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Variational Modeling of Porosity Waves
No full textMathematical models for finite-strain poroelasticity in an Eulerian formulation are studied by constructing their energy-variational structure, which gives rise to a class of saddle-point problems. This problem is discretized using an incremental time-stepping scheme and a mixed finite element approach, resulting in a monolithic, structure-preserving discretization. The Eulerian formulation is based on the inverse deformation, the so-called reference map. We present examples from geophysical applications, where elasticity and diffusive fluid flow are fully coupled and can be used to describe porosity waves, i.e., localized ascending fluid waves driven by gravitational forces
A brain-constrained neural model of cognition and language with NEST: transitioning from the Felix framework
No full textWe introduce a brain-constrained neurocomputational model designed to simulate higher cognitive functions of the human brain, implemented using NEST, a widely used open-source simulator optimised for high-performance spiking neural network simulations. Previously implemented in the custom-built C-based Felix simulation library, transitioning the model to NEST enhances accessibility, reproducibility, and computational efficiency. At the cellular level, the model comprises spiking excitatory neurons and local inhibitory neurons, whereas at the network level, it replicates the structural and functional organisation of 12 cortical regions spanning frontal, temporal, and occipital cortices, along with their associated inter-area connectivity. Additionally, global inhibition mechanisms and neuronal noise are integrated. Learning in the model follows biologically plausible Hebbian plasticity principles, incorporating both long-term potentiation and long-term depression. To validate the NEST implementation, we replicated previous simulation findings obtained with the Felix-based model. The new implementation successfully reproduced the same topographical distribution of cell assemblies following associative learning of object and action words within action and perception systems, replicating a range of previous neuroimaging results. Although the NEST model produced larger cell assemblies than Felix, the overall topographical patterns remained similar, indicating preservation of fundamental network characteristics. Moreover, the transition to NEST significantly enhanced computational efficiency, reducing simulation runtime nearly sixfold compared to Felix. This improvement in computational speed is crucial for expanding the model to include additional cortical regions, such as extending to the right hemisphere, which necessitates increased computational resources
Achieving fast and robust perfect entangling gates via reinforcement learning
No full textNoisy intermediate-scale quantum computers hold the promise of tackling complex and otherwise intractable computational challenges through the massive parallelism offered by qubits. Central to realizing the potential of quantum computing are perfect entangling (PE) two-qubit gates, which serve as a critical building block for universal quantum computation. In the context of quantum optimal control, shaping electromagnetic pulses to drive quantum gates is crucial for pushing gate performance toward theoretical limits. In this work, we leverage reinforcement learning (RL) techniques to discover near-optimal pulse shapes that yield PE gates. A collection of RL agents is trained within robust simulation environments, enabling the identification of effective control strategies even under noisy conditions. Selected agents are then validated on higher-fidelity simulations, illustrating how RL-based methods can reduce calibration overhead when compared to quantum optimal control techniques. Furthermore, the RL approach is hardware agnostic with the potential for broad applicability across various quantum computing platforms
Sepsis secondary to cystitis in a guinea pig (Cavia porcellus)
No full textCystitis is a frequent, often chronic and recurrent disease in guinea pigs (Cavia porcellus). This report describes a case of a 2-year-old, entire, female Abyssinian guinea pig with fatal cystitis. The animal was presented with progressive chronic cystitis and had previously been treated with several antibiotics and analgesics. Radiographs demonstrated a mineral-dense opacity in the urinary bladder, and urinalysis revealed numerous leukocytes. The animal received subcutaneous fluid boluses and a change of antibiotic treatment. The general condition deteriorated, and the animal died acutely 1 day after being admitted to the hospital. Pathology revealed severe, chronic-active, multifocal, purulent to fibrinous, haemorrhagic cystitis. A bacteriological examination of the urinary bladder wall and urinary bladder contents revealed Facklamia sourekii, Corynebacterium renale and Enterococcus casseliflavus. Myocarditis and steatitis were also noted, supporting sepsis secondary to cystitis as the cause of death
Comment on “Mapping photoisomerization dynamics on a three-state model potential energy surface in bacteriorhodopsin using femtosecond stimulated Raman spectroscopy” by Z. Wang, Y. Chen, J. Jiang, X. Zhao and W. Liu, Chem. Sci., 2025, 16, 3713
