@inbook{9132, abstract = {We see them in our everyday lives. They make skies and sunsets even more beautiful, inspiring painters all over the world. But what are clouds? What are the physical processes occurring within a cloud? Do they all look alike, or are there different types of clouds? Why? Beyond our small human scale, how are clouds distributed at large, planetary scales? How do they couple and interact with the large-scale circulation of the atmosphere? What do the physics of cloud formation tell us about the hydrological cycle, including mean and extreme precipitation, in our current climate and in a warming world? What role do they play in the global energetics of the planet, for instance by reflecting the incoming shortwave radiation from the Sun, and by reducing the outgoing longwave radiation to space, because of their high altitudes and thus cold temperatures? These are the questions that will be addressed in these five lectures.}, author = {Muller, Caroline J}, booktitle = {Fundamental Aspects of Turbulent Flows in Climate Dynamics}, editor = {Bouchet, Freddy and Schneider, Tapio and Venaille, Antoine and Salomon, Christophe}, isbn = {978-0-1988-5521-7}, publisher = {Oxford University Press}, title = {{Clouds in current and in a warming climate}}, doi = {10.1093/oso/9780198855217.003.0002}, volume = {109}, year = {2020}, } @unpublished{9150, abstract = {The goal of this study is twofold. First, we aim at developing a simple model as an interpretative framework for the water vapor isotopic variations in the tropical troposphere over the ocean. We use large-eddy simulations to justify the underlying assumptions of this simple model, to constrain its input parameters and to evaluate its results. Second, we aim at interpreting the depletion of the water vapor isotopic composition in the lower and mid-troposphere as precipitation increases, which is a salient feature in tropical oceanic observations. This feature constitutes a stringent test on the relevance of our interpretative framework. Previous studies, based on observations or on models with parameterized convection, have highlighted the roles of deep convective and meso-scale downdrafts, rain evaporation, rain-vapor diffusive exchanges and mixing processes. The interpretative framework that we develop is a two-column model representing the net ascent in clouds and the net descent in the environment. We show that the mechanisms for depleting the troposphere when precipitation rate increases all stem from the higher tropospheric relative humidity. First, when the relative humidity is larger, less snow sublimates before melting and a smaller fraction of rain evaporates. Both effects lead to more depleted rain evaporation and eventually more depleted water vapor. This mechanism dominates in regimes of large-scale ascent. Second, the entrainment of dry air into clouds reduces the vertical isotopic gradient and limits the depletion of tropospheric water vapor. This mechanism dominates in regimes of large-scale descent.}, author = {Risi, Camille and Muller, Caroline J and Blossey, Peter N.}, publisher = {ESSOAr}, title = {{Rain evaporation, snow melt and entrainment at the heart of water vapor isotopic variations in the tropical troposphere, according to large-eddy simulations and a two-column model}}, doi = {10.1002/essoar.10504670.1}, year = {2020}, } @article{9156, abstract = {The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.}, author = {Akopyan, Arseniy and Edelsbrunner, Herbert}, issn = {2544-7297}, journal = {Computational and Mathematical Biophysics}, number = {1}, pages = {74--88}, publisher = {De Gruyter}, title = {{The weighted Gaussian curvature derivative of a space-filling diagram}}, doi = {10.1515/cmb-2020-0101}, volume = {8}, year = {2020}, } @article{9157, abstract = {Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy.}, author = {Akopyan, Arseniy and Edelsbrunner, Herbert}, issn = {2544-7297}, journal = {Computational and Mathematical Biophysics}, number = {1}, pages = {51--67}, publisher = {De Gruyter}, title = {{The weighted mean curvature derivative of a space-filling diagram}}, doi = {10.1515/cmb-2020-0100}, volume = {8}, year = {2020}, } @article{9162, abstract = {Active navigation relies on effectively extracting information from the surrounding environment, and often features the tracking of gradients of a relevant signal—such as the concentration of molecules. Microfluidic networks of closed pathways pose the challenge of determining the shortest exit pathway, which involves the proper local decision-making at each bifurcating junction. Here, we focus on the basic decision faced at a T-junction by a microscopic particle, which orients among possible paths via its sensing of a diffusible substance's concentration. We study experimentally the navigation of colloidal particles following concentration gradients by diffusiophoresis. We treat the situation as a mean first passage time (MFPT) problem that unveils the important role of a separatrix in the concentration field to determine the statistics of path taking. Further, we use numerical experiments to study different strategies, including biomimetic ones such as run and tumble or Markovian chemotactic migration. The discontinuity in the MFPT at the junction makes it remarkably difficult for microscopic agents to follow the shortest path, irrespective of adopted navigation strategy. In contrast, increasing the size of the sensing agents improves the efficiency of short-path taking by harvesting information on a larger scale. It inspires the development of a run-and-whirl dynamics that takes advantage of the mathematical properties of harmonic functions to emulate particles beyond their own size.