@unpublished{21398,
  abstract     = {Seymour's decomposition theorem is a hallmark result in matroid theory presenting a structural characterization of the class of regular matroids. Formalization of matroid theory faces many challenges, most importantly that only a limited number of notions and results have been implemented so far. In this work, we formalize the proof of the forward (composition) direction of Seymour's theorem for regular matroids. To this end, we develop a library in Lean 4 that implements definitions and results about totally unimodular matrices, vector matroids, their standard representations, regular matroids, and 1-, 2-, and 3-sums of matrices and binary matroids given by their standard representations. Using this framework, we formally state Seymour's decomposition theorem and implement a formally verified proof of the composition direction in the setting where the matroids have finite rank and may have infinite ground sets.},
  author       = {Dvorak, Martin and Figueroa-Reid, Tristan and Hamadani, Rida and Hwang, Byung-Hak and Karunus, Evgenia and Kolmogorov, Vladimir and Meiburg, Alexander and Nelson, Alexander and Nelson, Peter and Sandey, Mark and Sergeev, Ivan},
  booktitle    = {arXiv},
  title        = {{Composition direction of Seymour's theorem for regular matroids — Formally verified}},
  doi          = {10.48550/arXiv.2509.20539},
  year         = {2025},
}

@unpublished{20286,
  abstract     = {Natural organisms utilize distributed actuation through their musculoskeletal
systems to adapt their gait for traversing diverse terrains or to morph their
bodies for varied tasks. A longstanding challenge in robotics is to emulate
this capability of natural organisms, which has motivated the development of
numerous soft robotic systems. However, such systems are generally optimized
for a single functionality, lack the ability to change form or function on
demand, or remain tethered to bulky control systems. To address these
limitations, we present a framework for designing and controlling robots that
utilize distributed actuation. We propose a novel building block that
integrates 3D-printed bones with liquid crystal elastomer (LCE) muscles as
lightweight actuators, enabling the modular assembly of musculoskeletal robots.
We developed LCE rods that contract in response to infrared radiation, thereby
providing localized, untethered control over the distributed skeletal network
and producing global deformations of the robot. To fully capitalize on the
extensive design space, we introduce two computational tools: one for
optimizing the robot's skeletal graph to achieve multiple target deformations,
and another for co-optimizing skeletal designs and control gaits to realize
desired locomotion. We validate our framework by constructing several robots
that demonstrate complex shape morphing, diverse control schemes, and
environmental adaptability. Our system integrates advances in modular material
building, untethered and distributed control, and computational design to
introduce a new generation of robots that brings us closer to the capabilities
of living organisms.},
  author       = {Bhargava, Manas and Hiraki, Takefumi and Strugaru, Irina-Malina and Zhang, Yuhan and Piovarci, Michael and Daraio, Chiara and Iwai, Daisuke and Bickel, Bernd},
  booktitle    = {arXiv},
  title        = {{Computational design and fabrication of modular robots with untethered control}},
  doi          = {10.48550/arXiv.2508.05410},
  year         = {2025},
}

@phdthesis{20371,
  abstract     = {Quantum mechanics reveals a world that defies classical determinism, where uncertainty, superposition, and fluctuations are fundamental aspects. Engineering devices that harness these quantum features requires not only precision, but also a deep understanding of how they interact with their surrounding environment. Superconducting circuits, which exploit
macroscopic quantum coherence in low-loss superconducting materials, provide a scalable platform for implementing such systems. Among the critical elements in these circuits, superinductors—high-impedance, dissipation-free inductive components—play a central role by suppressing charge fluctuations. They allow quantum states to be delocalized in phase space, protect qubits from environmental noise, and facilitate access to phenomena such as dual Josephson physics and ultra-strong coupling regimes. 
This thesis explores two complementary implementations of high-impedance circuits: geometric superinductors, demonstrating that high impedance can be achieved beyond kinetic inductance,
and Josephson junction chains, used to investigate both microwave mode properties and DC transport across the superconductor-to-insulator transition. 
Part I addresses geometric superinductors. Contrary to the common belief that high-impedance superconducting circuits require kinetic inductance, we demonstrate that purely geometric designs can achieve characteristic impedance exceeding the resistance quantum. By exploiting mutual coupling between adjacent turns, coil-based inductors achieve enhanced self-inductance, creating a reliable platform for qubits and resonators. Modeling, simulation, fabrication, and
characterization confirm that these elements behave as superinductor. With low loss, high linearity, and minimal stray capacitance, these elements are reproducible, free of uncontrolled tunneling events, and capable of strong magnetic coupling. This establishes geometric superinductors as robust, single-wave-function superconducting devices suitable for hardware protected qubits and hybrid systems.
Part II presents classical numerical simulations of a Quantum Phase Slip circuit to study dual Shapiro steps. The circuit consists of an ideal Quantum Phase Slip element embedded in a resistive-inductive environment with a parasitic capacitance.
Part III extends the investigation of high characteristic-impedance circuit elements to one-dimensional Josephson junction chains, which act as a quantum simulator for many-body physics and the superconductor–insulator transition. Different devices are realized on both sides of the DC phase transition, showing either a supercurrent branch or Coulomb blockade at zero bias. The effect of the crossover on microwave modes, however, remains insufficiently investigated. Studying these modes provides insight into the interplay between disorder and phase-slip events. Small differences in circuit component sizes determine which side of the transition a device falls on, making these results relevant not only for fundamental understanding but also for the design of quantum devices, emphasizing the crucial role of the
electromagnetic environment in stabilizing and controlling fragile quantum states. 
Together, these results illustrate how carefully engineered high characteristic-impedance elements provide a link between macroscopic circuits and the inherently uncertain quantum world, enabling experiments that probe, control, and ultimately exploit quantum fluctuations for applications in quantum information, metrology, solid state physics and beyond.

