li, Xiao-Huan and Dong, Qiao-Li},
issn = {1017-1398},
journal = {Numerical Algorithms},
pages = {365--388},
publisher = {Springer Nature},
title = {{An efficient projection-type method for monotone variational inequalities in Hilbert spaces}},
doi = {10.1007/s11075-019-00758-y},
volume = {84},
year = {2020},
}
@article{6649,
abstract = {While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.
},
author = {Benedikter, Niels P and Nam, Phan Thành and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
pages = {2097–2150},
publisher = {Springer Nature},
title = {{Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime}},
doi = {10.1007/s00220-019-03505-5},
volume = {374},
year = {2020},
}
@article{6748,
abstract = {Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.
Here we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge.},
author = {Javanmard, Adel and Mondelli, Marco and Montanari, Andrea},
journal = {Annals of Statistics},
number = {6},
pages = {3619--3642},
publisher = {Project Euclid},
title = {{Analysis of a two-layer neural network via displacement convexity}},
doi = {10.1214/20-AOS1945},
volume = {48},
year = {2020},
}
@article{6796,
abstract = {Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.},
author = {Stella, Federico and Urdapilleta, Eugenio and Luo, Yifan and Treves, Alessandro},
issn = {10981063},
journal = {Hippocampus},
number = {4},
pages = {302--313},
publisher = {Wiley},
title = {{Partial coherence and frustration in self-organizing spherical grids}},
doi = {10.1002/hipo.23144},
volume = {30},
year = {2020},
}