TY - GEN
AB - Here, we employ micro- and nanosized cellulose particles, namely paper fines and cellulose
nanocrystals, to induce hierarchical organization over a wide length scale. After processing
them into carbonaceous materials, we demonstrate that these hierarchically organized materials
outperform the best materials for supercapacitors operating with organic electrolytes reported
in literature in terms of specific energy/power (Ragone plot) while showing hardly any capacity
fade over 4,000 cycles. The highly porous materials feature a specific surface area as high as
2500 m2ˑg-1 and exhibit pore sizes in the range of 0.5 to 200 nm as proven by scanning electron
microscopy and N2 physisorption. The carbonaceous materials have been further investigated
by X-ray photoelectron spectroscopy and RAMAN spectroscopy. Since paper fines are an
underutilized side stream in any paper production process, they are a cheap and highly available
feedstock to prepare carbonaceous materials with outstanding performance in electrochemical
applications.
AU - Hobisch, Mathias A.
AU - Mourad, Eléonore
AU - Fischer, Wolfgang J.
AU - Prehal, Christian
AU - Eyley, Samuel
AU - Childress, Anthony
AU - Zankel, Armin
AU - Mautner, Andreas
AU - Breitenbach, Stefan
AU - Rao, Apparao M.
AU - Thielemans, Wim
AU - Freunberger, Stefan Alexander
AU - Eckhart, Rene
AU - Bauer, Wolfgang
AU - Spirk, Stefan
ID - 8081
TI - High specific capacitance supercapacitors from hierarchically organized all-cellulose composites
ER -
TY - JOUR
AB - Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.
AU - Lombardi, Fabrizio
AU - Wang, Jilin W.J.L.
AU - Zhang, Xiyun
AU - Ivanov, Plamen Ch
ID - 8105
JF - EPJ Web of Conferences
SN - 2100-014X
TI - Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality
VL - 230
ER -
TY - CONF
AB - Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.
AU - Edelsbrunner, Herbert
AU - Nikitenko, Anton
AU - Ölsböck, Katharina
AU - Synak, Peter
ID - 8135
SN - 21932808
T2 - Topological Data Analysis
TI - Radius functions on Poisson–Delaunay mosaics and related complexes experimentally
VL - 15
ER -
TY - GEN
AB - The main idea behind the Core Project is to teach first year students at IST scientific communication skills and let them practice by presenting their research within an interdisciplinary environment. Over the course of the first semester, students participated in seminars, where they shared their results with the colleagues from other fields and took part in discussions on relevant subjects. The main focus during this sessions was on delivering the information in a simplified and comprehensible way, going into the very basics of a subject if necessary. At the end, the students were asked to present their research in the written form to exercise their writing skills. The reports were gathered in this document. All of them were reviewed by the teaching assistants and write-ups illustrating unique stylistic features and, in general, an outstanding level of writing skills, were honorably mentioned in the section "Selected Reports".
AU - Maslov, Mikhail
AU - Kondrashov, Fyodor
AU - Artner, Christina
AU - Hennessey-Wesen, Mike
AU - Kavcic, Bor
AU - Machnik, Nick N
AU - Satapathy, Roshan K
AU - Tomanek, Isabella
ID - 8151
TI - Core Project Proceedings
ER -
TY - CHAP
AB - Understanding how the activity of membrane receptors and cellular signaling pathways shapes cell behavior is of fundamental interest in basic and applied research. Reengineering receptors to react to light instead of their cognate ligands allows for generating defined signaling inputs with high spatial and temporal precision and facilitates the dissection of complex signaling networks. Here, we describe fundamental considerations in the design of light-regulated receptor tyrosine kinases (Opto-RTKs) and appropriate control experiments. We also introduce methods for transient receptor expression in HEK293 cells, quantitative assessment of signaling activity in reporter gene assays, semiquantitative assessment of (in)activation time courses through Western blot (WB) analysis, and easy to implement light stimulation hardware.
AU - Kainrath, Stephanie
AU - Janovjak, Harald L
ED - Niopek, Dominik
ID - 8173
T2 - Photoswitching Proteins
TI - Design and application of light-regulated receptor tyrosine kinases
VL - 2173
ER -
TY - COMP
AU - Hauschild, Robert
ID - 8181
TI - Amplified centrosomes in dendritic cells promote immune cell effector functions
ER -
TY - JOUR
AB - Birch pollen allergy is among the most prevalent pollen allergies in Northern and Central Europe. This IgE-mediated disease can be treated with allergen immunotherapy (AIT), which typically gives rise to IgG antibodies inducing tolerance. Although the main mechanisms of allergen immunotherapy (AIT) are known, questions regarding possible Fc-mediated effects of IgG antibodies remain unanswered. This can mainly be attributed to the unavailability of appropriate tools, i.e., well-characterised recombinant antibodies (rAbs). We hereby aimed at providing human rAbs of several classes for mechanistic studies and as possible candidates for passive immunotherapy. We engineered IgE, IgG1, and IgG4 sharing the same variable region against the major birch pollen allergen Bet v 1 using Polymerase Incomplete Primer Extension (PIPE) cloning. We tested IgE functionality and IgG blocking capabilities using appropriate model cell lines. In vitro studies showed IgE engagement with FcεRI and CD23 and Bet v 1-dependent degranulation. Overall, we hereby present fully functional, human IgE, IgG1, and IgG4 sharing the same variable region against Bet v 1 and showcase possible applications in first mechanistic studies. Furthermore, our IgG antibodies might be useful candidates for passive immunotherapy of birch pollen allergy.
AU - Köhler, Verena K.
AU - Crescioli, Silvia
AU - Fazekas-Singer, Judit
AU - Bax, Heather J.
AU - Hofer, Gerhard
AU - Pranger, Christina L.
AU - Hufnagl, Karin
AU - Bianchini, Rodolfo
AU - Flicker, Sabine
AU - Keller, Walter
AU - Karagiannis, Sophia N.
AU - Jensen-Jarolim, Erika
ID - 8225
IS - 16
JF - International Journal of Molecular Sciences
SN - 1422-0067
TI - Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1
VL - 21
ER -
TY - JOUR
AU - Gotovina, Jelena
AU - Bianchini, Rodolfo
AU - Fazekas-Singer, Judit
AU - Herrmann, Ina
AU - Pellizzari, Giulia
AU - Haidl, Ian D.
AU - Hufnagl, Karin
AU - Karagiannis, Sophia N.
AU - Marshall, Jean S.
AU - Jensen‐Jarolim, Erika
ID - 8226
JF - Allergy
SN - 0105-4538
TI - Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro
ER -
TY - COMP
AB - Automated root growth analysis and tracking of root tips.
AU - Hauschild, Robert
ID - 8294
TI - RGtracker
ER -
TY - GEN
AB - Classic Byzantine fault-tolerant consensus protocols forfeit liveness in the face of asynchrony in order to preserve safety, whereas most deployed blockchain protocols forfeit safety in order to remain live. In this work, we achieve the best of both worlds by proposing a novel abstractions called the finality gadget. A finality gadget allows for transactions to always optimistically commit but informs the clients that these transactions might be unsafe. As a result, a blockchain can execute transactions optimistically and only commit them after they have been sufficiently and provably audited. In
this work, we formally model the finality gadget abstraction, prove that it is impossible to solve it deterministically in full asynchrony (even though it is stronger than consensus) and provide a partially synchronous protocol which is currently securing a major blockchain. This way we show that the protocol designer can decouple safety and liveness in order to speed up recovery from failures. We believe that there can be other types of finality gadgets that provide weaker safety (e.g., probabilistic) in order to gain more efficiency and this can depend on the probability that the network is not in synchrony.
AU - Stewart, Alistair
AU - Kokoris Kogias, Eleftherios
ID - 8307
T2 - arXiv
TI - GRANDPA: A Byzantine finality gadget
ER -
TY - CONF
AB - Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question.
In this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way.
Our core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001).
AU - Chakraborty, Suvradip
AU - Dziembowski, Stefan
AU - Nielsen, Jesper Buus
ID - 8322
SN - 03029743
T2 - Advances in Cryptology – CRYPTO 2020
TI - Reverse firewalls for actively secure MPCs
VL - 12171
ER -
TY - CONF
AB - Discrete Gaussian distributions over lattices are central to lattice-based cryptography, and to the computational and mathematical aspects of lattices more broadly. The literature contains a wealth of useful theorems about the behavior of discrete Gaussians under convolutions and related operations. Yet despite their structural similarities, most of these theorems are formally incomparable, and their proofs tend to be monolithic and written nearly “from scratch,” making them unnecessarily hard to verify, understand, and extend.
In this work we present a modular framework for analyzing linear operations on discrete Gaussian distributions. The framework abstracts away the particulars of Gaussians, and usually reduces proofs to the choice of appropriate linear transformations and elementary linear algebra. To showcase the approach, we establish several general properties of discrete Gaussians, and show how to obtain all prior convolution theorems (along with some new ones) as straightforward corollaries. As another application, we describe a self-reduction for Learning With Errors (LWE) that uses a fixed number of samples to generate an unlimited number of additional ones (having somewhat larger error). The distinguishing features of our reduction are its simple analysis in our framework, and its exclusive use of discrete Gaussians without any loss in parameters relative to a prior mixed discrete-and-continuous approach.
As a contribution of independent interest, for subgaussian random matrices we prove a singular value concentration bound with explicitly stated constants, and we give tighter heuristics for specific distributions that are commonly used for generating lattice trapdoors. These bounds yield improvements in the concrete bit-security estimates for trapdoor lattice cryptosystems.
AU - Genise, Nicholas
AU - Micciancio, Daniele
AU - Peikert, Chris
AU - Walter, Michael
ID - 8339
SN - 03029743
T2 - 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography
TI - Improved discrete Gaussian and subgaussian analysis for lattice cryptography
VL - 12110
ER -
TY - JOUR
AB - Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.
Results: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.
Conclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.
AU - Rampelt, Heike
AU - Sucec, Iva
AU - Bersch, Beate
AU - Horten, Patrick
AU - Perschil, Inge
AU - Martinou, Jean-Claude
AU - van der Laan, Martin
AU - Wiedemann, Nils
AU - Schanda, Paul
AU - Pfanner, Nikolaus
ID - 8402
JF - BMC Biology
KW - Biotechnology
KW - Plant Science
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Developmental Biology
KW - Cell Biology
KW - Physiology
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
KW - Structural Biology
KW - General Agricultural and Biological Sciences
SN - 1741-7007
TI - The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments
VL - 18
ER -
TY - GEN
AB - The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9·10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9·10·12 complex is the anchor point at the inner-membrane insertase complex TIM22. The mechanism of client transport by TIM9·10 has been resolved recently, but the structure and subunit composition of the TIM9·10·12 complex remains largely unresolved. Furthermore, the assembly process of the hexameric TIM chaperones from its subunits remained elusive. We investigate the structural and dynamical properties of the Tim subunits, and show that they are highly dynamic. In their non-assembled form, the subunits behave as intrinsically disordered proteins; when the conserved cysteines of the CX3C-Xn-CX3C motifs are formed, short marginally stable α-helices are formed, which are only fully stabilized upon hexamer formation to the mature chaperone. Subunits are in equilibrium between their hexamer-embedded and a free form, with exchange kinetics on a minutes time scale. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9·10·12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12) with a conserved hydrophobic client-binding groove and flexible N- and C-terminal tentacles.
