@article{20704,
  abstract     = {Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES.},
  author       = {Tuo, Ping and Zeng, Zezhu and Chen, Jiale and Cheng, Bingqing},
  issn         = {1549-9626},
  journal      = {Journal of Chemical Theory and Computation},
  number       = {22},
  pages        = {11427--11435},
  publisher    = {American Chemical Society},
  title        = {{Scalable multitemperature free energy sampling of classical Ising spin states}},
  doi          = {10.1021/acs.jctc.5c01248},
  volume       = {21},
  year         = {2025},
}

@article{22525,
  abstract     = {Cropland cultivation is fundamental to food security and plays a crucial role in the global water, energy, and carbon cycles. However, our understanding of how climate change will impact cropland functions is still limited. This knowledge gap is partly due to the simplifications made in terrestrial biosphere models (TBMs), which often overlook essential agricultural management practices such as irrigation and fertilizer application and simplify critical physiological crop processes.
Here, we demonstrate how, with minor, parsimonious enhancements to the TBM T&C, it is possible to accurately represent a complex cropland system. Our modified model, T&C-CROP, incorporates realistic agricultural management practices, including complex crop rotations and irrigation and fertilization regimes, along with their effects on soil biogeochemical cycling. We successfully validate T&C-CROP across four distinct agricultural sites, encompassing diverse cropping systems such as multi-crop rotations, monoculture, and managed grassland.
A comprehensive validation of T&C-CROP was conducted, encompassing water, energy, and carbon fluxes; leaf area index (LAI); and organ-specific yields. Our model effectively captured the heterogeneity in daily land surface energy balances across crop sites, achieving coefficients of determination of 0.77, 0.48, and 0.87 for observed versus simulated net radiation (Rn), sensible heat flux (H), and latent heat flux (LE), respectively. Seasonal, crop-specific gross primary production (GPP) was simulated with an average absolute bias of less than 10 %. Peak-season LAI was accurately represented, with an r2 of 0.67. Harvested yields (above-ground biomass, grain, and straw) were generally simulated within 10 %–20 % accuracy of observed values, although inter-annual variations in crop-specific growth were difficult to capture.},
  author       = {Buckley Paules, Jordi and Fatichi, Simone and Warring, Bonnie and Paschalis, Athanasios},
  issn         = {1991-9603},
  journal      = {Geoscientific Model Development},
  number       = {4},
  pages        = {1287--1305},
  publisher    = {Copernicus Publications},
  title        = {{T&C-CROP: representing mechanistic crop growth with a terrestrial biosphere model (T&C, v1.5) – model formulation and validation}},
  doi          = {10.5194/gmd-18-1287-2025},
  volume       = {18},
  year         = {2025},
}

@article{22557,
  abstract     = {The implementation of future geoengineering projects to counteract global warming trends or more generally changes in aerosol loads alter solar radiation reaching the Earth's surface. These changes could have effects on ecohydrological systems with impacts which are still poorly quantified. Here, we compute how changes in solar radiation affect global and local near-surface meteorological variables by using CMIP6 model results. Using climate model outputs, we compute climate sensitivities to solar radiation alterations. These sensitivities are then applied to local observations and used to construct two sets of numerical experiments: the first focuses on solar radiation changes only, and the second systematically modifies precipitation, air temperature, specific humidity, and wind speed using the CMIP6-derived sensitivities to radiation changes, i.e., including its land–atmosphere feedback. We use those scenarios as input to a mechanistic ecohydrological model to quantify the local responses of the energy and water budgets as well as vegetation productivity spanning different biomes and climates.
In the absence of land–atmosphere feedback, changes in solar radiation tend to reflect mostly in sensible heat changes, with minor effects on the hydrological cycle, and vegetation productivity correlates linearly with changes in solar radiation. When land–atmosphere feedback is included, changes in latent heat and hydrological variables are much more pronounced, mostly because of the temperature and vapor pressure deficit changes associated with solar radiation changes. Vegetation productivity tends to have an asymmetric response with a considerable decrease in gross primary production to a radiation reduction not accompanied by a similar increase at higher radiation. These results provide important insights into how ecosystems could respond to potential future changes in shortwave radiation including solar geoengineering programs.},
  author       = {Wang, Yiran and Meili, Naika and Fatichi, Simone},
  issn         = {1607-7938},
  journal      = {Hydrology and Earth System Sciences},
  number       = {2},
  pages        = {381--396},
  publisher    = {Copernicus Publications},
  title        = {{Ecohydrological responses to solar radiation changes}},
  doi          = {10.5194/hess-29-381-2025},
  volume       = {29},
  year         = {2025},
}

