TY - JOUR
AB - In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after.
AU - Baranov, Dmitry
AU - Šverko, Tara
AU - Moot, Taylor
AU - Keller, Helena R.
AU - Klein, Megan D.
AU - Vishnu, E. K.
AU - Balazs, Daniel
AU - Shulenberger, Katherine E.
ID - 9829
IS - 7
JF - ACS Nano
SN - 19360851
TI - News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience
VL - 15
ER -
TY - CONF
AB - In this paper, we study the power and limitations of component-stable algorithms in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari, Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space MPC algorithms, which are, informally, defined as algorithms for which the outputs reported by the nodes in different connected components are required to be independent. This very natural notion was introduced to capture most (if not all) of the known efficient MPC algorithms to date, and it was the first general class of MPC algorithms for which one can show non-trivial conditional lower bounds. In this paper we enhance the framework of component-stable algorithms and investigate its effect on the complexity of randomized and deterministic low-space MPC. Our key contributions include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and Uitto. This requires a very delicate amendment of the notion of component stability, which allows us to fill in gaps in the earlier arguments. 2) We also extend the framework to obtain conditional lower bounds for deterministic algorithms and fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate a collection of natural graph problems for which non-component-stable algorithms break the conditional lower bound obtained for component-stable algorithms. This implies that, for both deterministic and randomized algorithms, component-stable algorithms are conditionally weaker than the non-component-stable ones.
Altogether our results imply that component-stability might limit the computational power of the low-space MPC model, paving the way for improved upper bounds that escape the conditional lower bound setting of Ghaffari, Kuhn, and Uitto.
AU - Czumaj, Artur
AU - Davies, Peter
AU - Parter, Merav
ID - 9933
SN - 9781450385480
T2 - Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
TI - Component stability in low-space massively parallel computation
ER -
TY - CONF
AB - We present a deterministic O(log log log n)-round low-space Massively Parallel Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex graphs. In this model, every machine has sublinear local space of size n^φ for any arbitrary constant φ \in (0,1). Our algorithm works under the relaxed setting where each machine is allowed to perform exponential local computations, while respecting the n^φ space and bandwidth limitations.
Our key technical contribution is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized round complexity for the problem in the local model. Our derandomization employs a combination of tools, notably pseudorandom generators (PRG) and bounded-independence hash functions.
The achieved round complexity of O(logloglog n) rounds matches the bound of log(T_local ), which currently serves an upper bound barrier for all known randomized algorithms for locally-checkable problems in this model. Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the (Δ+1)-coloring problem have been known before.
AU - Czumaj, Artur
AU - Davies, Peter
AU - Parter, Merav
ID - 9935
SN - 978-1-4503-8548-0
T2 - Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
TI - Improved deterministic (Δ+1) coloring in low-space MPC
ER -
TY - JOUR
AB - Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry.
AU - Chaigne, Agathe
AU - Smith, Matthew B.
AU - Cavestany, R. L.
AU - Hannezo, Edouard B
AU - Chalut, Kevin J.
AU - Paluch, Ewa K.
ID - 9952
IS - 14
JF - Journal of Cell Science
SN - 00219533
TI - Three-dimensional geometry controls division symmetry in stem cell colonies
VL - 134
ER -
TY - CONF
AB - There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.
In this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the "correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model.
AU - Alistarh, Dan-Adrian
AU - Töpfer, Martin
AU - Uznański, Przemysław
ID - 9951
SN - 9781450385480
T2 - Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
TI - Comparison dynamics in population protocols
ER -
TY - JOUR
AB - Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart.
AU - Raso, Andrea
AU - Dirkx, Ellen
AU - Sampaio-Pinto, Vasco
AU - el Azzouzi, Hamid
AU - Cubero, Ryan J
AU - Sorensen, Daniel W.
AU - Ottaviani, Lara
AU - Olieslagers, Servé
AU - Huibers, Manon M.
AU - de Weger, Roel
AU - Siddiqi, Sailay
AU - Moimas, Silvia
AU - Torrini, Consuelo
AU - Zentillin, Lorena
AU - Braga, Luca
AU - Nascimento, Diana S.
AU - da Costa Martins, Paula A.
AU - van Berlo, Jop H.
AU - Zacchigna, Serena
AU - Giacca, Mauro
AU - De Windt, Leon J.