AU - Weinhäupl, Katharina
AU - Wang, Yong
AU - Hessel, Audrey
AU - Brennich, Martha
AU - Lindorff-Larsen, Kresten
AU - Schanda, Paul
ID - 8404
T2 - bioRxiv
TI - Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone
ER -
TY - BOOK
AB - Arnold diffusion, which concerns the appearance of chaos in classical mechanics, is one of the most important problems in the fields of dynamical systems and mathematical physics. Since it was discovered by Vladimir Arnold in 1963, it has attracted the efforts of some of the most prominent researchers in mathematics. The question is whether a typical perturbation of a particular system will result in chaotic or unstable dynamical phenomena. In this groundbreaking book, Vadim Kaloshin and Ke Zhang provide the first complete proof of Arnold diffusion, demonstrating that that there is topological instability for typical perturbations of five-dimensional integrable systems (two and a half degrees of freedom).
This proof realizes a plan John Mather announced in 2003 but was unable to complete before his death. Kaloshin and Zhang follow Mather’s strategy but emphasize a more Hamiltonian approach, tying together normal forms theory, hyperbolic theory, Mather theory, and weak KAM theory. Offering a complete, clean, and modern explanation of the steps involved in the proof, and a clear account of background material, this book is designed to be accessible to students as well as researchers. The result is a critical contribution to mathematical physics and dynamical systems, especially Hamiltonian systems.
AU - Kaloshin, Vadim
AU - Zhang, Ke
ID - 8414
SN - 9-780-6912-0253-2
TI - Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom
VL - 208
ER -
TY - GEN
AB - Chaperones are essential for assisting protein folding, and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding of how additional interactions enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1, and Tim23 which has an additional disordered hydrophilic domain. Combining NMR, SAXS and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity vs. specificity.
AU - Sučec, Iva
AU - Wang, Yong
AU - Dakhlaoui, Ons
AU - Weinhäupl, Katharina
AU - Jores, Tobias
AU - Costa, Doriane
AU - Hessel, Audrey
AU - Brennich, Martha
AU - Rapaport, Doron
AU - Lindorff-Larsen, Kresten
AU - Bersch, Beate
AU - Schanda, Paul
ID - 8403
T2 - bioRxiv
TI - Structural basis of client specificity in mitochondrial membrane-protein chaperones
ER -
TY - CONF
AB - We present the results of the ARCH 2020 friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. In its fourth edition, eight tools have been applied to solve eight different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.
AU - Althoff, Matthias
AU - Bak, Stanley
AU - Bao, Zongnan
AU - Forets, Marcelo
AU - Frehse, Goran
AU - Freire, Daniel
AU - Kochdumper, Niklas
AU - Li, Yangge
AU - Mitra, Sayan
AU - Ray, Rajarshi
AU - Schilling, Christian
AU - Schupp, Stefan
AU - Wetzlinger, Mark
ID - 8572
T2 - EPiC Series in Computing
TI - ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics
VL - 74
ER -
TY - CONF
AB - We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.
AU - Geretti, Luca
AU - Alexandre Dit Sandretto, Julien
AU - Althoff, Matthias
AU - Benet, Luis
AU - Chapoutot, Alexandre
AU - Chen, Xin
AU - Collins, Pieter
AU - Forets, Marcelo
AU - Freire, Daniel
AU - Immler, Fabian
AU - Kochdumper, Niklas
AU - Sanders, David
AU - Schilling, Christian
ID - 8571
T2 - EPiC Series in Computing
TI - ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics
VL - 74
ER -
TY - CONF
AB - A vector addition system with states (VASS) consists of a finite set of states and counters. A transition changes the current state to the next state, and every counter is either incremented, or decremented, or left unchanged. A state and value for each counter is a configuration; and a computation is an infinite sequence of configurations with transitions between successive configurations. A probabilistic VASS consists of a VASS along with a probability distribution over the transitions for each state. Qualitative properties such as state and configuration reachability have been widely studied for VASS. In this work we consider multi-dimensional long-run average objectives for VASS and probabilistic VASS. For a counter, the cost of a configuration is the value of the counter; and the long-run average value of a computation for the counter is the long-run average of the costs of the configurations in the computation. The multi-dimensional long-run average problem given a VASS and a threshold value for each counter, asks whether there is a computation such that for each counter the long-run average value for the counter does not exceed the respective threshold. For probabilistic VASS, instead of the existence of a computation, we consider whether the expected long-run average value for each counter does not exceed the respective threshold. Our main results are as follows: we show that the multi-dimensional long-run average problem (a) is NP-complete for integer-valued VASS; (b) is undecidable for natural-valued VASS (i.e., nonnegative counters); and (c) can be solved in polynomial time for probabilistic integer-valued VASS, and probabilistic natural-valued VASS when all computations are non-terminating.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Otop, Jan
ID - 8600
SN - 18688969
T2 - 31st International Conference on Concurrency Theory
TI - Multi-dimensional long-run average problems for vector addition systems with states
VL - 171
ER -
TY - CONF
AB - A graph game is a two-player zero-sum game in which the players move a token throughout a graph to produce an infinite path, which determines the winner or payoff of the game. In bidding games, both players have budgets, and in each turn, we hold an "auction" (bidding) to determine which player moves the token. In this survey, we consider several bidding mechanisms and study their effect on the properties of the game. Specifically, bidding games, and in particular bidding games of infinite duration, have an intriguing equivalence with random-turn games in which in each turn, the player who moves is chosen randomly. We show how minor changes in the bidding mechanism lead to unexpected differences in the equivalence with random-turn games.
AU - Avni, Guy
AU - Henzinger, Thomas A
ID - 8599
SN - 18688969
T2 - 31st International Conference on Concurrency Theory
TI - A survey of bidding games on graphs
VL - 171
ER -
TY - CONF
AB - The design and implementation of efficient concurrent data structures have
seen significant attention. However, most of this work has focused on
concurrent data structures providing good \emph{worst-case} guarantees. In real
workloads, objects are often accessed at different rates, since access
distributions may be non-uniform. Efficient distribution-adaptive data
structures are known in the sequential case, e.g. the splay-trees; however,
they often are hard to translate efficiently in the concurrent case.
In this paper, we investigate distribution-adaptive concurrent data
structures and propose a new design called the splay-list. At a high level, the
splay-list is similar to a standard skip-list, with the key distinction that
the height of each element adapts dynamically to its access rate: popular
elements ``move up,'' whereas rarely-accessed elements decrease in height. We
show that the splay-list provides order-optimal amortized complexity bounds for
a subset of operations while being amenable to efficient concurrent
implementation. Experimental results show that the splay-list can leverage
distribution-adaptivity to improve on the performance of classic concurrent
designs, and can outperform the only previously-known distribution-adaptive
design in certain settings.
AU - Aksenov, Vitaly
AU - Alistarh, Dan-Adrian
AU - Drozdova, Alexandra
AU - Mohtashami, Amirkeivan
ID - 8725
SN - 1868-8969
T2 - 34th International Symposium on Distributed Computing
TI - The splay-list: A distribution-adaptive concurrent skip-list
VL - 179
ER -
TY - JOUR
AB - Several realistic spin-orbital models for transition metal oxides go beyond the classical expectations and could be understood only by employing the quantum entanglement. Experiments on these materials confirm that spin-orbital entanglement has measurable consequences. Here, we capture the essential features of spin-orbital entanglement in complex quantum matter utilizing 1D spin-orbital model which accommodates SU(2)⊗SU(2) symmetric Kugel-Khomskii superexchange as well as the Ising on-site spin-orbit coupling. Building on the results obtained for full and effective models in the regime of strong spin-orbit coupling, we address the question whether the entanglement found on superexchange bonds always increases when the Ising spin-orbit coupling is added. We show that (i) quantum entanglement is amplified by strong spin-orbit coupling and, surprisingly, (ii) almost classical disentangled states are possible. We complete the latter case by analyzing how the entanglement existing for intermediate values of spin-orbit coupling can disappear for higher values of this coupling.
AU - Gotfryd, Dorota
AU - Paerschke, Ekaterina
AU - Wohlfeld, Krzysztof
AU - Oleś, Andrzej M.
ID - 8726
IS - 3
JF - Condensed Matter
SN - 2410-3896
TI - Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling
VL - 5
ER -
TY - CONF
AB - Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training.
AU - Alamdari, Par Alizadeh
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Lukina, Anna
ID - 9040
SN - 9783854480426
T2 - Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design
TI - Formal methods with a touch of magic
ER -
TY - JOUR
AB - From rock salt to nanoparticle superlattices, complex structure can emerge from simple building blocks that attract each other through Coulombic forces1-4. On the micrometre scale, however, colloids in water defy the intuitively simple idea of forming crystals from oppositely charged partners, instead forming non-equilibrium structures such as clusters and gels5-7. Although various systems have been engineered to grow binary crystals8-11, native surface charge in aqueous conditions has not been used to assemble crystalline materials. Here we form ionic colloidal crystals in water through an approach that we refer to as polymer-attenuated Coulombic self-assembly. The key to crystallization is the use of a neutral polymer to keep particles separated by well defined distances, allowing us to tune the attractive overlap of electrical double layers, directing particles to disperse, crystallize or become permanently fixed on demand. The nucleation and growth of macroscopic single crystals is demonstrated by using the Debye screening length to fine-tune assembly. Using a variety of colloidal particles and commercial polymers, ionic colloidal crystals isostructural to caesium chloride, sodium chloride, aluminium diboride and K4C60 are selected according to particle size ratios. Once fixed by simply diluting out solution salts, crystals are pulled out of the water for further manipulation, demonstrating an accurate translation from solution-phase assembly to dried solid structures. In contrast to other assembly approaches, in which particles must be carefully engineered to encode binding information12-18, polymer-attenuated Coulombic self-assembly enables conventional colloids to be used as model colloidal ions, primed for crystallization.
AU - Hueckel, Theodore
AU - Hocky, Glen M.
AU - Palacci, Jérémie A
AU - Sacanna, Stefano
ID - 9059
IS - 7804
JF - Nature
KW - Multidisciplinary
SN - 0028-0836
TI - Ionic solids from common colloids
VL - 580
ER -
TY - CHAP
AU - Schmid-Hempel, Paul
AU - Cremer, Sylvia M
ED - Starr, C
ID - 9096
SN - 9783319903064
T2 - Encyclopedia of Social Insects
TI - Parasites and Pathogens
ER -
TY - JOUR
AB - The goal of this study is to understand the mechanisms controlling the isotopic composition of the water vapor near the surface of tropical oceans, at the scale of about a hundred kilometers and a month. In the tropics, it has long been observed that the isotopic compositions of rain and vapor near the surface are more depleted when the precipitation rate is high. This is called the “amount effect.” Previous studies, based on observations or models with parameterized convection, have highlighted the roles of deep convective and mesoscale downdrafts and rain evaporation. But the relative importance of these processes has never been quantified. We hypothesize that it can be quantified using an analytical model constrained by large‐eddy simulations. Results from large‐eddy simulations confirm that the classical amount effect can be simulated only if precipitation rate changes result from changes in the large‐scale circulation. We find that the main process depleting the water vapor compared to the equilibrium with the ocean is the fact that updrafts stem from areas where the water vapor is more enriched. The main process responsible for the amount effect is the fact that when the large‐scale ascent increases, isotopic vertical gradients are steeper, so that updrafts and downdrafts deplete the subcloud layer more efficiently.
