TY - JOUR
AB - Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.
AU - Gurel, Nezihe Merve
AU - Kara, Kaan
AU - Stojanov, Alen
AU - Smith, Tyler
AU - Lemmin, Thomas
AU - Alistarh, Dan-Adrian
AU - Puschel, Markus
AU - Zhang, Ce
ID - 8268
JF - IEEE Transactions on Signal Processing
SN - 1053587X
TI - Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications
VL - 68
ER -
TY - JOUR
AU - He, Peng
AU - Zhang, Yuzhou
AU - Xiao, Guanghui
ID - 8271
IS - 9
JF - Molecular Plant
SN - 16742052
TI - Origin of a subgenome and genome evolution of allotetraploid cotton species
VL - 13
ER -
TY - JOUR
AB - By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.
AU - Grosjean, Galien M
AU - Wald, Sebastian
AU - Sobarzo Ponce, Juan Carlos A
AU - Waitukaitis, Scott R
ID - 8101
IS - 8
JF - Physical Review Materials
KW - electric charge
KW - tribocharging
KW - soft matter
KW - granular materials
KW - polymers
SN - 2475-9953
TI - Quantitatively consistent scale-spanning model for same-material tribocharging
VL - 4
ER -
TY - JOUR
AB - Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes.
AU - Kalinin, Nikita
AU - Shkolnikov, Mikhail
ID - 8325
IS - 9
JF - Communications in Mathematical Physics
SN - 00103616
TI - Sandpile solitons via smoothing of superharmonic functions
VL - 378
ER -
TY - JOUR
AB - Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
AU - Gutierrez-Fernandez, Javier
AU - Kaszuba, Karol
AU - Minhas, Gurdeep S.
AU - Baradaran, Rozbeh
AU - Tambalo, Margherita
AU - Gallagher, David T.
AU - Sazanov, Leonid A
ID - 8318
IS - 1
JF - Nature Communications
TI - Key role of quinone in the mechanism of respiratory complex I
VL - 11
ER -
TY - JOUR
AB - The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.
AU - Mukba, S. A.
AU - Vlasov, Petr
AU - Kolosov, P. M.
AU - Shuvalova, E. Y.
AU - Egorova, T. V.
AU - Alkalaeva, E. Z.
ID - 8320
IS - 4
JF - Molecular Biology
SN - 00268933
TI - Expanding the genetic code: Unnatural base pairs in biological systems
VL - 54
ER -
TY - JOUR
AB - The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.
AU - Mukba, S. A.
AU - Vlasov, Petr
AU - Kolosov, P. M.
AU - Shuvalova, E. Y.
AU - Egorova, T. V.
AU - Alkalaeva, E. Z.
ID - 8321
IS - 4
JF - Molekuliarnaia biologiia
SN - 00268984
TI - Expanding the genetic code: Unnatural base pairs in biological systems
VL - 54
ER -
TY - JOUR
AU - Pach, János
ID - 8323
JF - Discrete and Computational Geometry
SN - 01795376
TI - A farewell to Ricky Pollack
VL - 64
ER -
TY - JOUR
AB - Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER.
AU - Kubiasova, Karolina
AU - Montesinos López, Juan C
AU - Šamajová, Olga
AU - Nisler, Jaroslav
AU - Mik, Václav
AU - Semeradova, Hana
AU - Plíhalová, Lucie
AU - Novák, Ondřej
AU - Marhavý, Peter
AU - Cavallari, Nicola
AU - Zalabák, David
AU - Berka, Karel
AU - Doležal, Karel
AU - Galuszka, Petr
AU - Šamaj, Jozef
AU - Strnad, Miroslav
AU - Benková, Eva
AU - Plíhal, Ondřej
AU - Spíchal, Lukáš
ID - 8336
JF - Nature Communications
TI - Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum
VL - 11
ER -
TY - JOUR
AB - Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.