@article{22539,
  abstract     = {Urbanization is projected to add 2.5 billion more urban residents by 2050. The resulting increases in impervious surfaces leads to altered hydrologic processes through greater runoff and reduced transpiration. Urban landscapes, characterized by heterogeneous land covers and infiltration rates, complicates the modeling of the urban water cycle. Existing models tend to focus on event-scale floods and thereby overlooking long-term hydrological alterations, as they often oversimplify hydrological processes such as soil moisture dynamics or evapotranspiration.
Accurately projecting the long-term hydrological budget over cities is essential to better understand water resources availability for water sensitive urban design and to guide urban greening initiatives with the purpose of improving urban water management. Using Singapore —a densely populated tropical city-state committed to water harvesting— as a testbed, this study compares two modeling approaches to resolve the long-term urban hydrological budget. The Urban Tethys & Chloris (UT&C) model offers realistic representations of urban features, microclimate and hydrology, although it is computationally intensive. In contrast, the Tethys & Chloris (T&C) model, originally developed for natural environments, modified here to incorporate simplified urban features, is simpler and faster allowing fully distributed simulations.
Findings suggest that while UT&C results may offer a more reliable representation at local scales, accounting for microclimatic feedback and two-dimensional urban geometries, both models yield similar hydrological budget insights when integrated at the city scale – at least in the wet climate of Singapore. Vegetation fraction emerges as the primary control on total evapotranspiration. T&C’s reduced computational demand, and native support for distributed hydrological modeling make it well-suited for city-wide simulations. The overall study underscores the complexities and feasibility of modeling long-term hydrological processes in urban environments.},
  author       = {Lin Xu, Yexia and Meili, Naika and Fatichi, Simone},
  issn         = {1879-2707},
  journal      = {Journal of Hydrology},
  publisher    = {Elsevier},
  title        = {{Long-term hydrological budget over urban areas: approaches and challenges}},
  doi          = {10.1016/j.jhydrol.2025.134000},
  volume       = {662, Part B},
  year         = {2025},
}

@article{22562,
  abstract     = {Persistent multiyear drought (MYD) events pose a growing threat to nature and humans in a changing climate. We identified and inventoried global MYDs by detecting spatiotemporally contiguous climatic anomalies, showing that MYDs have become drier, hotter, and led to increasingly diminished vegetation greenness. The global terrestrial land affected by MYDs has increased at a rate of 49,279 ± 14,771 square kilometers per year from 1980 to 2018. Temperate grasslands have exhibited the greatest declines in vegetation greenness during MYDs, whereas boreal and tropical forests have had comparably minor responses. With MYDs becoming more common, this global quantitative inventory of the occurrence, severity, trend, and impact of MYDs provides an important benchmark for facilitating more effective and collaborative preparedness toward mitigation of and adaptation to such extreme events.},
  author       = {Chen, Liangzhi and Brun, Philipp and Buri, Pascal and Fatichi, Simone and Gessler, Arthur and McCarthy, Michael James and Pellicciotti, Francesca and Stocker, Benjamin and Karger, Dirk Nikolaus},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6731},
  pages        = {278--284},
  publisher    = {AAAS},
  title        = {{Global increase in the occurrence and impact of multiyear droughts}},
  doi          = {10.1126/science.ado4245},
  volume       = {387},
  year         = {2025},
}