AU - Risi, Camille
AU - Muller, Caroline J
AU - Blossey, Peter
ID - 9126
IS - 8
JF - Journal of Advances in Modeling Earth Systems
KW - Global and Planetary Change
KW - General Earth and Planetary Sciences
KW - Environmental Chemistry
SN - 1942-2466
TI - What controls the water vapor isotopic composition near the surface of tropical oceans? Results from an analytical model constrained by large‐eddy simulations
VL - 12
ER -
TY - JOUR
AB - Nearly all regions in the world are projected to become dryer in a warming climate. Here, we investigate the Mediterranean region, often referred to as a climate change “hot spot”. From regional climate simulations, it is shown that although enhanced warming and drying over land is projected, the spatial pattern displays high variability. Indeed, drying is largely caused by enhanced warming over land. However, in Northern Europe, soil moisture alleviates warming induced drying by up to 50% due to humidity uptake from land. In already arid regions, the Mediterranean Sea is generally the only humidity source, and drying is only due to land warming. However, over Sahara and the Iberian Peninsula, enhanced warming over land is insufficient to explain the extreme drying. These regions are also isolated from humidity advection by heat lows, which are cyclonic circulation anomalies associated with surface heating over land. The cyclonic circulation scales with the temperature gradient between land and ocean which increases with climate change, reinforcing the cyclonic circulation over Sahara and the Iberian Peninsula, both diverting the zonal advection of humidity to the south of the Iberian Peninsula. The dynamics are therefore key in the warming and drying of the Mediterranean region, with extreme aridification over the Sahara and Iberian Peninsula. In these regions, the risk for human health due to the thermal load which accounts for air temperature and humidity is therefore projected to increase significantly with climate change at a level of extreme danger.
AU - Drobinski, Philippe
AU - Da Silva, Nicolas
AU - Bastin, Sophie
AU - Mailler, Sylvain
AU - Muller, Caroline J
AU - Ahrens, Bodo
AU - Christensen, Ole B.
AU - Lionello, Piero
ID - 9127
IS - 9
JF - Regional Environmental Change
KW - Global and Planetary Change
SN - 1436-3798
TI - How warmer and drier will the Mediterranean region be at the end of the twenty-first century?
VL - 20
ER -
TY - JOUR
AB - This paper reviews recent important advances in our understanding of the response of precipitation extremes to warming from theory and from idealized cloud-resolving simulations. A theoretical scaling for precipitation extremes has been proposed and refined in the past decades, allowing to address separately the contributions from the thermodynamics, the dynamics and the microphysics. Theoretical constraints, as well as remaining uncertainties, associated with each of these three contributions to precipitation extremes, are discussed. Notably, although to leading order precipitation extremes seem to follow the thermodynamic theoretical expectation in idealized simulations, considerable uncertainty remains regarding the response of the dynamics and of the microphysics to warming, and considerable departure from this theoretical expectation is found in observations and in more realistic simulations. We also emphasize key outstanding questions, in particular the response of mesoscale convective organization to warming. Observations suggest that extreme rainfall often comes from an organized system in very moist environments. Improved understanding of the physical processes behind convective organization is needed in order to achieve accurate extreme rainfall prediction in our current, and in a warming climate.
AU - Muller, Caroline J
AU - Takayabu, Yukari
ID - 9128
IS - 3
JF - Environmental Research Letters
KW - Renewable Energy
KW - Sustainability and the Environment
KW - Public Health
KW - Environmental and Occupational Health
KW - General Environmental Science
SN - 1748-9326
TI - Response of precipitation extremes to warming: What have we learned from theory and idealized cloud-resolving simulations, and what remains to be learned?
VL - 15
ER -
TY - JOUR
AB - This study investigates the feedbacks between an interactive sea surface temperature (SST) and the self‐aggregation of deep convective clouds, using a cloud‐resolving model in nonrotating radiative‐convective equilibrium. The ocean is modeled as one layer slab with a temporally fixed mean but spatially varying temperature. We find that the interactive SST decelerates the aggregation and that the deceleration is larger with a shallower slab, consistent with earlier studies. The surface temperature anomaly in dry regions is positive at first, thus opposing the diverging shallow circulation known to favor self‐aggregation, consistent with the slower aggregation. But surprisingly, the driest columns then have a negative SST anomaly, thus strengthening the diverging shallow circulation and favoring aggregation. This diverging circulation out of dry regions is found to be well correlated with the aggregation speed. It can be linked to a positive surface pressure anomaly (PSFC), itself the consequence of SST anomalies and boundary layer radiative cooling. The latter cools and dries the boundary layer, thus increasing PSFC anomalies through virtual effects and hydrostasy. Sensitivity experiments confirm the key role played by boundary layer radiative cooling in determining PSFC anomalies in dry regions, and thus the shallow diverging circulation and the aggregation speed.
AU - Shamekh, S.
AU - Muller, Caroline J
AU - Duvel, J.‐P.
AU - D'Andrea, F.
ID - 9125
IS - 11
JF - Journal of Advances in Modeling Earth Systems
KW - Global and Planetary Change
KW - General Earth and Planetary Sciences
KW - Environmental Chemistry
SN - 1942-2466
TI - Self‐aggregation of convective clouds with interactive sea surface temperature
VL - 12
ER -
TY - GEN
AB - The couplings among clouds, convection, and circulation in trade-wind regimes remain a fundamental puzzle that limits our ability to constrain future climate change. Radiative heating plays an important role in these couplings. Here we calculate the clear-sky radiative profiles from 2001 in-situ soundings (978 dropsondes and 1023 radiosondes) collected during the EUREC4A field campaign, which took place south and east of Barbados in January–February 2020. We describe the method used to calculate these radiative profiles and present preliminary results sampling variability at multiple scales, from the variability across all soundings to groupings by diurnal cycle and mesoscale organization state, as well as individual soundings associated with elevated moisture layers. This clear-sky radiative profiles data set can provide important missing detail to what can be learned from calculations based on passive remote sensing and help in investigating the role of radiation in dynamic and thermodynamic variability in trade-wind regimes. All data are archived and freely available for public access on AERIS (Albright et al. (2020), https://doi.org/10.25326/78).
AU - Albright, Anna Lea
AU - Fildier, Benjamin
AU - Touzé-Peiffer, Ludovic
AU - Pincus, Robert
AU - Vial, Jessica
AU - Muller, Caroline J
ID - 9124
T2 - Earth System Science Data
TI - Atmospheric radiative profiles during EUREC4A
ER -
TY - CHAP
AB - Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.
AU - Westram, Anja M
AU - Faria, Rui
AU - Butlin, Roger
AU - Johannesson, Kerstin
ID - 9123
SN - 9780470016176
T2 - eLS
TI - Inversions and Evolution
ER -
TY - JOUR
AB - 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.
AU - Gandhi, Tanvi
AU - Mac Huang, Jinzi
AU - Aubret, Antoine
AU - Li, Yaocheng
AU - Ramananarivo, Sophie
AU - Vergassola, Massimo
AU - Palacci, Jérémie A
ID - 9162
IS - 10
JF - Physical Review Fluids
SN - 2469-990X
TI - Decision-making at a T-junction by gradient-sensing microscopic agents
VL - 5
ER -
TY - JOUR
AU - Speck, Thomas
AU - Tailleur, Julien
AU - Palacci, Jérémie A
ID - 9164
IS - 6
JF - New Journal of Physics
KW - General Physics and Astronomy
SN - 1367-2630
TI - Focus on active colloids and nanoparticles
VL - 22
ER -
TY - JOUR
AB - 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.
AU - Biswas, Ranita
AU - Largeteau-Skapin, Gaëlle
AU - Zrour, Rita
AU - Andres, Eric
ID - 9249
IS - 1
JF - Mathematical Morphology - Theory and Applications
SN - 2353-3390
TI - Digital objects in rhombic dodecahedron grid
VL - 4
ER -
TY - CONF
AB - 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⟶∞ .
AU - Pach, János
AU - Tardos, Gábor
AU - Tóth, Géza
ID - 9299
SN - 0302-9743
T2 - 28th International Symposium on Graph Drawing and Network Visualization
TI - Crossings between non-homotopic edges
VL - 12590
ER -
TY - JOUR
AB - In 1989, Rota made the following conjecture. Given n bases B1,…,Bn in an n-dimensional vector space V, one can always find n disjoint bases of V, each containing exactly one element from each Bi (we call such bases transversal bases). Rota’s basis conjecture remains wide open despite its apparent simplicity and the efforts of many researchers (e.g., the conjecture was recently the subject of the collaborative “Polymath” project). In this paper we prove that one can always find (1/2−o(1))n disjoint transversal bases, improving on the previous best bound of Ω(n/logn). Our results also apply to the more general setting of matroids.
AU - Bucić, Matija
AU - Kwan, Matthew Alan
AU - Pokrovskiy, Alexey
AU - Sudakov, Benny
ID - 9576
IS - 21
JF - International Mathematics Research Notices
SN - 1073-7928
TI - Halfway to Rota’s basis conjecture
VL - 2020
ER -
TY - JOUR
AB - An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clogn. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. Motivated by an old problem of Erd̋s and McKay, recently Narayanan, Sahasrabudhe, and Tomon conjectured that for any fixed C, every n-vertex C-Ramsey graph induces subgraphs of Θ(n2) different sizes. In this paper we prove this conjecture.
AU - Kwan, Matthew Alan
AU - Sudakov, Benny
ID - 9577
IS - 6
JF - International Mathematics Research Notices
SN - 1073-7928
TI - Ramsey graphs induce subgraphs of quadratically many sizes
VL - 2020
ER -
TY - JOUR
AB - 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.
AU - He, Xiaoyu
AU - Kwan, Matthew Alan
ID - 9573
IS - 3
JF - Bulletin of the London Mathematical Society
SN - 0024-6093
TI - Universality of random permutations
VL - 52
ER -
TY - CONF
AB - Second-order information, in the form of Hessian- or Inverse-Hessian-vector products, is a fundamental tool for solving optimization problems. Recently, there has been significant interest in utilizing this information in the context of deep
neural networks; however, relatively little is known about the quality of existing approximations in this context. Our work examines this question, identifies issues with existing approaches, and proposes a method called WoodFisher to compute a faithful and efficient estimate of the inverse Hessian. Our main application is to neural network compression, where we build on the classic Optimal Brain Damage/Surgeon framework. We demonstrate that WoodFisher significantly outperforms popular state-of-the-art methods for oneshot pruning. Further, even when iterative, gradual pruning is allowed, our method results in a gain in test accuracy over the state-of-the-art approaches, for standard image classification datasets such as ImageNet ILSVRC. We examine how our method can be extended to take into account first-order information, as well as
illustrate its ability to automatically set layer-wise pruning thresholds and perform compression in the limited-data regime. The code is available at the following link, https://github.com/IST-DASLab/WoodFisher.
AU - Singh, Sidak Pal
AU - Alistarh, Dan-Adrian
ID - 9632
SN - 10495258
T2 - Advances in Neural Information Processing Systems
TI - WoodFisher: Efficient second-order approximation for neural network compression
VL - 33
ER -
TY - JOUR
AB - Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.
AU - Edelsbrunner, Herbert
AU - Virk, Ziga
AU - Wagner, Hubert
ID - 9630
IS - 2
JF - Journal of Computational Geometry
TI - Topological data analysis in information space
VL - 11
ER -
TY - CONF
AB - The ability to leverage large-scale hardware parallelism has been one of the key enablers of the accelerated recent progress in machine learning. Consequently, there has been considerable effort invested into developing efficient parallel variants of classic machine learning algorithms. However, despite the wealth of knowledge on parallelization, some classic machine learning algorithms often prove hard to parallelize efficiently while maintaining convergence. In this paper, we focus on efficient parallel algorithms for the key machine learning task of inference on graphical models, in particular on the fundamental belief propagation algorithm. We address the challenge of efficiently parallelizing this classic paradigm by showing how to leverage scalable relaxed schedulers in this context. We present an extensive empirical study, showing that our approach outperforms previous parallel belief propagation implementations both in terms of scalability and in terms of wall-clock convergence time, on a range of practical applications.