AU - Antoniadi, Ioanna
AU - Novák, Ondřej
AU - Gelová, Zuzana
AU - Johnson, Alexander J
AU - Plíhal, Ondřej
AU - Simerský, Radim
AU - Mik, Václav
AU - Vain, Thomas
AU - Mateo-Bonmatí, Eduardo
AU - Karady, Michal
AU - Pernisová, Markéta
AU - Plačková, Lenka
AU - Opassathian, Korawit
AU - Hejátko, Jan
AU - Robert, Stéphanie
AU - Friml, Jiří
AU - Doležal, Karel
AU - Ljung, Karin
AU - Turnbull, Colin
ID - 8337
JF - Nature Communications
TI - Cell-surface receptors enable perception of extracellular cytokinins
VL - 11
ER -
TY - GEN
AB - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the
mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.
AU - Varzi, Alberto
AU - Thanner, Katharina
AU - Scipioni, Roberto
AU - Di Lecce, Daniele
AU - Hassoun, Jusef
AU - Dörfler, Susanne
AU - Altheus, Holger
AU - Kaskel, Stefan
AU - Prehal, Christian
AU - Freunberger, Stefan Alexander
ID - 8067
KW - Battery
KW - Lithium metal
KW - Lithium-sulphur
KW - Lithium-air
KW - All-solid-state
SN - 2664-1690
TI - Current status and future perspectives of Lithium metal batteries
ER -
TY - JOUR
AB - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.
AU - Varzi, Alberto
AU - Thanner, Katharina
AU - Scipioni, Roberto
AU - Di Lecce, Daniele
AU - Hassoun, Jusef
AU - Dörfler, Susanne
AU - Altheus, Holger
AU - Kaskel, Stefan
AU - Prehal, Christian
AU - Freunberger, Stefan Alexander
ID - 8361
IS - 12
JF - Journal of Power Sources
SN - 0378-7753
TI - Current status and future perspectives of lithium metal batteries
VL - 480
ER -
TY - GEN
AB - The present review addresses the technical advances and the theoretical developments to realize and rationalize attosecond-science experiments that reveal a new dynamical time scale (10−15-10−18 s), with a particular emphasis on molecular systems and the implications of attosecond processes for chemical dynamics. After a brief outline of the theoretical framework for treating non-perturbative phenomena in Section 2, we introduce the physical mechanisms underlying high-harmonic generation and attosecond technology. The relevant technological developments and experimental schemes are covered in Section 3. Throughout the remainder of the chapter, we report on selected applications in molecular attosecond physics, thereby addressing specific phenomena mediated by purely electronic dynamics: charge localization in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic spectroscopy, and delays in molecular photoionization.
AU - Baykusheva, Denitsa Rangelova
AU - Wörner, Hans Jakob
ID - 14028
TI - Attosecond molecular spectroscopy and dynamics
ER -
TY - JOUR
AB - Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.
AU - Arnold, Georg M
AU - Wulf, Matthias
AU - Barzanjeh, Shabir
AU - Redchenko, Elena
AU - Rueda Sanchez, Alfredo R
AU - Hease, William J
AU - Hassani, Farid
AU - Fink, Johannes M
ID - 8529
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface
VL - 11
ER -
TY - JOUR
AB - We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.
AU - Skrivan, Tomas
AU - Soderstrom, Andreas
AU - Johansson, John
AU - Sprenger, Christoph
AU - Museth, Ken
AU - Wojtan, Christopher J
ID - 8535
IS - 4
JF - ACM Transactions on Graphics
SN - 07300301
TI - Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces
VL - 39
ER -
TY - JOUR
AB - Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions.
AU - Su, C.
AU - Zhao, Gufang
AU - Zhong, C.