}, author = {Gandhi, Tanvi and Mac Huang, Jinzi and Aubret, Antoine and Li, Yaocheng and Ramananarivo, Sophie and Vergassola, Massimo and Palacci, Jérémie A}, issn = {2469-990X}, journal = {Physical Review Fluids}, number = {10}, publisher = {American Physical Society}, title = {{Decision-making at a T-junction by gradient-sensing microscopic agents}}, doi = {10.1103/physrevfluids.5.104202}, volume = {5}, year = {2020}, } @article{9164, author = {Speck, Thomas and Tailleur, Julien and Palacci, Jérémie A}, issn = {1367-2630}, journal = {New Journal of Physics}, keywords = {General Physics and Astronomy}, number = {6}, publisher = {IOP Publishing}, title = {{Focus on active colloids and nanoparticles}}, doi = {10.1088/1367-2630/ab90d9}, volume = {22}, year = {2020}, } @article{9194, abstract = {Quantum transduction, the process of converting quantum signals from one form of energy to another, is an important area of quantum science and technology. The present perspective article reviews quantum transduction between microwave and optical photons, an area that has recently seen a lot of activity and progress because of its relevance for connecting superconducting quantum processors over long distances, among other applications. Our review covers the leading approaches to achieving such transduction, with an emphasis on those based on atomic ensembles, opto-electro-mechanics, and electro-optics. We briefly discuss relevant metrics from the point of view of different applications, as well as challenges for the future.}, author = {Lauk, Nikolai and Sinclair, Neil and Barzanjeh, Shabir and Covey, Jacob P and Saffman, Mark and Spiropulu, Maria and Simon, Christoph}, issn = {2058-9565}, journal = {Quantum Science and Technology}, number = {2}, publisher = {IOP Publishing}, title = {{Perspectives on quantum transduction}}, doi = {10.1088/2058-9565/ab788a}, volume = {5}, year = {2020}, } @article{9195, abstract = {Quantum information technology based on solid state qubits has created much interest in converting quantum states from the microwave to the optical domain. Optical photons, unlike microwave photons, can be transmitted by fiber, making them suitable for long distance quantum communication. Moreover, the optical domain offers access to a large set of very well‐developed quantum optical tools, such as highly efficient single‐photon detectors and long‐lived quantum memories. For a high fidelity microwave to optical transducer, efficient conversion at single photon level and low added noise is needed. Currently, the most promising approaches to build such systems are based on second‐order nonlinear phenomena such as optomechanical and electro‐optic interactions. Alternative approaches, although not yet as efficient, include magneto‐optical coupling and schemes based on isolated quantum systems like atoms, ions, or quantum dots. Herein, the necessary theoretical foundations for the most important microwave‐to‐optical conversion experiments are provided, their implementations are described, and the current limitations and future prospects are discussed.}, author = {Lambert, Nicholas J. and Rueda Sanchez, Alfredo R and Sedlmeir, Florian and Schwefel, Harald G. L.}, issn = {2511-9044}, journal = {Advanced Quantum Technologies}, number = {1}, publisher = {Wiley}, title = {{Coherent conversion between microwave and optical photons - An overview of physical implementations}}, doi = {10.1002/qute.201900077}, volume = {3}, year = {2020}, } @article{9196, abstract = {In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces.}, author = {Hensel, Sebastian and Rosati, Tommaso}, issn = {1730-6337}, journal = {Studia Mathematica}, keywords = {General Mathematics}, number = {3}, pages = {251--297}, publisher = {Instytut Matematyczny}, title = {{Modelled distributions of Triebel–Lizorkin type}}, doi = {10.4064/sm180411-11-2}, volume = {252}, year = {2020}, } @article{9197, abstract = {In this paper we introduce and study all-pay bidding games, a class of two player, zero-sum games on graphs. The game proceeds as follows. We place a token on some vertex in the graph and assign budgets to the two players. Each turn, each player submits a sealed legal bid (non-negative and below their remaining budget), which is deducted from their budget and the highest bidder moves the token onto an adjacent vertex. The game ends once a sink is reached, and Player 