ID - 9874
IS - 1
JF - Nature Communications
TI - A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration
VL - 12
ER -
TY - JOUR
AB - Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology.
AU - Baldwin, Katherine T.
AU - Tan, Christabel X.
AU - Strader, Samuel T.
AU - Jiang, Changyu
AU - Savage, Justin T.
AU - Elorza-Vidal, Xabier
AU - Contreras, Ximena
AU - Rülicke, Thomas
AU - Hippenmeyer, Simon
AU - Estévez, Raúl
AU - Ji, Ru-Rong
AU - Eroglu, Cagla
ID - 9793
IS - 15
JF - Neuron
SN - 0896-6273
TI - HepaCAM controls astrocyte self-organization and coupling
VL - 109
ER -
TY - JOUR
AB - Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales.
AU - Sperl, Georg
AU - Narain, Rahul
AU - Wojtan, Christopher J
ID - 9818
IS - 4
JF - ACM Transactions on Graphics
SN - 07300301
TI - Mechanics-aware deformation of yarn pattern geometry
VL - 40
ER -
TY - COMP
AB - This archive contains the missing sweater mesh animations and displacement models for the code of "Mechanics-Aware Deformation of Yarn Pattern Geometry"
Code Repository: https://git.ist.ac.at/gsperl/MADYPG
AU - Sperl, Georg
AU - Narain, Rahul
AU - Wojtan, Christopher J
ID - 9327
TI - Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)
ER -
TY - JOUR
AB - Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress.
AU - Picard, Katherine
AU - Bisht, Kanchan
AU - Poggini, Silvia
AU - Garofalo, Stefano
AU - Golia, Maria Teresa
AU - Basilico, Bernadette
AU - Abdallah, Fatima
AU - Ciano Albanese, Naomi
AU - Amrein, Irmgard
AU - Vernoux, Nathalie
AU - Sharma, Kaushik
AU - Hui, Chin Wai
AU - C. Savage, Julie
AU - Limatola, Cristina
AU - Ragozzino, Davide
AU - Maggi, Laura
AU - Branchi, Igor
AU - Tremblay, Marie Ève
ID - 9953
JF - Brain, Behavior, and Immunity
SN - 08891591
TI - Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice
ER -
TY - DATA
AU - Vicoso, Beatriz
ID - 9949
TI - Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of gene expression in Artemia brine shrimp"
ER -
TY - JOUR
AB - The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars.
AU - Maskara, N.
AU - Michailidis, Alexios
AU - Ho, W. W.
AU - Bluvstein, D.
AU - Choi, S.
AU - Lukin, M. D.
AU - Serbyn, Maksym
ID - 9960
IS - 9
JF - Physical Review Letters
SN - 0031-9007
TI - Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving
VL - 127
ER -
TY - JOUR
AB - The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems.
AU - Sonner, Michael
AU - Serbyn, Maksym
AU - Papić, Zlatko
AU - Abanin, Dmitry A.
ID - 9961
IS - 8
JF - Physical Review B
SN - 2469-9950
TI - Thouless energy across the many-body localization transition in Floquet systems
VL - 104
ER -
TY - CONF
AB - Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths.
AU - Pietrzak, Krzysztof Z
AU - Salem, Iosif
AU - Schmid, Stefan
AU - Yeo, Michelle X
ID - 9969
SN - 978-1-6654-4501-6
TI - LightPIR: Privacy-preserving route discovery for payment channel networks
ER -
TY - JOUR
AB - Neurons can change their classical neurotransmitters during ontogeny, sometimes going through stages of dual release. Here, we explored the development of the neurotransmitter identity of neurons of the avian nucleus isthmi parvocellularis (Ipc), whose axon terminals are retinotopically arranged in the optic tectum (TeO) and exert a focal gating effect upon the ascending transmission of retinal inputs. Although cholinergic and glutamatergic markers are both found in Ipc neurons and terminals of adult pigeons and chicks, the mRNA expression of the vesicular acetylcholine transporter, VAChT, is weak or absent. To explore how the Ipc neurotransmitter identity is established during ontogeny, we analyzed the expression of mRNAs coding for cholinergic (ChAT, VAChT, and CHT) and glutamatergic (VGluT2 and VGluT3) markers in chick embryos at different developmental stages. We found that between E12 and E18, Ipc neurons expressed all cholinergic mRNAs and also VGluT2 mRNA; however, from E16 through posthatch stages, VAChT mRNA expression was specifically diminished. Our ex vivo deposits of tracer crystals and intracellular filling experiments revealed that Ipc axons exhibit a mature paintbrush morphology late in development, experiencing marked morphological transformations during the period of presumptive dual vesicular transmitter release. Additionally, although ChAT protein immunoassays increasingly label the growing Ipc axon, this labeling was consistently restricted to sparse portions of the terminal branches. Combined, these results suggest that the synthesis of glutamate and acetylcholine, and their vesicular release, is complexly linked to the developmental processes of branching, growing and remodeling of these unique axons.