ID - 8539
IS - 3
JF - Annales Scientifiques de l'Ecole Normale Superieure
SN - 0012-9593
TI - On the K-theory stable bases of the springer resolution
VL - 53
ER -
TY - CHAP
AB - This chapter presents an overview of the state of the art in attosecond time-resolved spectroscopy. The theoretical foundations of strong-field light–matter interaction and attosecond pulse generation are described. The enabling laser technologies are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization to the generation and characterization of attosecond pulses. The applications of attosecond pulses and pulse trains in electron- or ion-imaging experiments are presented, followed by attosecond electron spectroscopy in larger molecules. After this, high-harmonic spectroscopy and its applications to probing charge migration on attosecond time scales is reviewed. The rapidly evolving field of molecular photoionization delays is discussed. Finally, the applications of attosecond transient absorption to probing molecular dynamics are presented.
AU - Baykusheva, Denitsa Rangelova
AU - Wörner, Hans Jakob
ED - Marquardt, Roberto
ED - Quack, Martin
ID - 14000
SN - 9780128172353
T2 - Molecular Spectroscopy and Quantum Dynamics
TI - Attosecond Molecular Dynamics and Spectroscopy
ER -
TY - GEN
AB - This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request.
AU - Arnold, Georg M
AU - Wulf, Matthias
AU - Barzanjeh, Shabir
AU - Redchenko, Elena
AU - Rueda Sanchez, Alfredo R
AU - Hease, William J
AU - Hassani, Farid
AU - Fink, Johannes M
ID - 13056
TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface
ER -
TY - JOUR
AB - Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
AU - Andrei, Andreea
AU - Öztürk, Yavuz
AU - Khalfaoui-Hassani, Bahia
AU - Rauch, Juna
AU - Marckmann, Dorian
AU - Trasnea, Petru Iulian
AU - Daldal, Fevzi
AU - Koch, Hans-Georg
ID - 8579
IS - 9
JF - Membranes
TI - Cu homeostasis in bacteria: The ins and outs
VL - 10
ER -
TY - JOUR
AB - The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.
AU - Pinke, Gergely
AU - Zhou, Long
AU - Sazanov, Leonid A
ID - 8581
IS - 11
JF - Nature Structural and Molecular Biology
SN - 15459993
TI - Cryo-EM structure of the entire mammalian F-type ATP synthase
VL - 27
ER -
TY - CONF
AB - We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients.
AU - Graff, Grzegorz
AU - Graff, Beata
AU - Jablonski, Grzegorz
AU - Narkiewicz, Krzysztof
ID - 8580
SN - 9781728157511
T2 - 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities,
TI - The application of persistent homology in the analysis of heart rate variability
ER -
TY - JOUR
AB - Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.
AU - Tian, Anhao
AU - Kang, Bo
AU - Li, Baizhou
AU - Qiu, Biying
AU - Jiang, Wenhong
AU - Shao, Fangjie
AU - Gao, Qingqing
AU - Liu, Rui
AU - Cai, Chengwei
AU - Jing, Rui
AU - Wang, Wei
AU - Chen, Pengxiang
AU - Liang, Qinghui
AU - Bao, Lili
AU - Man, Jianghong
AU - Wang, Yan
AU - Shi, Yu
AU - Li, Jin
AU - Yang, Minmin
AU - Wang, Lisha
AU - Zhang, Jianmin
AU - Hippenmeyer, Simon
AU - Zhu, Junming
AU - Bian, Xiuwu
AU - Wang, Ying‐Jie
AU - Liu, Chong
ID - 8592
IS - 21
JF - Advanced Science
KW - General Engineering
KW - General Physics and Astronomy
KW - General Materials Science
KW - Medicine (miscellaneous)
KW - General Chemical Engineering
KW - Biochemistry
KW - Genetics and Molecular Biology (miscellaneous)
SN - 2198-3844
TI - Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting
VL - 7
ER -
TY - JOUR
AB - Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.
AU - Prehal, Christian
AU - Fitzek, Harald
AU - Kothleitner, Gerald
AU - Presser, Volker
AU - Gollas, Bernhard
AU - Freunberger, Stefan Alexander
AU - Abbas, Qamar
ID - 8568
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Persistent and reversible solid iodine electrodeposition in nanoporous carbons
VL - 11
ER -
TY - JOUR
AB - The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.