@article{22568,
  abstract     = {The recent surge in reservoir construction has increased global surface water storage, with Mainland
Southeast Asia (MSEA) being a significant hotspot. Such infrastructural evolution demands updates in water
management strategies and hydrological models. However, information on actual reservoir storage is hard to
acquire, especially for transboundary river basins. To date, no high-resolution spatiotemporal dataset on absolute
storage time series is available for reservoirs in MSEA. To address this gap, we present (1) a comprehensive openaccess database of absolute storage time series (sub-monthly) for 186 reservoirs (larger than 0.1 km3) in MSEA
spanning the period 1985–2023 and (2) an analysis of the reservoir storage dynamics. This dataset is derived
from remote sensing observations, integrating satellite-based water surface area extraction from high-resolution
(30 m) images and area–elevation–storage (A–E–S) relationships to estimate reservoir level and storage dynamics. The MSEA database includes static (area–elevation–storage curves, water frequency, and reservoir extent)
and dynamic (area, water level, and absolute storage time series) components for each reservoir. The 186 reservoirs collectively store around 175 km3 of water, with a minimum of 140 km3 and a maximum of 210 km3. They
cover an average area of 8700 km2, ranging from a minimum of 6500 km2 to a maximum of 10 000 km2. We show that the combined average reservoir storage increased from 70 to 160 km3 (+130 %) from 2008 to 2017, primarily contributed by reservoirs in the Irrawaddy, Red, Upper Mekong, and Lower Mekong basins. Our in situ validation provides a good match between estimated storage and in situ observations, with 50 % of the validation sites (10 out of 20) showing an R2 > 0.7 and an average nRMSE < 14 %. The indirect validation (based on altimetry-converted storage) shows even better results, with an R2 > 0.7 and an average nRMSE < 12 % for 70 % (14 out of 20) of the reservoirs. Furthermore, the analysis of the 2019–2020 drought event in the MSEA region reveals that nearly 30 %–40 % of the region experienced more than 5 months of drought, with the most significant impact on reservoirs in Cambodia and Thailand. As a result, storage departures ranged by up to −40 % in some reservoirs, highlighting significant impacts on water availability. Overall, this analysis demonstrates the potential of the inferred storage time series for assessing real-life water-related problems in Mainland Southeast Asia, with the possibility of applying the method to estimate reservoir storage time series in other parts of the world. The reservoir storage database in Mainland Southeast Asia (MSEA-Res database) and the associated Python code are publicly available on Zenodo at https://doi.org/10.5281/zenodo.14844580 (Mahto et al., 2025).},
  author       = {Mahto, Shanti Shwarup and Fatichi, Simone and Galelli, Stefano},
  issn         = {1866-3516},
  journal      = {Earth System Science Data},
  number       = {6},
  pages        = {2693--2712},
  publisher    = {Copernicus Publications},
  title        = {{A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res)}},
  doi          = {10.5194/essd-17-2693-2025},
  volume       = {17},
  year         = {2025},
}

@article{22572,
  abstract     = {Urban expansion alters landscape structure and hydrological processes, heightening pluvial flood risks in cities worldwide. This study integrates multi-temporal urban expansion data with the CAFlood cellular automata model to simulate rainfall events with multiple return periods (i.e., 1-in-10, 1-in-100, and 1-in-200 year return periods) across three different urban environments: Shenzhen (China), suburban Houston (United States), and Lausanne (Switzerland). To quantify how evolving urban morphology drives flood volume, we computed key landscape metrics describing impervious extent (percentage of impervious surface), green space shape complexity (Area-weighted Mean Shape Index), green space aggregation (Aggregation Index), and impervious edge complexity (Landscape Shape Index). Their effects on changes in flood volume were analysed with Generalised Additive Models stratified by levels of pre-expansion impervious cover. The results show that decreasing green space aggregation and impervious edge complexity are consistently significant indicators of increased flood volumes, particularly in areas with low pre-expansion impervious cover (<50 %). However, the influence of these two key morphological indicators decline as impervious coverage increases, with total imperviousness gradually becoming the dominant factor. Sensitivity experiments with synthetic urban fabrics confirm that maintaining compact, well-connected green spaces can limit the increase in flood volume even with when impervious surfaces expand equally. By explicitly linking the morphological changes in urban form to pluvial flood response across diverse climates and urbanisation context, this study moves beyond static approaches and provides actionable insights for planning flood-resilient urban growth.},
  author       = {Zhu, Yue and Burlando, Paolo and Zhang, Ye and Chi, Dengkai and Wang, Jing and Qiu, Yeshan and Bonatesta, Matteo and Zou, Wenyue and Geiß, Christian and Tan, Puay Yok and Fatichi, Simone},
  issn         = {2210-6715},
  journal      = {Sustainable Cities and Society},
  keywords     = {Urban morphology, Urban expansion, Pluvial flood, Flood resilience},
  publisher    = {Elsevier},
  title        = {{The influence of urban morphological changes on pluvial flooding during urban expansion}},
  doi          = {10.1016/j.scs.2025.107018},
  volume       = {135},
  year         = {2025},
}