1 pays Player 2 the outcome that is associated with the sink. The players attempt to maximize their expected outcome. Our games model settings where effort (of no inherent value) needs to be invested in an ongoing and stateful manner. On the negative side, we show that even in simple games on DAGs, optimal strategies may require a distribution over bids with infinite support. A central quantity in bidding games is the ratio of the players budgets. On the positive side, we show a simple FPTAS for DAGs, that, for each budget ratio, outputs an approximation for the optimal strategy for that ratio. We also implement it, show that it performs well, and suggests interesting properties of these games. Then, given an outcome c, we show an algorithm for finding the necessary and sufficient initial ratio for guaranteeing outcome c with probability 1 and a strategy ensuring such. Finally, while the general case has not previously been studied, solving the specific game in which Player 1 wins iff he wins the first two auctions, has been long stated as an open question, which we solve.}, author = {Avni, Guy and Ibsen-Jensen, Rasmus and Tkadlec, Josef}, isbn = {9781577358350}, issn = {2374-3468}, journal = {Proceedings of the AAAI Conference on Artificial Intelligence}, location = {New York, NY, United States}, number = {02}, pages = {1798--1805}, publisher = {Association for the Advancement of Artificial Intelligence}, title = {{All-pay bidding games on graphs}}, doi = {10.1609/aaai.v34i02.5546}, volume = {34}, year = {2020}, } @inproceedings{9202, abstract = {We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function.}, author = {Garcia Soto, Miriam and Prabhakar, Pavithra}, booktitle = {2020 IEEE Real-Time Systems Symposium}, issn = {2576-3172}, location = {Houston, TX, USA }, pages = {244--256}, publisher = {IEEE}, title = {{Hybridization for stability verification of nonlinear switched systems}}, doi = {10.1109/RTSS49844.2020.00031}, year = {2020}, } @inproceedings{9221, abstract = {Recent works have shown that gradient descent can find a global minimum for over-parameterized neural networks where the widths of all the hidden layers scale polynomially with N (N being the number of training samples). In this paper, we prove that, for deep networks, a single layer of width N following the input layer suffices to ensure a similar guarantee. In particular, all the remaining layers are allowed to have constant widths, and form a pyramidal topology. We show an application of our result to the widely used LeCun’s initialization and obtain an over-parameterization requirement for the single wide layer of order N2. }, author = {Nguyen, Quynh and Mondelli, Marco}, booktitle = {34th Conference on Neural Information Processing Systems}, location = {Vancouver, Canada}, pages = {11961–11972}, publisher = {Neural Information Processing Systems Foundation}, title = {{Global convergence of deep networks with one wide layer followed by pyramidal topology}}, volume = {33}, year = {2020}, } @misc{9222, author = {Katsaros, Georgios}, publisher = {Institute of Science and Technology Austria}, title = {{Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling}}, doi = {10.15479/AT:ISTA:9222}, year = {2020}, } @article{9249, abstract = {Rhombic dodecahedron is a space filling polyhedron which represents the close packing of spheres in 3D space and the Voronoi structures of the face centered cubic (FCC) lattice. In this paper, we describe a new coordinate system where every 3-integer coordinates grid point corresponds to a rhombic dodecahedron centroid. In order to illustrate the interest of the new coordinate system, we propose the characterization of 3D digital plane with its topological features, such as the interrelation between the thickness of the digital plane and the separability constraint we aim to obtain. We also present the characterization of 3D digital lines and study it as the intersection of multiple digital planes. Characterization of 3D digital sphere with relevant topological features is proposed as well along with the 48-symmetry appearing in the new coordinate system.}, author = {Biswas, Ranita and Largeteau-Skapin, Gaëlle and Zrour, Rita and Andres, Eric}, issn = {2353-3390}, journal = {Mathematical Morphology - Theory and Applications}, number = {1}, pages = {143--158}, publisher = {De Gruyter}, title = {{Digital objects in rhombic dodecahedron grid}}, doi = {10.1515/mathm-2020-0106}, volume = {4}, year = {2020}, } @inproceedings{9299, abstract = {We call a multigraph non-homotopic if it can be drawn in the plane in such a way that no two edges connecting the same pair of vertices can be continuously transformed into each other without passing through a vertex, and no loop can be shrunk to its end-vertex in the same way. It is easy to see that a non-homotopic multigraph on n>1 vertices can have arbitrarily many edges. We prove that the number of crossings between the edges of a non-homotopic multigraph with n vertices and m>4n edges is larger than cm2n for some constant c>0 , and that this bound is tight up to a polylogarithmic factor. We also show that the lower bound is not asymptotically sharp as n is fixed and m⟶∞ .