AU - Deichler, Alfonso
AU - Carrasco, Denisse
AU - Lopez-Jury, Luciana
AU - Vega Zuniga, Tomas A
AU - Marquez, Natalia
AU - Mpodozis, Jorge
AU - Marin, Gonzalo
ID - 8643
JF - Scientific Reports
TI - A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents
VL - 10
ER -
TY - JOUR
AB - Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.
AU - Esteban, Laura A
AU - Lonishin, Lyubov R
AU - Bobrovskiy, Daniil M
AU - Leleytner, Gregory
AU - Bogatyreva, Natalya S
AU - Kondrashov, Fyodor
AU - Ivankov, Dmitry N
ID - 8645
IS - 6
JF - Bioinformatics
SN - 1367-4803
TI - HypercubeME: Two hundred million combinatorially complete datasets from a single experiment
VL - 36
ER -
TY - JOUR
AB - Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.
AU - Merrin, Jack
ID - 8597
IS - 6
JF - Physical Biology
TI - Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide
VL - 17
ER -
TY - JOUR
AB - Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections.
AU - Henneberger, Christian
AU - Bard, Lucie
AU - Panatier, Aude
AU - Reynolds, James P.
AU - Kopach, Olga
AU - Medvedev, Nikolay I.
AU - Minge, Daniel
AU - Herde, Michel K.
AU - Anders, Stefanie
AU - Kraev, Igor
AU - Heller, Janosch P.
AU - Rama, Sylvain
AU - Zheng, Kaiyu
AU - Jensen, Thomas P.
AU - Sanchez-Romero, Inmaculada
AU - Jackson, Colin J.
AU - Janovjak, Harald L
AU - Ottersen, Ole Petter
AU - Nagelhus, Erlend Arnulf
AU - Oliet, Stephane H.R.
AU - Stewart, Michael G.
AU - Nägerl, U. VAlentin
AU - Rusakov, Dmitri A.
ID - 8674
IS - 5
JF - Neuron
SN - 08966273
TI - LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia
VL - 108
ER -
TY - JOUR
AB - Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules.
AU - Ghazaryan, Areg
AU - Lemeshko, Mikhail
AU - Volosniev, Artem
ID - 8652
JF - Communications Physics
SN - 2399-3650
TI - Filtering spins by scattering from a lattice of point magnets
VL - 3
ER -
TY - JOUR
AB - Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.
AU - Sznurkowska, Magdalena K.
AU - Hannezo, Edouard B
AU - Azzarelli, Roberta
AU - Chatzeli, Lemonia
AU - Ikeda, Tatsuro
AU - Yoshida, Shosei
AU - Philpott, Anna
AU - Simons, Benjamin D
ID - 8669
JF - Nature Communications
TI - Tracing the cellular basis of islet specification in mouse pancreas
VL - 11
ER -
TY - JOUR
AB - Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.
AU - Chaigne, Agathe
AU - Labouesse, Céline
AU - White, Ian J.
AU - Agnew, Meghan
AU - Hannezo, Edouard B
AU - Chalut, Kevin J.
AU - Paluch, Ewa K.
ID - 8672
IS - 2
JF - Developmental Cell
SN - 15345807
TI - Abscission couples cell division to embryonic stem cell fate
VL - 55
ER -
TY - JOUR
AB - In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.
AU - Fischer, Julian L
AU - Kniely, Michael
ID - 8697
IS - 11
JF - Nonlinearity
SN - 09517715
TI - Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model
VL - 33
ER -
TY - JOUR
AB - Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.
AU - Tsai, Tony Y.-C.
AU - Sikora, Mateusz K
AU - Xia, Peng
AU - Colak-Champollion, Tugba
AU - Knaut, Holger
AU - Heisenberg, Carl-Philipp J
AU - Megason, Sean G.