AU - Reyes‐Pinto, Rosana
AU - Ferrán, José L.
AU - Vega Zuniga, Tomas A
AU - González‐Cabrera, Cristian
AU - Luksch, Harald
AU - Mpodozis, Jorge
AU - Puelles, Luis
AU - Marín, Gonzalo J.
ID - 9955
JF - Journal of Comparative Neurology
SN - 0021-9967
TI - Change in the neurochemical signature and morphological development of the parvocellular isthmic projection to the avian tectum
ER -
TY - GEN
AB - Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.
AU - Cao, Deqing
AU - Shen, Xiaoxiao
AU - Wang, Aiping
AU - Yu, Fengjiao
AU - Wu, Yuping
AU - Shi, Siqi
AU - Freunberger, Stefan Alexander
AU - Chen, Yuhui
ID - 9978
KW - Catalysis
KW - Energy engineering
KW - Materials theory and modeling
T2 - Research Square
TI - Sharp kinetic acceleration potentials during mediated redox catalysis of insulators
ER -
TY - JOUR
AB - The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions
for further developments.
AU - De Nicola, Stefano
ID - 9981
IS - 3
JF - SciPost Physics
KW - General Physics and Astronomy
SN - 2542-4653
TI - Importance sampling scheme for the stochastic simulation of quantum spin dynamics
VL - 11
ER -
TY - JOUR
AB - The Landau–Pekar equations describe the dynamics of a strongly coupled polaron.
Here, we provide a class of initial data for which the associated effective Hamiltonian
has a uniform spectral gap for all times. For such initial data, this allows us to extend the
results on the adiabatic theorem for the Landau–Pekar equations and their derivation
from the Fröhlich model obtained in previous works to larger times.
AU - Feliciangeli, Dario
AU - Rademacher, Simone Anna Elvira
AU - Seiringer, Robert
ID - 9225
JF - Letters in Mathematical Physics
SN - 03779017
TI - Persistence of the spectral gap for the Landau–Pekar equations
VL - 111
ER -
TY - GEN
AB - Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.
AU - Samarasinghe, Ranmal A.
AU - Miranda, Osvaldo
AU - Buth, Jessie E.
AU - Mitchell, Simon
AU - Ferando, Isabella
AU - Watanabe, Momoko
AU - Kurdian, Arinnae
AU - Golshani, Peyman
AU - Plath, Kathrin
AU - Lowry, William E.
AU - Parent, Jack M.
AU - Mody, Istvan
AU - Novitch, Bennett G.
ID - 6995
SN - 1097-6256
TI - Identification of neural oscillations and epileptiform changes in human brain organoids
ER -
TY - GEN
AB - We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.
AU - Feliciangeli, Dario
AU - Seiringer, Robert
ID - 9787
T2 - arXiv
TI - The strongly coupled polaron on the torus: quantum corrections to the Pekar asymptotics
ER -
TY - GEN
AB - We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar.
AU - Feliciangeli, Dario
AU - Rademacher, Simone Anna Elvira
AU - Seiringer, Robert
ID - 9791
T2 - arXiv
TI - The effective mass problem for the Landau-Pekar equations
ER -
TY - THES
AB - Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.
AU - Huljev, Karla
ID - 9397
SN - 2663-337X
TI - Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation
ER -
TY - THES
AB - In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.
We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.
AU - Goharshady, Amir Kafshdar
ID - 8934
SN - 2663-337X
TI - Parameterized and algebro-geometric advances in static program analysis
ER -
TY - GEN
AB - We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.