}, author = {Pach, János and Tardos, Gábor and Tóth, Géza}, booktitle = {28th International Symposium on Graph Drawing and Network Visualization}, isbn = {9783030687656}, issn = {1611-3349}, location = {Virtual, Online}, pages = {359--371}, publisher = {Springer Nature}, title = {{Crossings between non-homotopic edges}}, doi = {10.1007/978-3-030-68766-3_28}, volume = {12590}, year = {2020}, } @article{9308, author = {Avvakumov, Sergey and Wagner, Uli and Mabillard, Isaac and Skopenkov, A. B.}, issn = {0036-0279}, journal = {Russian Mathematical Surveys}, number = {6}, pages = {1156--1158}, publisher = {IOP Publishing}, title = {{Eliminating higher-multiplicity intersections, III. Codimension 2}}, doi = {10.1070/RM9943}, volume = {75}, year = {2020}, } @misc{9326, abstract = {The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.}, author = {Gupta, Chitrak and Khaniya, Umesh and Chan, Chun and Dehez, Francois and Shekhar, Mrinal and Gunner, M. R. and Sazanov, Leonid A and Chipot, Christophe and Singharoy, Abhishek}, publisher = {American Chemical Society}, title = {{Charge transfer and chemo-mechanical coupling in respiratory complex I}}, doi = {10.1021/jacs.9b13450.s002}, year = {2020}, } @inproceedings{9415, abstract = {Optimizing convolutional neural networks for fast inference has recently become an extremely active area of research. One of the go-to solutions in this context is weight pruning, which aims to reduce computational and memory footprint by removing large subsets of the connections in a neural network. Surprisingly, much less attention has been given to exploiting sparsity in the activation maps, which tend to be naturally sparse in many settings thanks to the structure of rectified linear (ReLU) activation functions. In this paper, we present an in-depth analysis of methods for maximizing the sparsity of the activations in a trained neural network, and show that, when coupled with an efficient sparse-input convolution algorithm, we can leverage this sparsity for significant performance gains. To induce highly sparse activation maps without accuracy loss, we introduce a new regularization technique, coupled with a new threshold-based sparsification method based on a parameterized activation function called Forced-Activation-Threshold Rectified Linear Unit (FATReLU). We examine the impact of our methods on popular image classification models, showing that most architectures can adapt to significantly sparser activation maps without any accuracy loss. Our second contribution is showing that these these compression gains can be translated into inference speedups: we provide a new algorithm to enable fast convolution operations over networks with sparse activations, and show that it can enable significant speedups for end-to-end inference on a range of popular models on the large-scale ImageNet image classification task on modern Intel CPUs, with little or no retraining cost. }, author = {Kurtz, Mark and Kopinsky, Justin and Gelashvili, Rati and Matveev, Alexander and Carr, John and Goin, Michael and Leiserson, William and Moore, Sage and Nell, Bill and Shavit, Nir and Alistarh, Dan-Adrian}, booktitle = {37th International Conference on Machine Learning, ICML 2020}, issn = {2640-3498}, location = {Online}, pages = {5533--5543}, title = {{Inducing and exploiting activation sparsity for fast neural network inference}}, volume = {119}, year = {2020}, } @article{9526, abstract = {DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. Here, we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation of genes also activates antisense transcription, which is modestly enhanced by H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes.}, author = {Choi, Jaemyung and Lyons, David B. and Kim, M. Yvonne and Moore, Jonathan D. and Zilberman, Daniel}, issn = {1097-4164}, journal = {Molecular Cell}, number = {2}, pages = {310--323.e7}, publisher = {Elsevier}, title = {{DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts}}, doi = {10.1016/j.molcel.2019.10.011}, volume = {77}, year = {2020}, } @article{9573, abstract = {It is a classical fact that for any ε>0, a random permutation of length n=(1+ε)k2/4 typically contains a monotone subsequence of length k. As a far-reaching generalization, Alon conjectured that a random permutation of this same length n is typically k-universal, meaning that it simultaneously contains every pattern of length k. He also made the simple observation that for n=O(k2logk), a random length-n permutation is typically k-universal. We make the first significant progress towards Alon's conjecture by showing that n=2000k2loglogk suffices.}, author = {He, Xiaoyu and Kwan, Matthew Alan}, issn = {1469-2120}, journal = {Bulletin of the London Mathematical Society}, number = {3}, pages = {515--529}, publisher = {Wiley}, title = {{Universality of random permutations}}, doi = {10.1112/blms.12345}, volume = {52}, year = {2020}, }