AU - Aksenov, Vitaly
AU - Alistarh, Dan-Adrian
AU - Korhonen, Janne
ID - 9631
SN - 10495258
T2 - Advances in Neural Information Processing Systems
TI - Scalable belief propagation via relaxed scheduling
VL - 33
ER -
TY - JOUR
AB - The visualization of data is indispensable in scientific research, from the early stages when human insight forms to the final step of communicating results. In computational physics, chemistry and materials science, it can be as simple as making a scatter plot or as straightforward as looking through the snapshots of atomic positions manually. However, as a result of the "big data" revolution, these conventional approaches are often inadequate. The widespread adoption of high-throughput computation for materials discovery and the associated community-wide repositories have given rise to data sets that contain an enormous number of compounds and atomic configurations. A typical data set contains thousands to millions of atomic structures, along with a diverse range of properties such as formation energies, band gaps, or bioactivities.It would thus be desirable to have a data-driven and automated framework for visualizing and analyzing such structural data sets. The key idea is to construct a low-dimensional representation of the data, which facilitates navigation, reveals underlying patterns, and helps to identify data points with unusual attributes. Such data-intensive maps, often employing machine learning methods, are appearing more and more frequently in the literature. However, to the wider community, it is not always transparent how these maps are made and how they should be interpreted. Furthermore, while these maps undoubtedly serve a decorative purpose in academic publications, it is not always apparent what extra information can be garnered from reading or making them.This Account attempts to answer such questions. We start with a concise summary of the theory of representing chemical environments, followed by the introduction of a simple yet practical conceptual approach for generating structure maps in a generic and automated manner. Such analysis and mapping is made nearly effortless by employing the newly developed software tool ASAP. To showcase the applicability to a wide variety of systems in chemistry and materials science, we provide several illustrative examples, including crystalline and amorphous materials, interfaces, and organic molecules. In these examples, the maps not only help to sift through large data sets but also reveal hidden patterns that could be easily missed using conventional analyses.The explosion in the amount of computed information in chemistry and materials science has made visualization into a science in itself. Not only have we benefited from exploiting these visualization methods in previous works, we also believe that the automated mapping of data sets will in turn stimulate further creativity and exploration, as well as ultimately feed back into future advances in the respective fields.
AU - Cheng, Bingqing
AU - Griffiths, Ryan-Rhys
AU - Wengert, Simon
AU - Kunkel, Christian
AU - Stenczel, Tamas
AU - Zhu, Bonan
AU - Deringer, Volker L.
AU - Bernstein, Noam
AU - Margraf, Johannes T.
AU - Reuter, Karsten
AU - Csanyi, Gabor
ID - 9675
IS - 9
JF - Accounts of Chemical Research
SN - 0001-4842
TI - Mapping materials and molecules
VL - 53
ER -
TY - JOUR
AB - Predicting phase stabilities of crystal polymorphs is central to computational materials science and chemistry. Such predictions are challenging because they first require searching for potential energy minima and then performing arduous free-energy calculations to account for entropic effects at finite temperatures. Here, we develop a framework that facilitates such predictions by exploiting all the information obtained from random searches of crystal structures. This framework combines automated clustering, classification and visualisation of crystal structures with machine-learning estimation of their enthalpy and entropy. We demonstrate the framework on the technologically important system of TiO2, which has many polymorphs, without relying on prior knowledge of known phases. We find a number of new phases and predict the phase diagram and metastabilities of crystal polymorphs at 1600 K, benchmarking the results against full free-energy calculations.
AU - Reinhardt, Aleks
AU - Pickard, Chris J.
AU - Cheng, Bingqing
ID - 9666
IS - 22
JF - Physical Chemistry Chemical Physics
SN - 1463-9076
TI - Predicting the phase diagram of titanium dioxide with random search and pattern recognition
VL - 22
ER -
TY - JOUR
AB - Water molecules can arrange into a liquid with complex hydrogen-bond networks and at least 17 experimentally confirmed ice phases with enormous structural diversity. It remains a puzzle how or whether this multitude of arrangements in different phases of water are related. Here we investigate the structural similarities between liquid water and a comprehensive set of 54 ice phases in simulations, by directly comparing their local environments using general atomic descriptors, and also by demonstrating that a machine-learning potential trained on liquid water alone can predict the densities, lattice energies, and vibrational properties of the ices. The finding that the local environments characterising the different ice phases are found in water sheds light on the phase behavior of water, and rationalizes the transferability of water models between different phases.
AU - Monserrat, Bartomeu
AU - Brandenburg, Jan Gerit
AU - Engel, Edgar A.
AU - Cheng, Bingqing
ID - 9671
IS - 1
JF - Nature Communications
TI - Liquid water contains the building blocks of diverse ice phases
VL - 11
ER -
TY - CONF
AB - Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete.
AU - Chatterjee, Krishnendu
AU - Ibsen-Jensen, Rasmus
AU - Jecker, Ismael R
AU - Svoboda, Jakub
ID - 8533
SN - 18688969
T2 - 45th International Symposium on Mathematical Foundations of Computer Science
TI - Simplified game of life: Algorithms and complexity
VL - 170
ER -
TY - CONF
AB - A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs.
AU - Jecker, Ismael R
AU - Kupferman, Orna
AU - Mazzocchi, Nicolas
ID - 8534
SN - 18688969
T2 - 45th International Symposium on Mathematical Foundations of Computer Science
TI - Unary prime languages
VL - 170
ER -
TY - JOUR
AB - We prove some recent experimental observations of Dan Reznik concerning periodic billiard orbits in ellipses. For example, the sum of cosines of the angles of a periodic billiard polygon remains constant in the 1-parameter family of such polygons (that exist due to the Poncelet porism). In our proofs, we use geometric and complex analytic methods.
AU - Akopyan, Arseniy
AU - Schwartz, Richard
AU - Tabachnikov, Serge
ID - 8538
JF - European Journal of Mathematics
SN - 2199-675X
TI - Billiards in ellipses revisited
ER -
TY - GEN
AB - The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.
AU - Gao, Xiaofei
AU - Li, Jun-Liszt
AU - Chen, Xingjun
AU - Ci, Bo
AU - Chen, Fei
AU - Lu, Nannan
AU - Shen, Bo
AU - Zheng, Lijun
AU - Jia, Jie-Min
AU - Yi, Yating
AU - Zhang, Shiwen
AU - Shi, Ying-Chao
AU - Shi, Kaibin
AU - Propson, Nicholas E
AU - Huang, Yubin
AU - Poinsatte, Katherine
AU - Zhang, Zhaohuan
AU - Yue, Yuanlei
AU - Bosco, Dale B
AU - Lu, Ying-mei
AU - Yang, Shi-bing
AU - Adams, Ralf H.
AU - Lindner, Volkhard
AU - Huang, Fen
AU - Wu, Long-Jun
AU - Zheng, Hui
AU - Han, Feng
AU - Hippenmeyer, Simon
AU - Stowe, Ann M.
AU - Peng, Bo
AU - Margeta, Marta
AU - Wang, Xiaoqun
AU - Liu, Qiang
AU - Körbelin, Jakob
AU - Trepel, Martin
AU - Lu, Hui
AU - Zhou, Bo O.
AU - Zhao, Hu
AU - Su, Wenzhi
AU - Bachoo, Robert M.
AU - Ge, Woo-ping
ID - 8616
T2 - bioRxiv
TI - Reduction of neuronal activity mediated by blood-vessel regression in the brain
ER -
TY - GEN
AB - A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group "Open Science Strategy" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions.
AU - Mayer, Katja
AU - Rieck, Katharina
AU - Reichmann, Stefan
AU - Danowski, Patrick
AU - Graschopf, Anton
AU - König, Thomas
AU - Kraker, Peter
AU - Lehner, Patrick
AU - Reckling, Falk
AU - Ross-Hellauer, Tony
AU - Spichtinger, Daniel
AU - Tzatzanis, Michalis
AU - Schürz, Stefanie
ID - 8695
TI - Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria
ER -
TY - JOUR
AB - We develop algorithms and techniques to compute rigorous bounds for finite pieces of orbits of the critical points, for intervals of parameter values, in the quadratic family of one-dimensional maps fa(x)=a−x2. We illustrate the effectiveness of our approach by constructing a dynamically defined partition 𝒫 of the parameter interval Ω=[1.4,2] into almost 4×106 subintervals, for each of which we compute to high precision the orbits of the critical points up to some time N and other dynamically relevant quantities, several of which can vary greatly, possibly spanning several orders of magnitude. We also subdivide 𝒫 into a family 𝒫+ of intervals, which we call stochastic intervals, and a family 𝒫− of intervals, which we call regular intervals. We numerically prove that each interval ω∈𝒫+ has an escape time, which roughly means that some iterate of the critical point taken over all the parameters in ω has considerable width in the phase space. This suggests, in turn, that most parameters belonging to the intervals in 𝒫+ are stochastic and most parameters belonging to the intervals in 𝒫− are regular, thus the names. We prove that the intervals in 𝒫+ occupy almost 90% of the total measure of Ω. The software and the data are freely available at http://www.pawelpilarczyk.com/quadr/, and a web page is provided for carrying out the calculations. The ideas and procedures can be easily generalized to apply to other parameterized families of dynamical systems.
AU - Golmakani, Ali
AU - Koudjinan, Edmond
AU - Luzzatto, Stefano
AU - Pilarczyk, Pawel
ID - 8694
IS - 7
JF - Chaos
TI - Rigorous numerics for critical orbits in the quadratic family
VL - 30
ER -
TY - JOUR
AB - Given l>2ν>2d≥4, we prove the persistence of a Cantor--family of KAM tori of measure O(ε1/2−ν/l) for any non--degenerate nearly integrable Hamiltonian system of class Cl(D×Td), where D⊂Rd is a bounded domain, provided that the size ε of the perturbation is sufficiently small. This extends a result by D. Salamon in \cite{salamon2004kolmogorov} according to which we do have the persistence of a single KAM torus in the same framework. Moreover, it is well--known that, for the persistence of a single torus, the regularity assumption can not be improved.
AU - Koudjinan, Edmond
ID - 8691
IS - 6
JF - Journal of Differential Equations
KW - Analysis
SN - 0022-0396
TI - A KAM theorem for finitely differentiable Hamiltonian systems
VL - 269
ER -
TY - JOUR
AB - As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level.
AU - Danowski, Patrick
AU - Ferus, Andreas
AU - Hikl, Anna-Laetitia
AU - McNeill, Gerda
AU - Miniberger, Clemens
AU - Reding, Steve
AU - Zarka, Tobias
AU - Zojer, Michael
ID - 8706
IS - 2
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
TI - „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B
VL - 73
ER -
TY - JOUR
AB - Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.
For complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b).
AU - Laukoter, Susanne
AU - Amberg, Nicole
AU - Pauler, Florian
AU - Hippenmeyer, Simon
ID - 8978
IS - 3
JF - STAR Protocols
SN - 2666-1667
TI - Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy
VL - 1
ER -
TY - JOUR
AB - The fundamental and practical importance of particle stabilization has motivated various characterization methods for studying polymer brushes on particle surfaces. In this work, we show how one can perform sensitive measurements of neutral polymer coating on colloidal particles using a commercial zetameter and salt solutions. By systematically varying the Debye length, we study the mobility of the polymer-coated particles in an applied electric field and show that the electrophoretic mobility of polymer-coated particles normalized by the mobility of non-coated particles is entirely controlled by the polymer brush and independent of the native surface charge, here controlled with pH, or the surface–ion interaction. Our result is rationalized with a simple hydrodynamic model, allowing for the estimation of characteristics of the polymer coating: the brush length L, and the Brinkman length ξ, determined by its resistance to flows. We demonstrate that the Debye layer provides a convenient and faithful probe to the characterization of polymer coatings on particles. Because the method simply relies on a conventional zetameter, it is widely accessible and offers a practical tool to rapidly probe neutral polymer brushes, an asset in the development and utilization of polymer-coated colloidal particles.