ID - 8680
IS - 6512
JF - Science
KW - Multidisciplinary
SN - 0036-8075
TI - An adhesion code ensures robust pattern formation during tissue morphogenesis
VL - 370
ER -
TY - JOUR
AB - Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.
AU - Galan, Silvia
AU - Machnik, Nick N
AU - Kruse, Kai
AU - Díaz, Noelia
AU - Marti-Renom, Marc A
AU - Vaquerizas, Juan M
ID - 8707
JF - Nature Genetics
SN - 10614036
TI - CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction
VL - 52
ER -
TY - JOUR
AB - A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system.
AU - Lechner, Mathias
AU - Hasani, Ramin
AU - Amini, Alexander
AU - Henzinger, Thomas A
AU - Rus, Daniela
AU - Grosu, Radu
ID - 8679
JF - Nature Machine Intelligence
TI - Neural circuit policies enabling auditable autonomy
VL - 2
ER -
TY - JOUR
AB - The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].
AU - Zhang, Haonan
ID - 8670
IS - 10
JF - Journal of Mathematical Physics
SN - 00222488
TI - Equality conditions of data processing inequality for α-z Rényi relative entropies
VL - 61
ER -
TY - JOUR
AB - The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.
AU - Maoz, Ori
AU - Tkačik, Gašper
AU - Esteki, Mohamad Saleh
AU - Kiani, Roozbeh
AU - Schneidman, Elad
ID - 8698
IS - 40
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 00278424
TI - Learning probabilistic neural representations with randomly connected circuits
VL - 117
ER -
TY - CONF
AB - Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E.
AU - Lechner, Mathias
AU - Hasani, Ramin
AU - Rus, Daniela
AU - Grosu, Radu
ID - 8704
SN - 10504729
T2 - Proceedings - IEEE International Conference on Robotics and Automation
TI - Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme
ER -
TY - JOUR
AB - Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.
AU - Sokolova, E. E.
AU - Vlasov, Petr
AU - Egorova, T. V.
AU - Shuvalov, A. V.
AU - Alkalaeva, E. Z.
ID - 8700
IS - 5
JF - Molecular Biology
SN - 00268933
TI - The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes
VL - 54
ER -
TY - JOUR
AB - Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.
AU - Sokolova, E. E.
AU - Vlasov, Petr
AU - Egorova, T. V.
AU - Shuvalov, A. V.
AU - Alkalaeva, E. Z.
ID - 8701
IS - 5
JF - Molekuliarnaia biologiia
SN - 00268984
TI - The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes
VL - 54
ER -
TY - GEN
AB - A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources.
AU - Jamie A. P. Law-Smith, Jamie A. P. Law-Smith
AU - Everson, Rosa Wallace
AU - Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz
AU - Mink, Selma E. de
AU - Son, Lieke A. C. van
AU - Götberg, Ylva Louise Linsdotter
AU - Zellmann, Stefan
AU - Alejandro Vigna-Gómez, Alejandro Vigna-Gómez
AU - Renzo, Mathieu
AU - Wu, Samantha
AU - Schrøder, Sophie L.
AU - Foley, Ryan J.
AU - Tenley Hutchinson-Smith, Tenley Hutchinson-Smith
ID - 14096
T2 - arXiv
TI - Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics
ER -
TY - JOUR
AB - In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling.
AU - Paris, Eugenio
AU - Tseng, Yi
AU - Paerschke, Ekaterina
AU - Zhang, Wenliang
AU - Upton, Mary H
AU - Efimenko, Anna
AU - Rolfs, Katharina
AU - McNally, Daniel E
AU - Maurel, Laura
AU - Naamneh, Muntaser
AU - Caputo, Marco
AU - Strocov, Vladimir N
AU - Wang, Zhiming
AU - Casa, Diego
AU - Schneider, Christof W
AU - Pomjakushina, Ekaterina
AU - Wohlfeld, Krzysztof
AU - Radovic, Milan
AU - Schmitt, Thorsten
ID - 8699
IS - 40
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 00278424
TI - Strain engineering of the charge and spin-orbital interactions in Sr2IrO4
VL - 117
ER -
TY - JOUR
AB - Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.