@article{22499,
  abstract     = {Increasing urban tree cover is a common strategy to lower urban temperatures and indirectly the building energy demand for air-conditioning (AC). However, urban vegetation leads to increasing humidity with potential negative effects on the AC dehumidification loads in hot-humid climates, an effect that has so far been unexplored. Here, we included a building energy model into the urban ecohydrological model Urban Tethys-Chloris (UT&C-BEM) to quantify the AC energy reduction effects of trees in seven hot cities with varying background humidity. A numerical experiment was performed simulating various urban densities and tree cover scenarios in the city-climates of Riyadh, Phoenix, Dubai, New Delhi, Singapore, Lagos, and Tokyo. The relative contribution of tree shade, air temperature reduction, and humidity increase on the AC energy reduction was further quantified. We found that well-watered trees provide the largest average summer AC energy reduction of −17% in the hot-dry climate (Riyadh, Phoenix). As tree shade is the dominant factor leading to the AC energy reduction in all city-climates, humid cities also show an average summer AC energy reduction ranging from −6% to −9%. However, increasing humidity is affecting AC dehumidification loads, especially under higher ventilation rates in humid climates and in these cities, AC energy reduction is most efficient with up to 40% tree cover. Additionally, we found that trees effectively reduce peak AC energy consumption due to higher shading effects in those hours. These results can inform urban planning strategies to maximize reduction in the AC energy demand using urban trees.},
  author       = {Meili, Naika and Zheng, Xing and Takane, Yuya and Nakajima, Ko and Yamaguchi, Kazuki and Chi, Dengkai and Zhu, Yue and Wang, Jing and Qiu, Yeshan and Paschalis, Athanasios and Manoli, Gabriele and Burlando, Paolo and Tan, Puay Yok and Fatichi, Simone},
  issn         = {1942-2466},
  journal      = {Journal of Advances in Modeling Earth Systems},
  number       = {3},
  publisher    = {American Geophysical Union},
  title        = {{Modeling the effect of trees on energy demand for indoor cooling and dehumidification across cities and climates}},
  doi          = {10.1029/2024ms004590},
  volume       = {17},
  year         = {2025},
}

@phdthesis{20357,
  author       = {Ruzickova, Natalia},
  isbn         = {978-3-99078-066-4},
  issn         = {2663-337X},
  keywords     = {gene regulation, networks, omnigenic model, pancreas, collective behaviour},
  pages        = {156},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Effect propagation in biological networks}},
  doi          = {10.15479/AT-ISTA-20357},
  year         = {2025},
}