AU - Mühlböck, Fabian
AU - Henzinger, Thomas A
ID - 9946
KW - Run-time verification
KW - Software engineering
KW - Implicit specification
SN - 2664-1690
TI - Differential monitoring
ER -
TY - GEN
AB - We comment on two formal proofs of Fermat's sum of two squares theorem, written using the Mathematical Components libraries of the Coq proof assistant. The first one follows Zagier's celebrated one-sentence proof; the second follows David Christopher's recent new proof relying on partition-theoretic arguments. Both formal proofs rely on a general property of involutions of finite sets, of independent interest. The proof technique consists for the most part of automating recurrent tasks (such as case distinctions and computations on natural numbers) via ad hoc tactics.
AU - Dubach, Guillaume
AU - Mühlböck, Fabian
ID - 9281
T2 - arXiv
TI - Formal verification of Zagier's one-sentence proof
ER -
TY - JOUR
AB - Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.
AU - Velasquez, Silvia Melina
AU - Guo, Xiaoyuan
AU - Gallemi, Marçal
AU - Aryal, Bibek
AU - Venhuizen, Peter
AU - Barbez, Elke
AU - Dünser, Kai Alexander
AU - Darino, Martin
AU - Pӗnčík, Aleš
AU - Novák, Ondřej
AU - Kalyna, Maria
AU - Mouille, Gregory
AU - Benková, Eva
AU - Bhalerao, Rishikesh P.
AU - Mravec, Jozef
AU - Kleine-Vehn, Jürgen
ID - 9986
IS - 17
JF - International Journal of Molecular Sciences
KW - auxin
KW - growth
KW - cell wall
KW - xyloglucans
KW - hypocotyls
KW - gravitropism
SN - 1661-6596
TI - Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants
VL - 22
ER -
TY - GEN
AB - Insufficient understanding of the mechanism that reversibly converts sulphur into lithium sulphide (Li2S) via soluble polysulphides (PS) hampers the realization of high performance lithium-sulphur cells. Typically Li2S formation is explained by direct electroreduction of a PS to Li2S; however, this is not consistent with the size of the insulating Li2S deposits. Here, we use in situ small and wide angle X-ray scattering (SAXS/WAXS) to track the growth and dissolution of crystalline and amorphous deposits from atomic to sub-micron scales during charge and discharge. Stochastic modelling based on the SAXS data allows quantification of the chemical phase evolution during discharge and charge. We show that Li2S deposits predominantly via disproportionation of transient, solid Li2S2 to form primary Li2S crystallites and solid Li2S4 particles. We further demonstrate that this process happens in reverse during charge. These findings show that the discharge capacity and rate capability in Li-S battery cathodes are therefore limited by mass transport through the increasingly tortuous network of Li2S / Li2S4 / carbon pores rather than electron transport through a passivating surface film.
AU - Prehal, Christian
AU - Talian, Sara Drvarič
AU - Vizintin, Alen
AU - Amenitsch, Heinz
AU - Dominko, Robert
AU - Freunberger, Stefan Alexander
AU - Wood, Vanessa
ID - 9980
KW - Li2S
KW - Lithium Sulphur Batteries
KW - SAXS
KW - WAXS
TI - Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries
ER -
TY - THES
AB - The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.
AU - Hansen, Andi H
ID - 9962
KW - Neuronal migration
KW - Non-cell-autonomous
KW - Cell-autonomous
KW - Neurodevelopmental disease
SN - 2663-337X
TI - Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration
ER -
TY - THES
AB - This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.
AU - Peruzzo, Matilda
ID - 9920
KW - quantum computing
KW - superinductor
KW - quantum metrology
SN - 2663-337X
TI - Geometric superinductors and their applications in circuit quantum electrodynamics
ER -
TY - GEN
AB - There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wavefunction. In the other the junction is added in parallel, which gives rise to an extended phase variable, continuous wavefunctions and a rich energy level structure due to the loop topology. While the corresponding rf-SQUID Hamiltonian was introduced as a quadratic, quasi-1D potential approximation to describe the fluxonium qubit implemented with long Josephson junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasi-charge qubit with strongly enhanced zero point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high precision of the inductive and capacitive energy as guaranteed by top-down lithography - a key ingredient for intrinsically protected superconducting qubits. The geometric fluxonium also exhibits a large magnetic dipole, which renders it an interesting new candidate for quantum sensing applications.
