3,493 Works

Adaptive circuits in synthetic biology

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One of the most remarkable features of biological systems is their ability to adapt to the constantly changing environment. By harnessing principles of control theory, synthetic biologists are starting to mimic this adaptation in regulatory gene circuits. Doing so allows for the construction of systems that perform reliably under non-optimal conditions. Furthermore, making a system adaptive can make up for imperfect knowledge of the underlying biology and, hence, avoid unforeseen complications in the implementation. Here,...

Perovskite-type superlattices from lead halide perovskite nanocubes

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Atomically defined assemblies of dye molecules (such as H and J aggregates) have been of interest for more than 80 years because of the emergence of collective phenomena in their optical spectra1,2,3, their coherent long-range energy transport, their conceptual similarity to natural light-harvesting complexes4,5, and their potential use as light sources and in photovoltaics. Another way of creating versatile and controlled aggregates that exhibit collective phenomena involves the organization of colloidal semiconductor nanocrystals into long-range-ordered...

Mitotic disassembly and reassembly of nuclear pore complexes

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Nuclear pore complexes (NPCs) are huge protein assemblies within the nuclear envelope (NE) that serve as selective gates for macromolecular transport between nucleus and cytoplasm. When higher eukaryotic cells prepare for division, they rapidly disintegrate NPCs during NE breakdown such that nuclear and cytoplasmic components mix to enable the formation of a cytoplasmic mitotic spindle. At the end of mitosis, reassembly of NPCs is coordinated with the establishment of the NE around decondensing chromatin. We...

qcscine/swoose: Release 1.0.0

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Changes: parametrization of SFAM molecular mechanics model (large and small systems) GAFF molecular mechanics model interface through SCINE to xTB and Sparrow automated set-up of QM/MM calculations (including automated QM region selection) single-point calculations with the molecular mechanics models and with QM/MM models Hessian matrix available with MM models structure optimizations and molecular dynamics simulations with MM models and with QM/MM models library functions to build molecular machine learning models from quantum chemical reference data

Leveraging self-organizing maps with convolutional neural networks for virtual chemical library screening

Computer assisted drug design has been established as an important tool to support drug discovery projects through the efficient identification of relationships between small molecules and macromolecular targets. Machine learning (ML) algorithms in particular now play an integral role for hit identification screening campaigns due to their capability to screen large databases for promising new chemical entities and to reduce those large molecule repositories to a select few promising compounds to focus on. Currently, one...

Three-Dimensional Analytical Modeling of an Eddy-Current-Based Non-Contact Speed Sensor

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This paper presents a computationally efficient, three-dimensional electromagnetic model for eddy-current-based speed sensors featuring an injection coil, two or more pick-up coils and a magnetic yoke. The superposition of incident and reflected fields, which was adopted in previous works, is replaced by a direct formulation; and Maxwell's equations are solved for the magnetic flux density vector, rather than involving a higher-order vector potential. The injected current is accounted for in the boundary conditions, and special...

Benefiting from local rigidity in 3D point cloud processing

Incorporating 3D understanding and spatial reasoning into (intelligent) algorithms is crucial for solving several tasks in fields such as engineering geodesy, risk assessment, and autonomous driving. Humans are capable of reasoning about 3D spatial relations even from a single 2D image. However, making the priors that we rely on explicit and integrating them into computer programs is very challenging. Operating directly on 3D input data, such as 3D point clouds, alleviates the need to lift...

Nashian game theory is incompatible with quantum contextuality

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In this work, we design a novel game-theoretical framework capable of capturing the defining aspects of quantum theory. We introduce an original model and an algorithmic procedure that enables to express measurement scenarios encountered in quantum mechanics as multiplayer games and to translate physical notions of causality, correlation, and contextuality to particular aspects of game theory. Furthermore, inspired by the established correspondence, we investigate the causal consistency of games in extensive form with imperfect information...

Volcano-seismic 2020 unrest in Reykjanes Iceland: The MAGIC multi-parametric rapid response during Covid-19 lockdown

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The plate boundary between the American and Eurasian plates runs in southwest Iceland along a 5-10 km wide seismicity zone on the Reykjanes Peninsula. There, tectonic spreading events take place as continuous seismic release and seismic episodes (swarms and individual large events) with recurrence interval of about 40 years and volcanic episodes at intervals of 800-1000 years. The crust in Reykjanes is, therefore, particularly thin and hot and geothermal energy is currently harnesses in two...

Informing the design of courtyard street blocks using solar energy models: A case study of a university campus in Singapore

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This study discusses the interplays between urban form and energy performance using a case study in Singapore. We investigate educational urban quarters in the tropical climate of Singapore using simulation-based parametric geometric modelling. Three input variables of urban form were examined: street network orientation, street canyon width, and building depth. In total, 280 scenarios were generated using a quasi-Monte Carlo Saltelli sampler and Grasshopper. For each scenario, the City Energy Analyst, an open-source urban building...