@article{19593,
  abstract     = {Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, our knowledge about the safe usage of anti-inflammatory drugs during pregnancy is still limited. While human induced pluripotent stem cells (hIPSC)-derived brain organoid models have started to explore functional consequences upon viral stimulation, these models commonly lack microglia, which are susceptible to and promote inflammation. Furthermore, microglia are actively involved in neuronal development. Here, we generate hIPSC-derived microglia precursor cells and assemble them into retinal organoids. Once the outer plexiform layer forms, these hIPSC-derived microglia (iMG) fully integrate into the retinal organoids. Since the ganglion cell survival declines by this time in 3D-retinal organoids, we adapted the model into 2D and identify that the improved ganglion cell number significantly decreases only with iMG presence. In parallel, we applied the immunostimulant POLY(I:C) to mimic a fetal viral infection. While POLY(I:C) exposure alters the iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore, iMG significantly enhance the supernatant’s inflammatory secretome and increase retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated changes of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG are present. Mechanistically, ibuprofen targets the enzymes cyclooxygenase 1 and 2 (COX1/PTGS1 and COX2/PTGS2) simultaneously, from which iMG mainly express COX1. Selective COX1 blockage fails to restore the calcium peak amplitude upon POLY(I:C) stimulation, suggesting ibuprofen’s beneficial effect depends on the presence and interplay of COX1 and COX2. These findings underscore the importance of microglia in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.},
  author       = {Hübschmann, Verena and Korkut, Medina and Venturino, Alessandro and Maya-Arteaga, Juan Pablo and Siegert, Sandra},
  issn         = {1742-2094},
  journal      = {Journal of Neuroinflammation},
  number       = {1},
  publisher    = {Springer Nature},
  title        = {{Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids}},
  doi          = {10.1186/s12974-025-03366-x},
  volume       = {22},
  year         = {2025},
}

@phdthesis{20074,
  abstract     = {Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. 
In chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. 
In chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. 
In summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.},
  author       = {Hübschmann, Verena},
  isbn         = {978-3-99078-060-2},
  issn         = {2663-337X},
  pages        = {151},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Human microglia impact neuronal development in retinal organoids}},
  doi          = {10.15479/AT-ISTA-20074},
  year         = {2025},
}

@article{19372,
  abstract     = {We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field.},
  author       = {Brooks, Morris and Mitrouskas, David Johannes},
  issn         = {2690-1005},
  journal      = {Probability and Mathematical Physics},
  number       = {1},
  pages        = {281--325},
  publisher    = {Mathematical Sciences Publishers},
  title        = {{Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling}},
  doi          = {10.2140/pmp.2025.6.281},
  volume       = {6},
  year         = {2025},
}

@article{20342,
  abstract     = {Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata.},
  author       = {Boker, Udi and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E},
  issn         = {1860-5974},
  journal      = {Logical Methods in Computer Science},
  number       = {2},
  publisher    = {EPI Sciences},
  title        = {{Safety and liveness of quantitative properties and automata}},
  doi          = {10.46298/lmcs-21(2:2)2025},
  volume       = {21},
  year         = {2025},
}

@phdthesis{20147,
  abstract     = {Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.

In this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.


},
  author       = {Sarac, Naci E},
  issn         = {2663-337X},
  pages        = {149},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A monitoring-oriented theory and classification of quantitative specifications}},
  doi          = {10.15479/AT-ISTA-20147},
  year         = {2025},
}

@article{22579,
  abstract     = {Decades of research on the Mekong River basin have vastly expanded our knowledge of key hydrological and
ecological processes, in part thanks to the development of modelling tools. However, few of these models are
openly available to the research community or adhere to FAIR (Findable, Accessible, Interoperable, Reusable)
principles, particularly in the domain of hydrology, in turn limiting transparency, reproducibility, and broader
scientific engagement. Here, we address this gap and introduce VIC-Res Mekong, an open-source hydrologicalwater management model for the Mekong River basin. The model is implemented over a spatial domain
of ∼630,000 km2 and has a resolution of 0.0625 degrees. Water and energy budgets are simulated with
the Variable Infiltration Capacity (VIC) model, while streamflow routing is simulated with VIC-Res, which
explicitly accounts for the storage and release dynamics of reservoirs. This is of key importance for a basin
like the Mekong, where the active storage capacity of dams has increased from 20 km3 to nearly 80 km3 in the past fifteen years. To this purpose, VIC-Res Mekong integrates information from a database containing reservoir storage time series (inferred from satellite images) for 129 dams that accounts for more than 90% of total storage capacity. These data support both hindcast simulations and the derivation of reservoir operating rules, enabling a flexible and realistic representation of dam operations that allows to characterize in detail dam-induced hydrological alterations.},
  author       = {Eldardiry, Hisham and Mahto, Shanti Shwarup and Fatichi, Simone and Galelli, Stefano},
  issn         = {1873-6726},
  journal      = {Environmental Modelling & Software},
  keywords     = {VIC hydrologic model, Mekong river, Large-scale hydrology, Water resources management, Reservoir operations, Remote sensing},
  publisher    = {Elsevier},
  title        = {{VIC-Res Mekong: An open-source hydrological-water management model for the Mekong River basin}},
  doi          = {10.1016/j.envsoft.2025.106603},
  volume       = {193},
  year         = {2025},
}