AU - Peruzzo, Matilda
AU - Hassani, Farid
AU - Szep, Gregory
AU - Trioni, Andrea
AU - Redchenko, Elena
AU - Zemlicka, Martin
AU - Fink, Johannes M
ID - 9928
KW - Quantum physics
KW - Mesoscale and Nanoscale physics
T2 - arXiv
TI - Geometric superinductance qubits: controlling phase delocalization across a single Josephson junction
ER -
TY - JOUR
AB - AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity.
AU - Watson, Jake
AU - Pinggera, Alexandra
AU - Ho, Hinze
AU - Greger, Ingo H.
ID - 9985
IS - 1
JF - Nature Communications
TI - AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions
VL - 12
ER -
TY - JOUR
AB - In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors.
AU - Wirth, Melchior
AU - Zhang, Haonan
ID - 9973
JF - Communications in Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0010-3616
TI - Complete gradient estimates of quantum Markov semigroups
ER -
TY - CHAP
AB - Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data.
AU - Xia, Peng
AU - Heisenberg, Carl-Philipp J
ED - Dosch, Roland
ID - 9245
KW - Tissue tension
KW - Morphogenesis
KW - Laser ablation
KW - Zebrafish folliculogenesis
KW - Granulosa cells
SN - 1064-3745
T2 - Germline Development in the Zebrafish
TI - Quantifying tissue tension in the granulosa layer after laser surgery
VL - 2218
ER -
TY - GEN
AB - The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects.
AU - B R, Mallikarjun
AU - Tewari, Ayush
AU - Oh, Tae-Hyun
AU - Weyrich, Tim
AU - Bickel, Bernd
AU - Seidel, Hans-Peter
AU - Pfister, Hanspeter
AU - Matusik, Wojciech
AU - Elgharib, Mohamed
AU - Theobalt, Christian
ID - 9957
T2 - Computer Vision Foundation
TI - Monocular reconstruction of neural face reflectance fields
ER -
TY - CONF
AB - Stateless model checking (SMC) is one of the standard approaches to the verification of concurrent programs. As scheduling non-determinism creates exponentially large spaces of thread interleavings, SMC attempts to partition this space into equivalence classes and explore only a few representatives from each class. The efficiency of this approach depends on two factors: (a) the coarseness of the partitioning, and (b) the time to generate representatives in each class. For this reason, the search for coarse partitionings that are efficiently explorable is an active research challenge. In this work we present RVF-SMC , a new SMC algorithm that uses a novel reads-value-from (RVF) partitioning. Intuitively, two interleavings are deemed equivalent if they agree on the value obtained in each read event, and read events induce consistent causal orderings between them. The RVF partitioning is provably coarser than recent approaches based on Mazurkiewicz and “reads-from” partitionings. Our experimental evaluation reveals that RVF is quite often a very effective equivalence, as the underlying partitioning is exponentially coarser than other approaches. Moreover, RVF-SMC generates representatives very efficiently, as the reduction in the partitioning is often met with significant speed-ups in the model checking task.
AU - Agarwal, Pratyush
AU - Chatterjee, Krishnendu
AU - Pathak, Shreya
AU - Pavlogiannis, Andreas
AU - Toman, Viktor
ID - 9987
SN - 0302-9743
T2 - 33rd International Conference on Computer-Aided Verification
TI - Stateless model checking under a reads-value-from equivalence
VL - 12759
ER -
TY - JOUR
AB - Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms.
AU - Schmid, Laura
AU - Shati, Pouya
AU - Hilbe, Christian
AU - Chatterjee, Krishnendu
ID - 9997
IS - 1
JF - Scientific Reports
KW - Multidisciplinary
TI - The evolution of indirect reciprocity under action and assessment generosity
VL - 11
ER -
TY - GEN
AB - We propose a new weak solution concept for (two-phase) mean curvature flow which enjoys both (unconditional) existence and (weak-strong) uniqueness properties. These solutions are evolving varifolds, just as in Brakke's formulation, but are coupled to the phase volumes by a simple transport equation. First, we show that, in the exact same setup as in Ilmanen's proof [J. Differential Geom. 38, 417-461, (1993)], any limit point of solutions to the Allen-Cahn equation is a varifold solution in our sense. Second, we prove that any calibrated flow in the sense of Fischer et al. [arXiv:2003.05478] - and hence any classical solution to mean curvature flow - is unique in the class of our new varifold solutions. This is in sharp contrast to the case of Brakke flows, which a priori may disappear at any given time and are therefore fatally non-unique. Finally, we propose an extension of the solution concept to the multi-phase case which is at least guaranteed to satisfy a weak-strong uniqueness principle.