No full textThe article by Wang et al. (Chem. Sci., 2025, 16, 3713) reports an experimental study of the photo-isomerization dynamics of the all-trans protonated Schiff base of retinal (AT-PSBR) in bacteriorhodopsin (bR), based on femtosecond stimulated Raman spectroscopy. In the present comment, we point out a misinterpretation of a new interesting high-frequency vibrational mode, conceptual flaws, like interpreting the data in a C2h symmetry framework, and most importantly the neglect of basic properties of AT-PSBR in bR, which were established over the past 30 years. The comment ends with a few suggestions on how to substantiate the new findings within a correct experimental and theoretical framework
Simple setup for in situ electrochemical electron paramagnetic resonance spectroscopy to study organic energy-storage materials
No full textThe design and application of a cost-effective, customisable electrochemical cell suitable for in situ X-band (9–10 GHz) Electron Paramagnetic Resonance (EPR) experiments is demonstrated. The cell is optimized for investigating electrochemical parameters of redox-active polymer films at room temperature using polar organic electrolytes. The polymer film to be studied is directly deposited onto the surface of a platinum wire acting as the working electrode. The three-electrode cylindrical cell design with mutual arrangement of the electrodes, inspired by the “ultramicroelectrode concept”, provides enhanced electrochemical response by minimizing ohmic drop while maintaining flexibility for a wide range of experimental setups. The cell performance is demonstrated using a redox conducting polymeric cathode material for organic radical batteries, namely poly[N,N″-bis(3-(4-oxy(2,2,6,6-tetramethylpiperidin-1-oxyl)butoxy)salicylidene)ethylenediiminato nickel(II)], as a test material. Continuous-wave EPR experiments using a portable benchtop spectrometer at a fixed magnetic field allow detecting the material's state of charge, initialisation of oxidation and reduction processes, as well as estimating electrochemical properties. The cell design presented here enables potentiostatic, galvanostatic, and potentiodynamic measurement modes, while offering the possibility of customisation through 3D printing and the use of various electrode materials
Pál’s Isominwidth Problem in the Hyperbolic Space
No full textThe paper focuses on possible hyperbolic versions of the classical Pál isominwidth
inequality in R2 from 1921, which states that for a fixed minimal width, the regular
triangle has minimal area. We note that the isominwidth problem is still wide open in
Rn for n ≥ 3. Recent work on the isominwidth problem on the sphere S2 shows that
the solution is the regular spherical triangle when the width is at most π2
according to
Bezdek and Blekherman, while Freyer and Sagmeister proved that the minimizer is
the polar of a spherical Reuleaux triangle when the minimal width is greater than π2
.
In this paper, the hyperbolic isominwidth problem is discussed with respect to the
probably most natural notion of width due to Lassak in the hyperbolic space Hn
where strips bounded by a supporting hyperplane and a corresponding hypersphere
are considered. On the one hand, we show that the volume of a convex body of
given minimal Lassak width w > 0 in Hn might be arbitrarily small; therefore, the
isominwidth problem for convex bodies inHn does not make sense. On the other hand,
in the two-dimensional case, we prove that among horocyclically convex bodies of
given Lassak width in H2, the area is minimized by the regular horocyclic triangle. In
addition, we also verify a stability version of the last result
Design of Thermoresponsive pNIPAM and dPG-Click Hydrogels for Human Cell Cultivation
No full textThe extracellular matrix (ECM) plays a central role in regulating cell behavior, tissue morphogenesis,
and differentiation through a combination of biochemical and mechanical cues. However, most
conventional cell-culture substrate materials are chemically poorly defined and exhibit batch-to-batch
variability, hindering mechanistic investigations into how individual matrix parameters influence
cellular decision-making. To overcome these limitations, this thesis presents the design and
characterization of a fully synthetic, tunable hydrogel platform that enables systematic exploration of
cell–matrix interactions under defined and reproducible conditions.
In the first part of this work, hydrogels were synthesized via strain-promoted alkyne–azide cycloaddition
(SPAAC) between dendritic polyglycerol-bicyclononyne (dPG-BCN) and azide-functionalized
pNIPAM-co-PEG copolymers. This bioorthogonal click chemistry provided independent control over
matrix stiffness, viscoelasticity, and biochemical functionality. The platform supported long-term three
dimensional culture of human induced pluripotent stem cells (hiPSCs) and guided their differentiation
into hepatic organoids. Functionalization with cyclic RGD peptides revealed that matrix adhesiveness
alone was sufficient to direct lineage specification via integrin-mediated activation of the TGF-β
signaling cascade, identifying a mechanosensitive integrin–MMP–TGF-β axis as a key regulator of
hepatic fate decisions.
In the second part, the hydrogel chemistry was expanded using a thiol–maleimide coupling approach,
and sulfate groups were introduced as a biomimetic, charge-tunable component. These hydrogels
exhibited enhanced mechanical stability, slower enzymatic degradation, and selective molecular
diffusion profiles as demonstrated by fluorescence recovery after photobleaching (FRAP) compared to
the unsulfated hydrogel. Sulfation significantly improved cell viability and adhesion in both two- and
three-dimensional cultures, highlighting the importance of electrostatic interactions in modulating cell
matrix communication.