AU - Kampjut, Domen
AU - Sazanov, Leonid A
ID - 8737
IS - 6516
JF - Science
TI - The coupling mechanism of mammalian respiratory complex I
VL - 370
ER -
TY - CONF
AB - Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)
achieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for
decentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show
that eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy.
AU - Li, Shigang
AU - Tal Ben-Nun, Tal Ben-Nun
AU - Girolamo, Salvatore Di
AU - Alistarh, Dan-Adrian
AU - Hoefler, Torsten
ID - 8722
T2 - Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
TI - Taming unbalanced training workloads in deep learning with partial collective operations
ER -
TY - JOUR
AB - Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
AU - Schulte, Linda
AU - Mao, Jiafei
AU - Reitz, Julian
AU - Sreeramulu, Sridhar
AU - Kudlinzki, Denis
AU - Hodirnau, Victor-Valentin
AU - Meier-Credo, Jakob
AU - Saxena, Krishna
AU - Buhr, Florian
AU - Langer, Julian D.
AU - Blackledge, Martin
AU - Frangakis, Achilleas S.
AU - Glaubitz, Clemens
AU - Schwalbe, Harald
ID - 8744
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Cysteine oxidation and disulfide formation in the ribosomal exit tunnel
VL - 11
ER -
TY - JOUR
AB - Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites
produced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3.
AU - Zhang, Yu
AU - Liu, Yu
AU - Calcabrini, Mariano
AU - Xing, Congcong
AU - Han, Xu
AU - Arbiol, Jordi
AU - Cadavid, Doris
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 8747
IS - 40
JF - Journal of Materials Chemistry C
TI - Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks
VL - 8
ER -
TY - GEN
AB - The Habitable Exoplanet Observatory, or HabEx, has been designed to be the Great Observatory of the 2030s. For the first time in human history, technologies have matured sufficiently to enable an affordable space-based telescope mission capable of discovering and characterizing Earthlike planets orbiting nearby bright sunlike stars in order to search for signs of habitability and biosignatures. Such a mission can also be equipped with instrumentation that will enable broad and exciting general astrophysics and planetary science not possible from current or planned facilities. HabEx is a space telescope with unique imaging and multi-object spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR. These capabilities allow for a broad suite of compelling science that cuts across the entire NASA astrophysics portfolio. HabEx has three primary science goals: (1) Seek out nearby worlds and explore their habitability; (2) Map out nearby planetary systems and understand the diversity of the worlds they contain; (3) Enable new explorations of astrophysical systems from our own solar system to external galaxies by extending our reach in the UV through near-IR. This Great Observatory science will be selected through a competed GO program, and will account for about 50% of the HabEx primary mission. The preferred HabEx architecture is a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph and a starshade, each with their own dedicated instrument.
AU - Gaudi, B. Scott
AU - Seager, Sara
AU - Mennesson, Bertrand
AU - Kiessling, Alina
AU - Warfield, Keith
AU - Cahoy, Kerri
AU - Clarke, John T.
AU - Shawn Domagal-Goldman, Shawn Domagal-Goldman
AU - Feinberg, Lee
AU - Guyon, Olivier
AU - Kasdin, Jeremy
AU - Mawet, Dimitri
AU - Plavchan, Peter
AU - Robinson, Tyler
AU - Rogers, Leslie
AU - Scowen, Paul
AU - Somerville, Rachel
AU - Stapelfeldt, Karl
AU - Stark, Christopher
AU - Stern, Daniel
AU - Turnbull, Margaret
AU - Amini, Rashied
AU - Kuan, Gary
AU - Martin, Stefan
AU - Morgan, Rhonda
AU - Redding, David
AU - Stahl, H. Philip
AU - Webb, Ryan
AU - Oscar Alvarez-Salazar, Oscar Alvarez-Salazar
AU - Arnold, William L.