AU - Hensel, Sebastian
AU - Laux, Tim
ID - 10011
KW - Mean curvature flow
KW - gradient flows
KW - varifolds
KW - weak solutions
KW - weak-strong uniqueness
KW - calibrated geometry
KW - gradient-flow calibrations
T2 - arXiv
TI - A new varifold solution concept for mean curvature flow: Convergence of the Allen-Cahn equation and weak-strong uniqueness
ER -
TY - JOUR
AB - Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology.
AU - Schmitt, Heather M.
AU - Fehrman, Rachel L.
AU - Maes, Margaret E
AU - Yang, Huan
AU - Guo, Lian Wang
AU - Schlamp, Cassandra L.
AU - Pelzel, Heather R.
AU - Nickells, Robert W.
ID - 10000
IS - 10
JF - Investigative Ophthalmology and Visual Science
SN - 0146-0404
TI - Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression
VL - 62
ER -
TY - JOUR
AB - We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice.
AU - Koroteev, Peter
AU - Pushkar, Petr
AU - Smirnov, Andrey V.
AU - Zeitlin, Anton M.
ID - 9998
IS - 5
JF - Selecta Mathematica
SN - 1022-1824
TI - Quantum K-theory of quiver varieties and many-body systems
VL - 27
ER -
TY - JOUR
AB - We study systems of nonlinear partial differential equations of parabolic type, in which the elliptic operator is replaced by the first-order divergence operator acting on a flux function, which is related to the spatial gradient of the unknown through an additional implicit equation. This setting, broad enough in terms of applications, significantly expands the paradigm of nonlinear parabolic problems. Formulating four conditions concerning the form of the implicit equation, we first show that these conditions describe a maximal monotone p-coercive graph. We then establish the global-in-time and large-data existence of a (weak) solution and its uniqueness. To this end, we adopt and significantly generalize Minty’s method of monotone mappings. A unified theory, containing several novel tools, is developed in a way to be tractable from the point of view of numerical approximations.
AU - Bulíček, Miroslav
AU - Maringová, Erika
AU - Málek, Josef
ID - 10005
IS - 09
JF - Mathematical Models and Methods in Applied Sciences
KW - Nonlinear parabolic systems
KW - implicit constitutive theory
KW - weak solutions
KW - existence
KW - uniqueness
SN - 0218-2025
TI - On nonlinear problems of parabolic type with implicit constitutive equations involving flux
VL - 31
ER -
TY - JOUR
AB - Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.
AU - Friml, Jiří
ID - 10016
JF - Cold Spring Harbor Perspectives in Biology
SN - 1943-0264
TI - Fourteen stations of auxin
ER -
TY - GEN
AB - In order to study integral points of bounded log-anticanonical height on weak del Pezzo surfaces, we classify weak del Pezzo pairs. As a representative example, we consider a quartic del Pezzo surface of singularity type A1 + A3 and prove an analogue of Manin's conjecture for integral points with respect to its singularities and its lines.
AU - Derenthal, Ulrich
AU - Wilsch, Florian Alexander
ID - 10018
KW - Integral points
KW - del Pezzo surface
KW - universal torsor
KW - Manin’s conjecture
T2 - arXiv
TI - Integral points on singular del Pezzo surfaces
ER -
TY - THES
AB - The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis.
AU - Hensel, Sebastian
ID - 10007
SN - 2663-337X
TI - Curvature driven interface evolution: Uniqueness properties of weak solution concepts
ER -
TY - GEN
AB - We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction of a gradient-flow calibration in the sense of the recent work of Fischer et al. [arXiv:2003.05478] for any such cluster. This extends the two-dimensional construction to the three-dimensional case of surfaces meeting along triple junctions.
AU - Hensel, Sebastian
AU - Laux, Tim
ID - 10013
T2 - arXiv
TI - Weak-strong uniqueness for the mean curvature flow of double bubbles
ER -
TY - JOUR
AB - Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2
Thr31 phosphorylation site for growth regulation in the Arabidopsis root tip.