Positron Emission Tomography in Animal Models of Alzheimer's Disease Amyloidosis: Translational Implications

Animal models of Alzheimer's disease amyloidosis that recapitulate cerebral amyloid-beta pathology have been widely used in preclinical research and have greatly enabled the mechanistic understanding of Alzheimer's disease and the development of therapeutics. Comprehensive deep phenotyping of the pathophysiological and biochemical features in these animal models is essential. Recent advances in positron emission tomography have allowed the non-invasive visualization of the alterations in the brain of animal models and in patients with Alzheimer's disease. These...

iGSE-C$_{\mathrm{x}}$ – a New Normalized Steinmetz Model for Class II Multilayer Ceramic Capacitors

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Ferroelectric Class II ceramic capacitors allow for highly compact converter realizations, but are showing relatively high losses for large-signal excitations which must be taken into account in the system dimensioning. Recent literature introduced the iGSE-C Q , a Steinmetz model based on the macroscopic capacitor Q-U hysteresis, allowing to accurately predict the losses of X7R capacitors. However, the model is specific for each single device, i.e., is insufficient to characterize losses in devices of the...

Learning efficient navigation in vortical flow fields

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Efficient point-to-point navigation in the presence of a background flow field is important for robotic applications such as ocean surveying. In such applications, robots may only have knowledge of their immediate surroundings or be faced with time-varying currents, which limits the use of optimal control techniques. Here, we apply a recently introduced Reinforcement Learning algorithm to discover time-efficient navigation policies to steer a fixed-speed swimmer through unsteady two-dimensional flow fields. The algorithm entails inputting environmental...

Urban scale digital twins and urban planning decision-making: Big data and network society

The paper examines the impact of the virtual public sphere on how urban spaces are experienced and conceived in our data-driven society. It places particular emphasis on urban scale digital twins, which are virtual replicas of cities that are used to simulate environments and develop scenarios in response to policy problems. The paper also investigates the shift from the technical to the socio-technical perspective within the field of smart cities. Despite the aspirations of urban...

Histone variant H2A.Z regulates zygotic genome activation

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During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development; still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that...

Impact of Tetrabutylammonium on the Oxidation of Bromide by Ozone

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The reaction of ozone with sea-salt derived bromide is relevant for marine boundary layer atmospheric chemistry. The oxidation of bromide by ozone is enhanced at aqueous interfaces. Ocean surface water and sea spray aerosol are enriched in organic compounds, which may also have a significant effect on this reaction at the interface. Here, we assess the surface propensity of cationic tetrabutylammonium at the aqueous liquid-vapor interface by liquid microjet X-ray photoelectron spectroscopy (XPS) and the...

Increasing the deterrence of airport security checks by managing expectations through communication: a hypothetical scenario experiment

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Selective security screenings are discussed as a potential strategy to reduce costs and waiting times at airports, while keeping security high. However, the limited literature suggests that traditional security screenings, where all passengers are screened, are perceived as more deterrent for criminal activity and more secure from passengers' perspectives. The goal of this study was to investigate whether targeted communication on an airport's website can counteract the detrimental effect of randomised airport security checks on...

Domain adaptation under structural causal models

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Domain adaptation (DA) arises as an important problem in statistical machine learning when the source data used to train a model is different from the target data used to test the model. Recent advances in DA have mainly been application-driven and have largely relied on the idea of a common subspace for source and target data. To understand the empirical successes and failures of DA methods, we propose a theoretical framework via structural causal models...

The refined quantum extremal surface prescription from the asymptotic equipartition property

Information theoretic ideas have provided numerous insights in the progress of fundamental physics, especially in our pursuit of quantum gravity. In particular, the holographic entanglement entropy is a very useful tool in studying AdS/CFT, and its efficacy is manifested in the recent black hole page curve calculation. On the other hand, the one-shot information theoretic entropies, such as the smooth min/max-entropies, are less discussed in AdS/CFT. They are however more fundamental entropy measures from the...

Monitoring the binding and insertion of a single transmembrane protein by an insertase

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Cells employ highly conserved families of insertases and translocases to insert and fold proteins into membranes. How insertases insert and fold membrane proteins is not fully known. To investigate how the bacterial insertase YidC facilitates this process, we here combine single-molecule force spectroscopy and fluorescence spectroscopy approaches, and molecular dynamics simulations. We observe that within 2 ms, the cytoplasmic α-helical hairpin of YidC binds the polypeptide of the membrane protein Pf3 at high conformational variability and...

Industrialising timber craftsmanship: Early glulam within the traditional timber construction in Switzerland

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Early glue laminated timber in Switzerland was used for many functions: industrial but also regular buildings such as sport halls, cultural buildings and housing. Integration of the new practice was only achieved by involving existing traditional players. Contractors had to bring together a long-standing knowledge of local timber craftsmanship and the patented glulam technology. The paper traces the early onsite construction practice of glulam by looking at the handling of the contractor for both fields,...

A Century of Fractionated Radiotherapy: How Mathematical Oncology Can Break the Rules

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Radiotherapy is involved in 50% of all cancer treatments and 40% of cancer cures. Most of these treatments are delivered in fractions of equal doses of radiation (Fractional Equivalent Dosing (FED)) in days to weeks. This treatment paradigm has remained unchanged in the past century and does not account for the development of radioresistance during treatment. Even if under-optimized, deviating from a century of successful therapy delivered in FED can be difficult. One way of...

Visual Representation and Stereotypes in News Media

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We propose a new method for measuring gender and ethnic stereotypes in news reports. By combining computer vision and natural language processing tools, the method allows us to analyze both images and text as well as the interaction between the two. We apply this approach to over 2 million web articles published in the New York Times and Fox News between 2000 and 2020. We find that in both outlets, men and whites are generally...

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