AU - Arya, Manan
AU - Balasubramanian, Bala
AU - Baysinger, Mike
AU - Bell, Ray
AU - Below, Chris
AU - Benson, Jonathan
AU - Blais, Lindsey
AU - Booth, Jeff
AU - Bourgeois, Robert
AU - Bradford, Case
AU - Brewer, Alden
AU - Brooks, Thomas
AU - Cady, Eric
AU - Caldwell, Mary
AU - Calvet, Rob
AU - Carr, Steven
AU - Chan, Derek
AU - Cormarkovic, Velibor
AU - Coste, Keith
AU - Cox, Charlie
AU - Danner, Rolf
AU - Davis, Jacqueline
AU - Dewell, Larry
AU - Dorsett, Lisa
AU - Dunn, Daniel
AU - East, Matthew
AU - Effinger, Michael
AU - Eng, Ron
AU - Freebury, Greg
AU - Garcia, Jay
AU - Gaskin, Jonathan
AU - Greene, Suzan
AU - Hennessy, John
AU - Hilgemann, Evan
AU - Hood, Brad
AU - Holota, Wolfgang
AU - Howe, Scott
AU - Huang, Pei
AU - Hull, Tony
AU - Hunt, Ron
AU - Hurd, Kevin
AU - Johnson, Sandra
AU - Kissil, Andrew
AU - Knight, Brent
AU - Kolenz, Daniel
AU - Kraus, Oliver
AU - Krist, John
AU - Li, Mary
AU - Lisman, Doug
AU - Mandic, Milan
AU - Mann, John
AU - Marchen, Luis
AU - Colleen Marrese-Reading, Colleen Marrese-Reading
AU - McCready, Jonathan
AU - McGown, Jim
AU - Missun, Jessica
AU - Miyaguchi, Andrew
AU - Moore, Bradley
AU - Nemati, Bijan
AU - Nikzad, Shouleh
AU - Nissen, Joel
AU - Novicki, Megan
AU - Perrine, Todd
AU - Pineda, Claudia
AU - Polanco, Otto
AU - Putnam, Dustin
AU - Qureshi, Atif
AU - Richards, Michael
AU - Riggs, A. J. Eldorado
AU - Rodgers, Michael
AU - Rud, Mike
AU - Saini, Navtej
AU - Scalisi, Dan
AU - Scharf, Dan
AU - Schulz, Kevin
AU - Serabyn, Gene
AU - Sigrist, Norbert
AU - Sikkia, Glory
AU - Singleton, Andrew
AU - Shaklan, Stuart
AU - Smith, Scott
AU - Southerd, Bart
AU - Stahl, Mark
AU - Steeves, John
AU - Sturges, Brian
AU - Sullivan, Chris
AU - Tang, Hao
AU - Taras, Neil
AU - Tesch, Jonathan
AU - Therrell, Melissa
AU - Tseng, Howard
AU - Valente, Marty
AU - Buren, David Van
AU - Villalvazo, Juan
AU - Warwick, Steve
AU - Webb, David
AU - Westerhoff, Thomas
AU - Wofford, Rush
AU - Wu, Gordon
AU - Woo, Jahning
AU - Wood, Milana
AU - Ziemer, John
AU - Arney, Giada
AU - Anderson, Jay
AU - Jesús Maíz-Apellániz, Jesús Maíz-Apellániz
AU - Bartlett, James
AU - Belikov, Ruslan
AU - Bendek, Eduardo
AU - Cenko, Brad
AU - Douglas, Ewan
AU - Dulz, Shannon
AU - Evans, Chris
AU - Faramaz, Virginie
AU - Feng, Y. Katherina
AU - Ferguson, Harry
AU - Follette, Kate
AU - Ford, Saavik
AU - García, Miriam
AU - Geha, Marla
AU - Gelino, Dawn
AU - Götberg, Ylva Louise Linsdotter
AU - Hildebrandt, Sergi
AU - Hu, Renyu
AU - Jahnke, Knud
AU - Kennedy, Grant
AU - Kreidberg, Laura
AU - Isella, Andrea
AU - Lopez, Eric
AU - Marchis, Franck
AU - Macri, Lucas
AU - Marley, Mark
AU - Matzko, William
AU - Mazoyer, Johan
AU - McCandliss, Stephan
AU - Meshkat, Tiffany
AU - Mordasini, Christoph
AU - Morris, Patrick
AU - Nielsen, Eric
AU - Newman, Patrick
AU - Petigura, Erik
AU - Postman, Marc
AU - Reines, Amy
AU - Roberge, Aki
AU - Roederer, Ian
AU - Ruane, Garreth
AU - Schwieterman, Edouard
AU - Sirbu, Dan