AU - Nikonorova, N
AU - Murphy, E
AU - Fonseca de Lima, CF
AU - Zhu, S
AU - van de Cotte, B
AU - Vu, LD
AU - Balcerowicz, D
AU - Li, Lanxin
AU - Kong, X
AU - De Rop, G
AU - Beeckman, T
AU - Friml, Jiří
AU - Vissenberg, K
AU - Morris, PC
AU - Ding, Z
AU - De Smet, I
ID - 10015
JF - Cells
KW - primary root
KW - (phospho)proteomics
KW - auxin
KW - (receptor) kinase
SN - 2073-4409
TI - The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators
VL - 10
ER -
TY - CONF
AB - We present a faster symbolic algorithm for the following central problem in probabilistic verification: Compute the maximal end-component (MEC) decomposition of Markov decision processes (MDPs). This problem generalizes the SCC decomposition problem of graphs and closed recurrent sets of Markov chains. The model of symbolic algorithms is widely used in formal verification and model-checking, where access to the input model is restricted to only symbolic operations (e.g., basic set operations and computation of one-step neighborhood). For an input MDP with n vertices and m edges, the classical symbolic algorithm from the 1990s for the MEC decomposition requires O(n2) symbolic operations and O(1) symbolic space. The only other symbolic algorithm for the MEC decomposition requires O(nm−−√) symbolic operations and O(m−−√) symbolic space. A main open question is whether the worst-case O(n2) bound for symbolic operations can be beaten. We present a symbolic algorithm that requires O˜(n1.5) symbolic operations and O˜(n−−√) symbolic space. Moreover, the parametrization of our algorithm provides a trade-off between symbolic operations and symbolic space: for all 0<ϵ≤1/2 the symbolic algorithm requires O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space ( O˜ hides poly-logarithmic factors). Using our techniques we present faster algorithms for computing the almost-sure winning regions of ω -regular objectives for MDPs. We consider the canonical parity objectives for ω -regular objectives, and for parity objectives with d -priorities we present an algorithm that computes the almost-sure winning region with O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space, for all 0<ϵ≤1/2 .
AU - Chatterjee, Krishnendu
AU - Dvorak, Wolfgang
AU - Henzinger, Monika
AU - Svozil, Alexander
ID - 10002
KW - Computer science
KW - Computational modeling
KW - Markov processes
KW - Probabilistic logic
KW - Formal verification
KW - Game Theory
SN - 1043-6871
T2 - Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science
TI - Symbolic time and space tradeoffs for probabilistic verification
ER -
TY - CONF
AB - Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs.
AU - Chatterjee, Krishnendu
AU - Doyen, Laurent
ID - 10004
KW - Computer science
KW - Heuristic algorithms
KW - Memory management
KW - Automata
KW - Markov processes
KW - Probability distribution
KW - Complexity theory
SN - 1043-6871
T2 - Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science
TI - Stochastic processes with expected stopping time
ER -
TY - CONF
AB - In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision.
AU - Henzinger, Thomas A
AU - Sarac, Naci E
ID - 10003
KW - Computer science
KW - Runtime
KW - Registers
KW - Time factors
KW - Monitoring
SN - 1043-6871
T2 - Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science
TI - Quantitative and approximate monitoring
ER -
TY - JOUR
AB - In this paper, we introduce a random environment for the exclusion process in obtained by assigning a maximal occupancy to each site. This maximal occupancy is allowed to randomly vary among sites, and partial exclusion occurs. Under the assumption of ergodicity under translation and uniform ellipticity of the environment, we derive a quenched hydrodynamic limit in path space by strengthening the mild solution approach initiated in Nagy (2002) and Faggionato (2007). To this purpose, we prove, employing the technology developed for the random conductance model, a homogenization result in the form of an arbitrary starting point quenched invariance principle for a single particle in the same environment, which is a result of independent interest. The self-duality property of the partial exclusion process allows us to transfer this homogenization result to the particle system and, then, apply the tightness criterion in Redig et al. (2020).
AU - Floreani, Simone
AU - Redig, Frank
AU - Sau, Federico
ID - 10024
JF - Stochastic Processes and their Applications
KW - hydrodynamic limit
KW - random environment
KW - random conductance model
KW - arbitrary starting point quenched invariance principle
KW - duality
KW - mild solution
SN - 0304-4149
TI - Hydrodynamics for the partial exclusion process in random environment
VL - 142
ER -
TY - THES
AB - This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author.
AU - Feliciangeli, Dario
ID - 9733
SN - 2663-337X
TI - The polaron at strong coupling
ER -