AU - Youssef, Mena
AU - Morin, Alexandre
AU - Aubret, Antoine
AU - Sacanna, Stefano
AU - Palacci, Jérémie A
ID - 9054
IS - 17
JF - Soft Matter
KW - General Chemistry
KW - Condensed Matter Physics
SN - 1744-683X
TI - Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt
VL - 16
ER -
TY - JOUR
AB - In the quest for alternate and efficient electrode materials, ternary metal electrocatalysts (TMEs), part of the perovskite family, were synthesized and tested for methanol electro-oxidation in alkaline media. La0.5Ca0.5MO3 (M = Ni, Co, or Mn) was synthesized via sol-gel method. X-ray diffraction analysis revealed that the perovskite crystal structure possesses characteristic sharp and crystalline peaks for all synthesized ternary electrocatalysts. The average particle size calculated using Debye–Scherrer equation was in the order of La0.5Ca0.5NiO3 (LCNO) > La0.5Ca0.5CoO3 (LCCO)> La0.5Ca0.5MnO3 (LCMO). The elemental composition of as prepared sample, LCCO was investigated via x-ray fluorescence spectroscopy. The qualitative and quantitative analysis revealed the presence of La, Ca and Co in parent crystal structure with percentage compositions of 9.0, 3.12 and 87.82% respectively. The particle size distribution was homogenous, as determined by scanning electron and transmission electron microscopes. The electrocatalytic activity of the synthesized ternary electrocatalysts was studied electrochemically by cyclic voltammetry. The calculated diffusion coefficient values showed that electrode surface of LCNO and LCCO have limited efficiency for diffusion related phenomenon. The heterogeneous rate constants inferred better electrode kinetics of LCCO and LCNO which exhibited good electrocatalytic behavior; sharp anodic peaks were observed in the potential range of +0.3 to 0.6 V and +0.6 to 0.8 V, respectively. Methanol electro-oxidation was found minimal in case of LCMO sample. We have observed that Co substitution at B-site of perovskite electrode materials attains better electrochemical properties, thus in relation with reported literature.
AU - Hussain, Tayyaba
AU - Nauman, Muhammad
AU - Sabahat, Sana
AU - Arif, Saira
ID - 9069
IS - 12
JF - Materials Research Express
KW - Electronic
KW - Optical and Magnetic Materials
KW - Surfaces
KW - Coatings and Films
KW - Polymers and Plastics
KW - Metals and Alloys
KW - Biomaterials
SN - 2053-1591
TI - Synthesis of ternary electrocatalysts for exploration of methanol electro-oxidation in alkaline media
VL - 6
ER -
TY - JOUR
AB - Gadolinium silicide (Gd5Si4) nanoparticles are an interesting class of materials due to their high magnetization, low Curie temperature, low toxicity in biological environments and their multifunctional properties. We report the magnetic and magnetothermal properties of gadolinium silicide (Gd5Si4) nanoparticles prepared by surfactant-assisted ball milling of arc melted bulk ingots of the compound. Using different milling times and speeds, a wide range of crystallite sizes (13–43 nm) could be produced and a reduction in Curie temperature (TC) from 340 K to 317 K was achieved, making these nanoparticles suitable for self-controlled magnetic hyperthermia applications. The magnetothermal effect was measured in applied AC magnetic fields of amplitude 164–239 Oe and frequencies 163–519 kHz. All particles showed magnetic heating with a strong dependence of the specific absorption rate (SAR) on the average crystallite size. The highest SAR of 3.7 W g−1 was measured for 43 nm sized nanoparticles of Gd5Si4. The high SAR and low TC, (within the therapeutic range for magnetothermal therapy) makes the Gd5Si4 behave like self-regulating heat switches that would be suitable for self-controlled magnetic hyperthermia applications after biocompatibility and cytotoxicity tests.
AU - Nauman, Muhammad
AU - Alnasir, Muhammad Hisham
AU - Hamayun, Muhammad Asif
AU - Wang, YiXu
AU - Shatruk, Michael
AU - Manzoor, Sadia
ID - 9067
IS - 47
JF - RSC Advances
KW - General Chemistry
KW - General Chemical Engineering
SN - 2046-2069
TI - Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles
VL - 10
ER -
TY - CONF
AB - We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball’s volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the "wrapping effect" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG’s superior performance compared to LRT, CAPD, and Flow*.
AU - Gruenbacher, Sophie
AU - Cyranka, Jacek
AU - Lechner, Mathias
AU - Islam, Md Ariful
AU - Smolka, Scott A.
AU - Grosu, Radu
ID - 9103
SN - 07431546
T2 - Proceedings of the 59th IEEE Conference on Decision and Control
TI - Lagrangian reachtubes: The next generation
VL - 2020
ER -
TY - JOUR
AB - We investigate the role of a warm sea surface temperature (SST) anomaly (hot spot of typically 3 to 5 K) on the aggregation of convection using cloud-resolving simulations in a nonrotating framework. It is well known that SST gradients can spatially organize convection. Even with uniform SST, the spontaneous self-aggregation of convection is possible above a critical SST (here 295 K), arising mainly from radiative feedbacks. We investigate how a circular hot spot helps organize convection, and how self-aggregation feedbacks modulate this organization. The hot spot significantly accelerates aggregation, particularly for warmer/larger hot spots, and extends the range of SSTs for which aggregation occurs; however, at cold SST (290 K) the aggregated cluster disaggregates if we remove the hot spot. A large convective instability over the hot spot leads to stronger convection and generates a large-scale circulation which forces the subsidence drying outside the hot spot. Indeed, convection over the hot spot brings the atmosphere toward a warmer temperature. The warmer temperatures are imprinted over the whole domain by gravity waves and subsidence warming. The initial transient warming and concomitant subsidence drying suppress convection outside the hot spot, thus driving the aggregation. The hot-spot-induced large-scale circulation can enforce the aggregation even without radiative feedbacks for hot spots sufficiently large/warm. The strength of the large-scale circulation, which defines the speed of aggregation, is a function of the hot spot fractional area. At equilibrium, once the aggregation is well established, the moist convective region with upward midtropospheric motion, centered over the hot spot, has an area surprisingly independent of the hot spot size.
AU - Shamekh, Sara
AU - Muller, Caroline J
AU - Duvel, Jean-Philippe
AU - D’Andrea, Fabio
ID - 9129
IS - 11
JF - Journal of the Atmospheric Sciences
KW - Atmospheric Science
SN - 0022-4928
TI - How do ocean warm anomalies favor the aggregation of deep convective clouds?
VL - 77
ER -
TY - CHAP
AB - 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.
AU - Muller, Caroline J
ED - Bouchet, Freddy
ED - Schneider, Tapio
ED - Venaille, Antoine
ED - Salomon, Christophe
ID - 9132
SN - 978-0-1988-5521-7
T2 - Fundamental Aspects of Turbulent Flows in Climate Dynamics
TI - Clouds in current and in a warming climate
VL - 109
ER -
TY - GEN
AB - 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.
AU - Risi, Camille
AU - Muller, Caroline J
AU - Blossey, Peter N.
ID - 9150
TI - 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
ER -
TY - JOUR
AB - Bending-active structures are able to efficiently produce complex curved shapes from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match specific bending requests, namely the global curvature of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arch that fits a bounding box of 3.90x3.96x3.25 meters. This case study serves to test the applicability of this methodology at the architectural scale. The structure is validated via FE analyses and the fabrication of the full scale prototype.
AU - Laccone, Francesco
AU - Malomo, Luigi
AU - Perez Rodriguez, Jesus
AU - Pietroni, Nico
AU - Ponchio, Federico
AU - Bickel, Bernd
AU - Cignoni, Paolo
ID - 9208
IS - 9
JF - SN Applied Sciences
TI - A bending-active twisted-arch plywood structure: Computational design and fabrication of the FlexMaps Pavilion
VL - 2
ER -
TY - CONF
AB - 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.
AU - Nguyen, Quynh
AU - Mondelli, Marco
ID - 9221
T2 - 34th Conference on Neural Information Processing Systems
TI - Global convergence of deep networks with one wide layer followed by pyramidal topology
VL - 33
ER -
TY - CONF
AB - 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.
AU - Kurtz, Mark
AU - Kopinsky, Justin
AU - Gelashvili, Rati
AU - Matveev, Alexander
AU - Carr, John
AU - Goin, Michael
AU - Leiserson, William
AU - Moore, Sage
AU - Nell, Bill
AU - Shavit, Nir
AU - Alistarh, Dan-Adrian
ID - 9415
SN - 2640-3498
T2 - 37th International Conference on Machine Learning, ICML 2020
TI - Inducing and exploiting activation sparsity for fast neural network inference
VL - 119
ER -
TY - JOUR
AB - 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.
AU - Choi, Jaemyung
AU - Lyons, David B.
AU - Kim, M. Yvonne
AU - Moore, Jonathan D.
AU - Zilberman, Daniel
ID - 9526
IS - 2
JF - Molecular Cell
SN - 1097-2765
TI - DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts
VL - 77
ER -
TY - JOUR
AB - We show that for any n divisible by 3, almost all order-n Steiner triple systems admit a decomposition of almost all their triples into disjoint perfect matchings (that is, almost all Steiner triple systems are almost resolvable).
AU - Ferber, Asaf
AU - Kwan, Matthew Alan
ID - 9583
JF - Forum of Mathematics
TI - Almost all Steiner triple systems are almost resolvable
VL - 8
ER -
TY - JOUR
AB - How long a monotone path can one always find in any edge-ordering of the complete graph Kn? This appealing question was first asked by Chvátal and Komlós in 1971, and has since attracted the attention of many researchers, inspiring a variety of related problems. The prevailing conjecture is that one can always find a monotone path of linear length, but until now the best known lower bound was n2/3-o(1). In this paper we almost close this gap, proving that any edge-ordering of the complete graph contains a monotone path of length n1-o(1).
AU - Bucić, Matija
AU - Kwan, Matthew Alan
AU - Pokrovskiy, Alexey
AU - Sudakov, Benny
AU - Tran, Tuan
AU - Wagner, Adam Zsolt
ID - 9578
IS - 2
JF - Israel Journal of Mathematics
SN - 0021-2172
TI - Nearly-linear monotone paths in edge-ordered graphs
VL - 238
ER -
TY - JOUR
AB - The problem of finding dense induced bipartite subgraphs in H-free graphs has a long history, and was posed 30 years ago by Erdős, Faudree, Pach and Spencer. In this paper, we obtain several results in this direction. First we prove that any H-free graph with minimum degree at least d contains an induced bipartite subgraph of minimum degree at least cH log d/log log d, thus nearly confirming one and proving another conjecture of Esperet, Kang and Thomassé. Complementing this result, we further obtain optimal bounds for this problem in the case of dense triangle-free graphs, and we also answer a question of Erdœs, Janson, Łuczak and Spencer.
AU - Kwan, Matthew Alan
AU - Letzter, Shoham
AU - Sudakov, Benny
AU - Tran, Tuan
ID - 9582
IS - 2
JF - Combinatorica
SN - 0209-9683
TI - Dense induced bipartite subgraphs in triangle-free graphs
VL - 40
ER -
TY - JOUR
AB - We show that for any 𝑛 divisible by 3, almost all order- 𝑛 Steiner triple systems have a perfect matching (also known as a parallel class or resolution class). In fact, we prove a general upper bound on the number of perfect matchings in a Steiner triple system and show that almost all Steiner triple systems essentially attain this maximum. We accomplish this via a general theorem comparing a uniformly random Steiner triple system to the outcome of the triangle removal process, which we hope will be useful for other problems. Our methods can also be adapted to other types of designs; for example, we sketch a proof of the theorem that almost all Latin squares have transversals.