AU - Spalding, Christopher
AU - Teplitz, Harry
AU - Tumlinson, Jason
AU - Turner, Neal
AU - Werk, Jessica
AU - Wofford, Aida
AU - Wyatt, Mark
AU - Young, Amber
AU - Zellem, Rob
ID - 14095
T2 - arXiv
TI - The habitable exoplanet observatory (HabEx) mission concept study final report
ER -
TY - JOUR
AB - Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring.
AU - Kaveh, Kamran
AU - McAvoy, Alex
AU - Chatterjee, Krishnendu
AU - Nowak, Martin A.
ID - 8767
IS - 11
JF - PLOS Computational Biology
KW - Ecology
KW - Modelling and Simulation
KW - Computational Theory and Mathematics
KW - Genetics
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
KW - Molecular Biology
KW - Cellular and Molecular Neuroscience
SN - 1553-734X
TI - The Moran process on 2-chromatic graphs
VL - 16
ER -
TY - CONF
AB - Efficiently handling time-triggered and possibly nondeterministic switches
for hybrid systems reachability is a challenging task. In this paper we present
an approach based on conservative set-based enclosure of the dynamics that can
handle systems with uncertain parameters and inputs, where the uncertainties
are bound to given intervals. The method is evaluated on the plant model of an
experimental electro-mechanical braking system with periodic controller. In
this model, the fast-switching controller dynamics requires simulation time
scales of the order of nanoseconds. Accurate set-based computations for
relatively large time horizons are known to be expensive. However, by
appropriately decoupling the time variable with respect to the spatial
variables, and enclosing the uncertain parameters using interval matrix maps
acting on zonotopes, we show that the computation time can be lowered to 5000
times faster with respect to previous works. This is a step forward in formal
verification of hybrid systems because reduced run-times allow engineers to
introduce more expressiveness in their models with a relatively inexpensive
computational cost.
AU - Forets, Marcelo
AU - Freire, Daniel
AU - Schilling, Christian
ID - 8750
SN - 9781728191485
T2 - 18th ACM-IEEE International Conference on Formal Methods and Models for System Design
TI - Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions
ER -
TY - JOUR
AB - We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels.
AU - Maas, Jan
AU - Mielke, Alexander
ID - 8758
IS - 6
JF - Journal of Statistical Physics
SN - 00224715
TI - Modeling of chemical reaction systems with detailed balance using gradient structures
VL - 181
ER -
TY - GEN
AB - This dataset comprises all data shown in the figures of the submitted article "Surpassing the resistance quantum with a geometric superinductor". Additional raw data are available from the corresponding author on reasonable request.
AU - Peruzzo, Matilda
AU - Trioni, Andrea
AU - Hassani, Farid
AU - Zemlicka, Martin
AU - Fink, Johannes M
ID - 13070
TI - Surpassing the resistance quantum with a geometric superinductor
ER -