The combined findings demonstrate that synthetic hydrogels can be rationally designed to decouple and
quantify the effects of stiffness, adhesiveness, charge density, and viscoelasticity on stem-cell function.
Beyond their fundamental value for understanding ECM-guided morphogenesis, these chemically
defined and scalable materials provide a promising foundation for translational applications in
regenerative medicine, drug testing, and tissue engineering. By replacing the ECM using rational
designed hydrogels, this work contributes to the next generation of biomaterials capable of guiding
cellular identity and function by design
Optimal estimation retrieval framework for daytime clear-sky total column water vapour from MTG-FCI near-infrared measurements
No full textA retrieval of total column water vapour (TCWV) from the new daytime, clear-sky near-infrared (NIR) measurements of the Flexible Combined Imager (FCI) onboard the geostationary satellite Meteosat Third Generation Imager (MTG-I, Meteosat-12) is presented. The retrieval algorithm is based on the differential absorption technique, relating TCWV amounts to the radiance ratio of a non-absorbing band at 0.865 µm and a nearby water vapour (WV) absorbing band at 0.914 µm. The sensitivity of the band ratio to WV amount increases towards the surface which means that the whole atmospheric column down to the boundary-layer moisture variability can be observed well.
The retrieval framework is based on an optimal estimation (OE) method, providing pixel-based uncertainty estimates. It builds on well-established algorithms for other passive imagers with similar spectral band settings. Transferring knowledge gained in their development onto FCI required new approaches. The absence of additional, adjacent window bands to estimate the surface reflectance within FCI's absorbing channel is mitigated using a principal component regression (PCR) from the bands at 0.51, 0.64, 0.865, 1.61, and 2.25 µm.
We utilize synergistic observations from Sentinel-3 Ocean and Land Colour Instrument (OLCI) and Sea and Land Surface Temperature Radiometer (SLSTR) to generate “FCI-like” measurements. OLCI bands were complemented with SLSTR bands, enabling evaluation of the retrieval's robustness and global performance of the PCR. Furthermore, this enabled algorithm testing under realistic conditions using well-characterized data, at a time when a long-term, fully calibrated FCI Level 1c dataset was not available. We built a forward model for two FCI equivalent OLCI bands at 0.865 and 0.9 µm. A long-term validation of OLCI against a single atmospheric radiation measurement (ARM) reference site without the PCR resulted in a bias of 1.85 kg m−2, centred root-mean-square deviation (cRMSD) of 1.26 kg m−2, and a Pearson correlation coefficient (r) of 0.995.
A first verification of the OLCI/SLSTR “FCI-like” TCWV against well-established ground-based TCWV products concludes with a wet bias between 0.33–2.84 kg m−2, a cRMSD between 1.46–2.21 kg m−2, and r between 0.98–0.99. In this set of comparisons, only land pixels were considered. Furthermore, a dataset of FCI Level 1c observations with a preliminary calibration was processed. The TCWV processed for these FCI measurements aligns well with reanalysis TCWV and collocated OLCI/SLSTR TCWV but shows a dry bias. A more rigorous validation and assessment will be done once a longer record of FCI data is available.
TCWV observations derived from geostationary satellite measurements enhance monitoring of WV distributions and associated meteorological phenomena from synoptic scales down to local scales. Such observations are of special interest for the advancement of nowcasting techniques and numerical weather prediction (NWP) accuracy as well as process-studies
Maximum entropy networks show that plant–arbuscular mycorrhizal fungi associations are anti-nested and modular
No full text- There is uncertainty in whether there is a common pattern of nestedness and modularity in plant–arbuscular mycorrhizal (AM) fungi associations, partly because of limitations arising from the use of null models that randomly rewire the observed connections to test for non-random patterns in the network.
- Here, we overcome these limitations by generating null association matrices using maximum entropy network modelling, and specifically the bipartite binary configuration model (BiCM) with degree distributions as soft constraints. This was used to test the hypothesis that nestedness and modularity are prevalent in plant–AM fungi associations.
- In contrast to past findings, we found most plant–AM fungi associations were anti-nested and modular. This pattern was almost universal, being consistent across habitat types, multiple spatial scales, and multiple levels of plant node aggregation, from communities and species to populations. Anti-nestedness can easily emerge from modularity when network patterns are determined by the identity of the plant and AM fungal nodes.
- Our findings emphasize the need for experiments that test the factors that cause the observed network structure and how that structure determines the function and stability of plant–AM fungi association networks