AU - Kwan, Matthew Alan
ID - 9581
IS - 6
JF - Proceedings of the London Mathematical Society
SN - 0024-6115
TI - Almost all Steiner triple systems have perfect matchings
VL - 121
ER -
TY - JOUR
AB - Macroscopic models of nucleation provide powerful tools for understanding activated phase transition processes. These models do not provide atomistic insights and can thus sometimes lack material-specific descriptions. Here, we provide a comprehensive framework for constructing a continuum picture from an atomistic simulation of homogeneous nucleation. We use this framework to determine the equilibrium shape of the solid nucleus that forms inside bulk liquid for a Lennard-Jones potential. From this shape, we then extract the anisotropy of the solid-liquid interfacial free energy, by performing a reverse Wulff construction in the space of spherical harmonic expansions. We find that the shape of the nucleus is nearly spherical and that its anisotropy can be perfectly described using classical models.
AU - Cheng, Bingqing
AU - Ceriotti, Michele
AU - Tribello, Gareth A.
ID - 9658
IS - 4
JF - The Journal of Chemical Physics
SN - 0021-9606
TI - Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification
VL - 152
ER -
TY - JOUR
AB - Equilibrium molecular dynamics simulations, in combination with the Green-Kubo (GK) method, have been extensively used to compute the thermal conductivity of liquids. However, the GK method relies on an ambiguous definition of the microscopic heat flux, which depends on how one chooses to distribute energies over atoms. This ambiguity makes it problematic to employ the GK method for systems with nonpairwise interactions. In this work, we show that the hydrodynamic description of thermally driven density fluctuations can be used to obtain the thermal conductivity of a bulk fluid unambiguously, thereby bypassing the need to define the heat flux. We verify that, for a model fluid with only pairwise interactions, our method yields estimates of thermal conductivity consistent with the GK approach. We apply our approach to compute the thermal conductivity of a nonpairwise additive water model at supercritical conditions, and of a liquid hydrogen system described by a machine-learning interatomic potential, at 33 GPa and 2000 K.
AU - Cheng, Bingqing
AU - Frenkel, Daan
ID - 9664
IS - 13
JF - Physical Review Letters
SN - 0031-9007
TI - Computing the heat conductivity of fluids from density fluctuations
VL - 125
ER -
TY - JOUR
AB - Hydrogen, the simplest and most abundant element in the Universe, develops a remarkably complex behaviour upon compression^1. Since Wigner predicted the dissociation and metallization of solid hydrogen at megabar pressures almost a century ago^2, several efforts have been made to explain the many unusual properties of dense hydrogen, including a rich and poorly understood solid polymorphism^1,3-5, an anomalous melting line6 and the possible transition to a superconducting state^7. Experiments at such extreme conditions are challenging and often lead to hard-to-interpret and controversial observations, whereas theoretical investigations are constrained by the huge computational cost of sufficiently accurate quantum mechanical calculations. Here we present a theoretical study of the phase diagram of dense hydrogen that uses machine learning to 'learn' potential-energy surfaces and interatomic forces from reference calculations and then predict them at low computational cost, overcoming length- and timescale limitations. We reproduce both the re-entrant melting behaviour and the polymorphism of the solid phase. Simulations using our machine-learning-based potentials provide evidence for a continuous molecular-to-atomic transition in the liquid, with no first-order transition observed above the melting line. This suggests a smooth transition between insulating and metallic layers in giant gas planets, and reconciles existing discrepancies between experiments as a manifestation of supercritical behaviour.
AU - Cheng, Bingqing
AU - Mazzola, Guglielmo
AU - Pickard, Chris J.
AU - Ceriotti, Michele
ID - 9685
IS - 7824
JF - Nature
SN - 0028-0836
TI - Evidence for supercritical behaviour of high-pressure liquid hydrogen
VL - 585
ER -
TY - JOUR
AB - Obtaining detailed information about high mountain snowpacks is often limited by insufficient ground-based observations and uncertainty in the (re)distribution of solid precipitation. We utilize high-resolution optical images from Pléiades satellites to generate a snow depth map, at a spatial resolution of 4 m, for a high mountain catchment of central Chile. Results are negatively biased (median difference of −0.22 m) when compared against observations from a terrestrial Light Detection And Ranging scan, though replicate general snow depth variability well. Additionally, the Pléiades dataset is subject to data gaps (17% of total pixels), negative values for shallow snow (12%), and noise on slopes >40–50° (2%). We correct and filter the Pléiades snow depths using surface classification techniques of snow-free areas and a random forest model for data gap filling. Snow depths (with an estimated error of ~0.36 m) average 1.66 m and relate well to topographical parameters such as elevation and northness in a similar way to previous studies. However, estimations of snow depth based upon topography (TOPO) or physically based modeling (DBSM) cannot resolve localized processes (i.e., avalanching or wind scouring) that are detected by Pléiades, even when forced with locally calibrated data. Comparing these alternative model approaches to corrected Pléiades snow depths reveals total snow volume differences between −28% (DBSM) and +54% (TOPO) for the catchment and large differences across most elevation bands. Pléiades represents an important contribution to understanding snow accumulation at sparsely monitored catchments, though ideally requires a careful systematic validation procedure to identify catchment-scale biases and errors in the snow depth derivation.
AU - Shaw, Thomas E.
AU - Gascoin, Simon
AU - Mendoza, Pablo A.
AU - Pellicciotti, Francesca
AU - McPhee, James
ID - 12598
IS - 2
JF - Water Resources Research
KW - Water Science and Technology
SN - 0043-1397
TI - Snow depth patterns in a high mountain Andean catchment from satellite optical tristereoscopic remote sensing
VL - 56
ER -
TY - JOUR
AB - Information about end-of-winter spatial distribution of snow depth is important for seasonal forecasts of spring/summer streamflow in high-mountain regions. Nevertheless, such information typically relies upon extrapolation from a sparse network of observations at low elevations. Here, we test the potential of high-resolution snow depth data derived from optical stereophotogrammetry of Pléiades satellites for improving the representation of snow depth initial conditions (SDICs) in a glacio-hydrological model and assess potential improvements in the skill of snowmelt and streamflow simulations in a high-elevation Andean catchment. We calibrate model parameters controlling glacier mass balance and snow cover evolution using ground-based and satellite observations, and consider the relative importance of accurate estimates of SDICs compared to model parameters and forcings. We find that Pléiades SDICs improve the simulation of snow-covered area, glacier mass balance, and monthly streamflow compared to alternative SDICs based upon extrapolation of meteorological variables or statistical methods to estimate SDICs based upon topography. Model simulations are found to be sensitive to SDICs in the early spring (up to 48% variability in modeled streamflow compared to the best estimate model), and to temperature gradients in all months that control albedo and melt rates over a large elevation range (>2,400 m). As such, appropriately characterizing the distribution of total snow volume with elevation is important for reproducing total streamflow and the proportions of snowmelt. Therefore, optical stereo-photogrammetry offers an advantage for obtaining SDICs that aid both the timing and magnitude of streamflow simulations, process representation (e.g., snow cover evolution) and has the potential for large spatial domains.
AU - Shaw, Thomas E.
AU - Caro, Alexis
AU - Mendoza, Pablo
AU - Ayala, Álvaro
AU - Pellicciotti, Francesca
AU - Gascoin, Simon
AU - McPhee, James
ID - 12594
IS - 8
JF - Water Resources Research
KW - Water Science and Technology
SN - 0043-1397
TI - The utility of optical satellite winter snow depths for initializing a glacio‐hydrological model of a High‐Elevation, Andean catchment
VL - 56
ER -
TY - JOUR
AB - As glaciers adjust their size in response to climate variations, long-term changes in meltwater production can be expected, affecting the local availability of water resources. We investigate glacier runoff in the period 1955–2016 in the Maipo River basin (4843 km2, 33.0–34.3∘ S, 69.8–70.5∘ W), in the semiarid Andes of Chile. The basin contains more than 800 glaciers, which cover 378 km2 in total (inventoried in 2000). We model the mass balance and runoff contribution of 26 glaciers with the physically oriented and fully distributed TOPKAPI (Topographic Kinematic Approximation and Integration)-ETH glacio-hydrological model and extrapolate the results to the entire basin. TOPKAPI-ETH is run at a daily time step using several glaciological and meteorological datasets, and its results are evaluated against streamflow records, remotely sensed snow cover, and geodetic mass balances for the periods 1955–2000 and 2000–2013. Results show that in 1955–2016 glacier mass balance had a general decreasing trend as a basin average but also had differences between the main sub-catchments. Glacier volume decreased by one-fifth (from 18.6±4.5 to 14.9±2.9 km3). Runoff from the initially glacierized areas was 177±25 mm yr−1 (16±7 % of the total contributions to the basin), but it shows a decreasing sequence of maxima, which can be linked to the interplay between a decrease in precipitation since the 1980s and the reduction of ice melt. Glaciers in the Maipo River basin will continue retreating because they are not in equilibrium with the current climate. In a hypothetical constant climate scenario, glacier volume would reduce to 81±38 % of the year 2000 volume, and glacier runoff would be 78±30 % of the 1955–2016 average. This would considerably decrease the drought mitigation capacity of the basin.
AU - Ayala, Álvaro
AU - Farías-Barahona, David
AU - Huss, Matthias
AU - Pellicciotti, Francesca
AU - McPhee, James
AU - Farinotti, Daniel
ID - 12596
IS - 6
JF - The Cryosphere
KW - Earth-Surface Processes
KW - Water Science and Technology
SN - 1994-0424
TI - Glacier runoff variations since 1955 in the Maipo River basin, in the semiarid Andes of central Chile
VL - 14
ER -
TY - JOUR
AB - We examine the spatial patterns of near-surface air temperature (Ta) over a melting glacier using a multi-annual dataset from McCall Glacier, Alaska. The dataset consists of a 10-year (2005–2014) meteorological record along the glacier centreline up to an upper glacier cirque, spanning an elevation difference of 900 m. We test the validity of on-glacier linear lapse rates, and a model that calculates Ta based on the influence of katabatic winds and other heat sources along the glacier flow line. During the coldest hours of each summer (10% of time), average lapse rates across the entire glacier range from −4.7 to −6.7°C km−1, with a strong relationship between Ta and elevation (R2 > 0.7). During warm conditions, Ta shows more complex, non-linear patterns that are better explained by the flow line-dependent model, reducing errors by up to 0.5°C compared with linear lapse rates, although more uncertainty might be associated with these observations due to occasionally poor sensor ventilation. We conclude that Ta spatial distribution can vary significantly from year to year, and from one glacier section to another. Importantly, extrapolations using linear lapse rates from the ablation zone might lead to large underestimations of Ta on the upper glacier areas.
AU - Troxler, Patrick
AU - Ayala, Álvaro
AU - Shaw, Thomas E.
AU - Nolan, Matt
AU - Brock, Ben W.