@article{22586,
  abstract     = {Extreme rainfall events that break previous records are occurring more frequently worldwide, leading to severe flooding and infrastructure damage. Conventional flood design approaches, based on extreme value analysis (EVA) of limited historical data, often fail to anticipate such unprecedented extremes. Here, we present a stochastic approach that leverages the Advanced Weather Generator (AWE-GEN) to simulate a large ensemble of 100-year hourly rainfall time series, explicitly accounting for internal climate variability. By excluding the record-breaking event year during calibration, we assess the ability of our proposed method to reproduce unseen record-breaking events. We evaluated this approach using data from 2703 rain stations across nine countries. Our results show that the stochastic approach captures record-breaking events more reliably than EVA, achieving success rates exceeding 85% for 3–12-hour durations at a 100-year return period threshold. This framework provides a more robust way for estimating rainfall extremes and supports the design of resilient infrastructure under deep uncertainty.},
  author       = {Chen, Mengzhu and Mahto, Shanti Shwarup and He, Xiaogang and Jun, Changhyun and Paschalis, Athanasios and Peleg, Nadav and Mascaro, Giuseppe and Fatichi, Simone},
  issn         = {2948-2100},
  journal      = {npj Natural Hazards},
  publisher    = {Springer Nature},
  title        = {{Record-breaking rainfall: a stochastic approach for its prediction}},
  doi          = {10.1038/s44304-025-00148-6},
  volume       = {2},
  year         = {2025},
}

@article{19701,
  abstract     = {Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.},
  author       = {Tkačik, Gašper and Wolde, Pieter Rein Ten},
  issn         = {1936-1238},
  journal      = {Annual Review of Biophysics},
  pages        = {249--274},
  publisher    = {Annual Reviews},
  title        = {{Information processing in biochemical networks}},
  doi          = {10.1146/annurev-biophys-060524-102720},
  volume       = {54},
  year         = {2025},
}

@article{20048,
  abstract     = {During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.},
  author       = {Moriyama, Yuuta and Mitsui, Toshiyuki and Heisenberg, Carl-Philipp J},
  issn         = {1477-9129},
  journal      = {Development},
  number       = {12},
  publisher    = {Company of Biologists},
  title        = {{Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation}},
  doi          = {10.1242/dev.204261},
  volume       = {152},
  year         = {2025},
}

@article{21343,
  abstract     = {The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],
such that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.
Given a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all
quadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common
root in Fp. Using recent work of Landesman, an application to the average size of the odd part
of the class group of quadratic number fields is also given},
  author       = {Browning, Timothy D and Chan, Yik Tung},
  issn         = {2270-518X},
  journal      = {Journal de l'Ecole Polytechnique - Mathematiques},
  pages        = {1677--1691},
  publisher    = {Ecole Polytechnique},
  title        = {{Solubility of a resultant equation and applications}},
  doi          = {10.5802/jep.320},
  volume       = {12},
  year         = {2025},
}

@article{20249,
  abstract     = {We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces.},
  author       = {Browning, Timothy D and Wilsch, Florian Alexander},
  issn         = {1420-9020},
  journal      = {Selecta Mathematica New Series},
  number       = {4},
  publisher    = {Springer Nature},
  title        = {{Integral points on cubic surfaces: heuristics and numerics}},
  doi          = {10.1007/s00029-025-01074-1},
  volume       = {31},
  year         = {2025},
}