AU - Pellicciotti, Francesca
ID - 12597
IS - 257
JF - Journal of Glaciology
KW - Earth-Surface Processes
SN - 0022-1430
TI - Modelling spatial patterns of near-surface air temperature over a decade of melt seasons on McCall Glacier, Alaska
VL - 66
ER -
TY - JOUR
AB - The seasonal dynamic changes of Tibetan glaciers have seen little prior investigation, despite the increase in geodetic studies of multi-year changes. This study compares seasonal glacier dynamics (“cold” and “warm” seasons) in the ablation zone of Parlung No. 4 Glacier, a temperate glacier in the monsoon-influenced southeastern Tibetan Plateau, by using repeat unpiloted aerial vehicle (UAV) surveys combined with Structure-from-Motion (SfM) photogrammetry and ground stake measurements. Our results showed that the surveyed ablation zone had a mean change of −2.7 m of ice surface elevation during the period of September 2018 to October 2019 but is characterized by significant seasonal cyclic variations with ice surface elevation lifting (+2.0 m) in the cold season (September 2018 to June 2019) but lowering (−4.7 m) in the warm season (June 2019 to October 2019). Over an annual timescale, surface lowering was greatly suppressed by the resupply of ice from the glacier’s accumulation area—the annual emergence velocity compensates for about 55% of surface ablation in our study area. Cold season emergence velocities (3.0 ± 1.2 m) were ~5-times larger than those observed in the warm season (0.6 ± 1.0 m). Distinct spring precipitation patterns may contribute to these distinct seasonal signals. Such seasonal dynamic conditions are possibly critical for different glacier responses to climate change in this region of the Tibetan Plateau, and perhaps further afield.
AU - Yang, Wei
AU - Zhao, Chuanxi
AU - Westoby, Matthew
AU - Yao, Tandong
AU - Wang, Yongjie
AU - Pellicciotti, Francesca
AU - Zhou, Jianmin
AU - He, Zhen
AU - Miles, Evan
ID - 12595
IS - 15
JF - Remote Sensing
SN - 2072-4292
TI - Seasonal dynamics of a temperate Tibetan glacier revealed by high-resolution UAV photogrammetry and in situ measurements
VL - 12
ER -
TY - JOUR
AB - Mountains are the water towers of the world, supplying a substantial part of both natural and anthropogenic water demands1,2. They are highly sensitive and prone to climate change3,4, yet their importance and vulnerability have not been quantified at the global scale. Here we present a global water tower index (WTI), which ranks all water towers in terms of their water-supplying role and the downstream dependence of ecosystems and society. For each water tower, we assess its vulnerability related to water stress, governance, hydropolitical tension and future climatic and socio-economic changes. We conclude that the most important (highest WTI) water towers are also among the most vulnerable, and that climatic and socio-economic changes will affect them profoundly. This could negatively impact 1.9 billion people living in (0.3 billion) or directly downstream of (1.6 billion) mountainous areas. Immediate action is required to safeguard the future of the world’s most important and vulnerable water towers.
AU - Immerzeel, W. W.
AU - Lutz, A. F.
AU - Andrade, M.
AU - Bahl, A.
AU - Biemans, H.
AU - Bolch, T.
AU - Hyde, S.
AU - Brumby, S.
AU - Davies, B. J.
AU - Elmore, A. C.
AU - Emmer, A.
AU - Feng, M.
AU - Fernández, A.
AU - Haritashya, U.
AU - Kargel, J. S.
AU - Koppes, M.
AU - Kraaijenbrink, P. D. A.
AU - Kulkarni, A. V.
AU - Mayewski, P. A.
AU - Nepal, S.
AU - Pacheco, P.
AU - Painter, T. H.
AU - Pellicciotti, Francesca
AU - Rajaram, H.
AU - Rupper, S.
AU - Sinisalo, A.
AU - Shrestha, A. B.
AU - Viviroli, D.
AU - Wada, Y.
AU - Xiao, C.
AU - Yao, T.
AU - Baillie, J. E. M.
ID - 12599
IS - 7790
JF - Nature
SN - 0028-0836
TI - Importance and vulnerability of the world’s water towers
VL - 577
ER -
TY - JOUR
AB - Rock debris can accumulate on glacier surfaces and dramatically reduce glacier melt. The structure of a debris cover is unique to each glacier and sensitive to climate. Despite this, debris cover has been omitted from global glacier models and forecasts of their response to a changing climate. Fundamental to resolving these omissions is a global map of debris cover and an estimate of its future spatial evolution. Here we use Landsat imagery and a detailed correction to the Randolph Glacier Inventory to show that 7.3% of mountain glacier area is debris covered and over half of Earth’s debris is concentrated in three regions: Alaska (38.6% of total debris-covered area), Southwest Asia (12.6%) and Greenland (12.0%). We use a set of new metrics, which include stage, the current position of a glacier on its trajectory towards reaching its spatial carrying capacity of debris cover, to quantify the state of glaciers. Debris cover is present on 44% of Earth’s glaciers and prominent (>1.0 km2) on 15%. Of Earth’s glaciers, 20% have a substantial percentage of debris cover for which the net stage is 36% and the bulk of individual glaciers have evolved beyond an optimal moraine configuration favourable for debris-cover expansion. Use of this dataset in global-scale models will enable improved estimates of melt over 10.6% of the global glacier domain.
AU - Herreid, Sam
AU - Pellicciotti, Francesca
ID - 12593
IS - 9
JF - Nature Geoscience
KW - General Earth and Planetary Sciences
SN - 1752-0894
TI - The state of rock debris covering Earth’s glaciers
VL - 13
ER -
TY - CONF
AB - The family of feedback alignment (FA) algorithms aims to provide a more biologically motivated alternative to backpropagation (BP), by substituting the computations that are unrealistic to be implemented in physical brains. While FA algorithms have been shown to work well in practice, there is a lack of rigorous theory proofing their learning capabilities. Here we introduce the first feedback alignment algorithm with provable learning guarantees. In contrast to existing work, we do not require any assumption about the size or depth of the network except that it has a single output neuron, i.e., such as for binary classification tasks. We show that our FA algorithm can deliver its theoretical promises in practice, surpassing the learning performance of existing FA methods and matching backpropagation in binary classification tasks. Finally, we demonstrate the limits of our FA variant when the number of output neurons grows beyond a certain quantity.
AU - Lechner, Mathias
ID - 10672
T2 - 8th International Conference on Learning Representations
TI - Learning representations for binary-classification without backpropagation
ER -
TY - CONF
AB - A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that
gives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to
generate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on
depth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.
AU - Henderson, Paul M
AU - Lampert, Christoph
ID - 8188
SN - 9781713829546
T2 - 34th Conference on Neural Information Processing Systems
TI - Unsupervised object-centric video generation and decomposition in 3D
VL - 33
ER -
TY - JOUR
AB - Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.
AU - Bloomer, Rebecca H.
AU - Hutchison, Claire E.
AU - Bäurle, Isabel
AU - Walker, James
AU - Fang, Xiaofeng
AU - Perera, Pumi
AU - Velanis, Christos N.
AU - Gümüs, Serin
AU - Spanos, Christos
AU - Rappsilber, Juri
AU - Feng, Xiaoqi
AU - Goodrich, Justin
AU - Dean, Caroline
ID - 12188
IS - 28
JF - Proceedings of the National Academy of Sciences
KW - Multidisciplinary
SN - 0027-8424
TI - The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2
VL - 117
ER -
TY - JOUR
AB - Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.
AU - Christophorou, Nicolas
AU - She, Wenjing
AU - Long, Jincheng
AU - Hurel, Aurélie
AU - Beaubiat, Sébastien
AU - Idir, Yassir
AU - Tagliaro-Jahns, Marina
AU - Chambon, Aurélie
AU - Solier, Victor
AU - Vezon, Daniel
AU - Grelon, Mathilde
AU - Feng, Xiaoqi
AU - Bouché, Nicolas
AU - Mézard, Christine
ID - 12189
IS - 6
JF - PLOS Genetics
KW - Cancer Research
KW - Genetics (clinical)
KW - Genetics
KW - Molecular Biology
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 1553-7404
TI - AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization
VL - 16
ER -
TY - JOUR
AB - Let be a sequence of points on an elliptic curve defined over a number field K. In this paper, we study the denominators of the x-coordinates of this sequence. We prove that, if Q is a torsion point of prime order, then for n large enough there always exists a primitive divisor. Later on, we show the link between the study of the primitive divisors and a Lang-Trotter conjecture. Indeed, given two points P and Q on the elliptic curve, we prove a lower bound for the number of primes p such that P is in the orbit of Q modulo p.
AU - Verzobio, Matteo
ID - 12310
IS - 4
JF - Journal of Number Theory
KW - Algebra and Number Theory
SN - 0022-314X
TI - Primitive divisors of sequences associated to elliptic curves
VL - 209
ER -
TY - GEN
AB - We investigate the structural similarities between liquid water and 53 ices, including 20 known crystalline phases. We base such similarity comparison on the local environments that consist of atoms within a certain cutoff radius of a central atom. We reveal that liquid water explores the local environments of the diverse ice phases, by directly comparing the environments in these phases using general atomic descriptors, and also by demonstrating that a machine-learning potential trained on liquid water alone can predict the densities, the lattice energies, and vibrational properties of the
ices. The finding that the local environments characterising the different ice phases are found in water sheds light on water phase behaviors, and rationalizes the transferability of water models between different phases.
AU - Monserrat, Bartomeu
AU - Brandenburg, Jan Gerit
AU - Engel, Edgar A.
AU - Cheng, Bingqing
ID - 9699
T2 - arXiv
TI - Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well
ER -
TY - JOUR
AB - Desorption electrospray ionization (DESI), easy ambient sonic-spray ionization (EASI) and low-temperature plasma (LTP) ionization are powerful ambient ionization techniques for mass spectrometry. However, every single method has its limitation in terms of polarity and molecular weight of analyte molecules. After the miniaturization of every possible component of the different ion sources, we finally were able to embed two emitters and an ion transfer tubing into a small, hand-held device. The pen-like interface is connected to the mass spectrometer and a separate control unit via a bundle of flexible tubing and cables. The novel device allows the user to ionize an extended range of chemicals by simple switching between DESI, voltage-free EASI, or LTP ionization as well as to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The interface was successfully tested using different types of chemicals, pharmaceuticals, and real life samples. Moreover, the combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging mass spectrometry, which we name “interactive mass spectrometry imaging (IMSI)”.
AU - Meisenbichler, Christina
AU - Kluibenschedl, Florian
AU - Müller, Thomas
ID - 12940
IS - 21
JF - Analytical Chemistry
KW - Analytical Chemistry
SN - 0003-2700
TI - A 3-in-1 hand-held ambient mass spectrometry interface for identification and 2D localization of chemicals on surfaces
VL - 92
ER -
TY - JOUR
AB - Linear tetrapyrroles, called phyllobilins, are obtained as major catabolites upon chlorophyll degradation. Primarily, colorless phylloleucobilins featuring four deconjugated pyrrole units were identified. Their yellow counterparts, phylloxanthobilins, were discovered more recently. Although the two catabolites differ only by one double bond, physicochemical properties are very distinct. Moreover, the presence of the double bond seems to enhance physiologically relevant bioactivities: in contrast to phylloleucobilin, we identified a potent anti-proliferative activity for a phylloxanthobilin, and show that this natural product induces apoptotic cell death and a cell cycle arrest in cancer cells. Interestingly, upon modifying inactive phylloleucobilin by esterification, an anti-proliferative activity can be observed that increases with the chain lengths of the alkyl esters. We provide first evidence for anti-cancer activity of phyllobilins, report a novel plant source for a phylloxanthobilin, and by using paper spray MS, show that these bioactive yellow chlorophyll catabolites are more prevalent in Nature than previously assumed.
AU - Karg, Cornelia A.
AU - Wang, Pengyu
AU - Kluibenschedl, Florian
AU - Müller, Thomas
AU - Allmendinger, Lars
AU - Vollmar, Angelika M.
AU - Moser, Simone
ID - 12939
IS - 29
JF - European Journal of Organic Chemistry
KW - Organic Chemistry
KW - Physical and Theoretical Chemistry
SN - 1434-193X
TI - Phylloxanthobilins are abundant linear tetrapyrroles from chlorophyll breakdown with activities against cancer cells
VL - 2020
ER -
TY - BOOK
AB - This booklet is a collection of abstracts presented at the AHPC conference.
ED - Schlögl, Alois
ED - Kiss, Janos
ED - Elefante, Stefano
ID - 7474
SN - 978-3-99078-004-6
TI - Austrian High-Performance-Computing meeting (AHPC2020)
ER -
TY - CONF
AB - Quantization converts neural networks into low-bit fixed-point computations which can be carried out by efficient integer-only hardware, and is standard practice for the deployment of neural networks on real-time embedded devices. However, like their real-numbered counterpart, quantized networks are not immune to malicious misclassification caused by adversarial attacks. We investigate how quantization affects a network’s robustness to adversarial attacks, which is a formal verification question. We show that neither robustness nor non-robustness are monotonic with changing the number of bits for the representation and, also, neither are preserved by quantization from a real-numbered network. For this reason, we introduce a verification method for quantized neural networks which, using SMT solving over bit-vectors, accounts for their exact, bit-precise semantics. We built a tool and analyzed the effect of quantization on a classifier for the MNIST dataset. We demonstrate that, compared to our method, existing methods for the analysis of real-numbered networks often derive false conclusions about their quantizations, both when determining robustness and when detecting attacks, and that existing methods for quantized networks often miss attacks. Furthermore, we applied our method beyond robustness, showing how the number of bits in quantization enlarges the gender bias of a predictor for students’ grades.
AU - Giacobbe, Mirco
AU - Henzinger, Thomas A
AU - Lechner, Mathias
ID - 7808
SN - 03029743
T2 - International Conference on Tools and Algorithms for the Construction and Analysis of Systems
TI - How many bits does it take to quantize your neural network?
VL - 12079
ER -
TY - CONF
AB - Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary.
AU - Boissonnat, Jean-Daniel
AU - Wintraecken, Mathijs
ID - 7952
SN - 1868-8969
T2 - 36th International Symposium on Computational Geometry
TI - The topological correctness of PL-approximations of isomanifolds
VL - 164
ER -
TY - JOUR
AB - Scanning nanoscale superconducting quantum interference devices (nanoSQUIDs)
are of growing interest for highly sensitive quantitative imaging of magnetic,
spintronic, and transport properties of low-dimensional systems. Utilizing
specifically designed grooved quartz capillaries pulled into a sharp pipette,
we have fabricated the smallest SQUID-on-tip (SOT) devices with effective
diameters down to 39 nm. Integration of a resistive shunt in close proximity to
the pipette apex combined with self-aligned deposition of In and Sn, have
resulted in SOT with a flux noise of 42 n$\Phi_0$Hz$^{-1/2}$, yielding a record
low spin noise of 0.29 $\mu_B$Hz$^{-1/2}$. In addition, the new SOTs function
at sub-Kelvin temperatures and in high magnetic fields of over 2.5 T.
Integrating the SOTs into a scanning probe microscope allowed us to image the
stray field of a single Fe$_3$O$_4$ nanocube at 300 mK. Our results show that
the easy magnetization axis direction undergoes a transition from the (111)
direction at room temperature to an in-plane orientation, which could be
attributed to the Verwey phase transition in Fe$_3$O$_4$.
AU - Anahory, Y.
AU - Naren, H. R.
AU - Lachman, E. O.
AU - Sinai, S. Buhbut
AU - Uri, A.
AU - Embon, L.
AU - Yaakobi, E.
AU - Myasoedov, Y.
AU - Huber, M. E.
AU - Klajn, Rafal
AU - Zeldov, E.
ID - 13341
IS - 5
JF - Nanoscale
TI - SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging
VL - 12
ER -
TY - CONF
AB - Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7990
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)
VL - 164
ER -
TY - CONF
AB - In a straight-line embedded triangulation of a point set P in the plane, removing an inner edge and—provided the resulting quadrilateral is convex—adding the other diagonal is called an edge flip. The (edge) flip graph has all triangulations as vertices, and a pair of triangulations is adjacent if they can be obtained from each other by an edge flip. The goal of this paper is to contribute to a better understanding of the flip graph, with an emphasis on its connectivity.
For sets in general position, it is known that every triangulation allows at least edge flips (a tight bound) which gives the minimum degree of any flip graph for n points. We show that for every point set P in general position, the flip graph is at least -vertex connected. Somewhat more strongly, we show that the vertex connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum number of flippable edges in any triangulation of P, provided P is large enough. Finally, we exhibit some of the geometry of the flip graph by showing that the flip graph can be covered by 1-skeletons of polytopes of dimension (products of associahedra).
A corresponding result ((n – 3)-vertex connectedness) can be shown for the bistellar flip graph of partial triangulations, i.e. the set of all triangulations of subsets of P which contain all extreme points of P. This will be treated separately in a second part.
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7807
SN - 9781611975994
T2 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
TI - Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)
VL - 2020-January
ER -
TY - GEN
AB - The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.
AU - Simon, Alexis
AU - Fraisse, Christelle
AU - El Ayari, Tahani
AU - Liautard-Haag, Cathy
AU - Strelkov, Petr
AU - Welch, John
AU - Bierne, Nicolas
ID - 13073
TI - How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels
ER -
TY - GEN
AB - Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.
AU - Arnoux, Stephanie
AU - Fraisse, Christelle
AU - Sauvage, Christopher
ID - 13065
TI - VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species
ER -
TY - JOUR
AB - In nature, light is harvested by photoactive proteins to drive a range of biological processes, including photosynthesis, phototaxis, vision, and ultimately life. Bacteriorhodopsin, for example, is a protein embedded within archaeal cell membranes that binds the chromophore retinal within its hydrophobic pocket. Exposure to light triggers regioselective photoisomerization of the confined retinal, which in turn initiates a cascade of conformational changes within the protein, triggering proton flux against the concentration gradient, providing the microorganisms with the energy to live. We are inspired by these functions in nature to harness light energy using synthetic photoswitches under confinement. Like retinal, synthetic photoswitches require some degree of conformational flexibility to isomerize. In nature, the conformational change associated with retinal isomerization is accommodated by the structural flexibility of the opsin host, yet it results in steric communication between the chromophore and the protein. Similarly, we strive to design systems wherein isomerization of confined photoswitches results in steric communication between a photoswitch and its confining environment. To achieve this aim, a balance must be struck between molecular crowding and conformational freedom under confinement: too much crowding prevents switching, whereas too much freedom resembles switching of isolated molecules in solution, preventing communication.
In this Account, we discuss five classes of synthetic light-switchable compounds—diarylethenes, anthracenes, azobenzenes, spiropyrans, and donor–acceptor Stenhouse adducts—comparing their behaviors under confinement and in solution. The environments employed to confine these photoswitches are diverse, ranging from planar surfaces to nanosized cavities within coordination cages, nanoporous frameworks, and nanoparticle aggregates. The trends that emerge are primarily dependent on the nature of the photoswitch and not on the material used for confinement. In general, we find that photoswitches requiring less conformational freedom for switching are, as expected, more straightforward to isomerize reversibly under confinement. Because these compounds undergo only small structural changes upon isomerization, however, switching does not propagate into communication with their environment. Conversely, photoswitches that require more conformational freedom are more challenging to switch under confinement but also can influence system-wide behavior.
Although we are primarily interested in the effects of geometric constraints on photoswitching under confinement, additional effects inevitably emerge when a compound is removed from solution and placed within a new, more crowded environment. For instance, we have found that compounds that convert to zwitterionic isomers upon light irradiation often experience stabilization of these forms under confinement. This effect results from the mutual stabilization of zwitterions that are brought into close proximity on surfaces or within cavities. Furthermore, photoswitches can experience preorganization under confinement, influencing the selectivity and efficiency of their photoreactions. Because intermolecular interactions arising from confinement cannot be considered independently from the effects of geometric constraints, we describe all confinement effects concurrently throughout this Account.
AU - Grommet, Angela B.
AU - Lee, Lucia M.
AU - Klajn, Rafal
ID - 13361
IS - 11
JF - Accounts of Chemical Research
KW - General Medicine
KW - General Chemistry
SN - 0001-4842
TI - Molecular photoswitching in confined spaces
VL - 53
ER -
TY - JOUR
AB - Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure–property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage’s cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments.
AU - Gemen, Julius
AU - Ahrens, Johannes
AU - Shimon, Linda J. W.
AU - Klajn, Rafal
ID - 13362
IS - 41
JF - Journal of the American Chemical Society
KW - Colloid and Surface Chemistry
KW - Biochemistry
KW - General Chemistry
KW - Catalysis
SN - 0002-7863
TI - Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage
VL - 142
ER -
TY - JOUR
AB - Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions.
AU - Canton, Martina
AU - Grommet, Angela B.
AU - Pesce, Luca
AU - Gemen, Julius
AU - Li, Shiming
AU - Diskin-Posner, Yael
AU - Credi, Alberto
AU - Pavan, Giovanni M.
AU - Andréasson, Joakim
AU - Klajn, Rafal
ID - 13364
IS - 34
JF - Journal of the American Chemical Society
KW - Colloid and Surface Chemistry
KW - Biochemistry
KW - General Chemistry
KW - Catalysis
SN - 0002-7863
TI - Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage
VL - 142
ER -
TY - JOUR
AB - Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions.
AU - Pesce, Luca
AU - Perego, Claudio
AU - Grommet, Angela B.
AU - Klajn, Rafal
AU - Pavan, Giovanni M.
ID - 13365
IS - 21
JF - Journal of the American Chemical Society
KW - Colloid and Surface Chemistry
KW - Biochemistry
KW - General Chemistry
KW - Catalysis
SN - 0002-7863
TI - Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage
VL - 142
ER -
TY - JOUR
AB - Scanning nanoscale superconducting quantum interference devices (nanoSQUIDs) are of growing interest for highly sensitive quantitative imaging of magnetic, spintronic, and transport properties of low-dimensional systems. Utilizing specifically designed grooved quartz capillaries pulled into a sharp pipette, we have fabricated the smallest SQUID-on-tip (SOT) devices with effective diameters down to 39 nm. Integration of a resistive shunt in close proximity to the pipette apex combined with self-aligned deposition of In and Sn, has resulted in SOTs with a flux noise of 42 nΦ0 Hz−1/2, yielding a record low spin noise of 0.29 μB Hz−1/2. In addition, the new SOTs function at sub-Kelvin temperatures and in high magnetic fields of over 2.5 T. Integrating the SOTs into a scanning probe microscope allowed us to image the stray field of a single Fe3O4 nanocube at 300 mK. Our results show that the easy magnetization axis direction undergoes a transition from the 〈111〉 direction at room temperature to an in-plane orientation, which could be attributed to the Verwey phase transition in Fe3O4.
AU - Anahory, Y.
AU - Naren, H. R.
AU - Lachman, E. O.
AU - Buhbut Sinai, S.
AU - Uri, A.
AU - Embon, L.
AU - Yaakobi, E.
AU - Myasoedov, Y.
AU - Huber, M. E.
AU - Klajn, Rafal
AU - Zeldov, E.
ID - 13368
IS - 5
JF - Nanoscale
KW - General Materials Science
SN - 2040-3364
TI - SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging
VL - 12
ER -
TY - JOUR
AB - Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand.
AU - Moreno, Silvia
AU - Sharan, Priyanka
AU - Engelke, Johanna
AU - Gumz, Hannes
AU - Boye, Susanne
AU - Oertel, Ulrich
AU - Wang, Peng
AU - Banerjee, Susanta
AU - Klajn, Rafal
AU - Voit, Brigitte
AU - Lederer, Albena
AU - Appelhans, Dietmar
ID - 13363
IS - 37
JF - Small
KW - Biomaterials
KW - Biotechnology
KW - General Materials Science
KW - General Chemistry
SN - 1613-6810
TI - Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors
VL - 16
ER -