},
  author       = {Trioni, Andrea},
  isbn         = {978-3-99078-067-1},
  issn         = {2663-337X},
  pages        = {202},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains}},
  doi          = {10.15479/AT-ISTA-20371},
  year         = {2025},
}

@inproceedings{20008,
  abstract     = {We study the complexity of a class of promise graph homomorphism problems. For a fixed graph H, the H-colouring problem is to decide whether a given graph has a homomorphism to H. By a result of Hell and Nešetřil, this problem is NP-hard for any non-bipartite loop-less graph H. Brakensiek and Guruswami [SODA 2018] conjectured the hardness extends to promise graph homomorphism problems as follows: fix a pair of non-bipartite loop-less graphs G, H such that there is a homomorphism from G to H, it is NP-hard to distinguish between graphs that are G-colourable and those that are not H-colourable. We confirm this conjecture in the cases when both G and H are 4-colourable. This is a common generalisation of previous results of Khanna, Linial, and Safra [Comb. 20(3): 393-415 (2000)] and of Krokhin and Opršal [FOCS 2019]. The result is obtained by combining the algebraic approach to promise constraint satisfaction with methods of topological combinatorics and equivariant obstruction theory.},
  author       = {Avvakumov, Sergey and Filakovský, Marek and Opršal, Jakub and Tasinato, Gianluca and Wagner, Uli},
  booktitle    = {Proceedings of the 57th Annual ACM Symposium on Theory of Computing},
  isbn         = {9798400715105},
  issn         = {0737-8017},
  location     = {Prague, Czechia},
  pages        = {72--83},
  publisher    = {Association for Computing Machinery},
  title        = {{Hardness of 4-colouring G-colourable graphs}},
  doi          = {10.1145/3717823.3718154},
  year         = {2025},
}

@article{18112,
  abstract     = {It is conjectured that the only integrable metrics on the two-dimensional torus are Liouville metrics. In this paper, we study a deformative version of this conjecture: we consider integrable deformations of a non-flat Liouville metric in a conformal class and show that for a fairly large class of such deformations, the deformed metric is again Liouville. The principal idea of the argument is that the preservation of rational invariant tori in the foliation of the phase space forces a linear combination on the Fourier coefficients of the deformation to vanish. Showing that the resulting linear system is non-degenerate will then yield the claim. Since our method of proof immediately carries over to higher dimensional tori, we obtain analogous statements in this more general case. To put our results in perspective, we review existing results about integrable metrics on the torus.},
  author       = {Henheik, Sven Joscha},
  issn         = {1469-4417},
  journal      = {Ergodic Theory and Dynamical Systems},
  number       = {2},
  pages        = {467--503},
  publisher    = {Cambridge University Press},
  title        = {{Deformational rigidity of integrable metrics on the torus}},
  doi          = {10.1017/etds.2024.48},
  volume       = {45},
  year         = {2025},
}

@article{19001,
  abstract     = {We consider two Hamiltonians that are close to each other, H1≈H2, and analyze the time-decay of the corresponding Loschmidt echo M(t):=|⟨ψ0,eitH2e−itH1ψ0⟩|2 that expresses the effect of an imperfect time reversal on the initial state ψ0. Our model Hamiltonians are deformed Wigner matrices that do not share a common eigenbasis. The main tools for our results are two-resolvent laws for such H1 and H2.},
  author       = {Erdös, László and Henheik, Sven Joscha and Kolupaiev, Oleksii},
  issn         = {1573-0530},
  journal      = {Letters in Mathematical Physics},
  publisher    = {Springer Nature},
  title        = {{Loschmidt echo for deformed Wigner matrices}},
  doi          = {10.1007/s11005-025-01904-5},
  volume       = {115},
  year         = {2025},
}

@article{19548,
  abstract     = {We consider the BCS energy gap „.T / (essentially given by „.T /  .T; p/,
the BCS order parameter) at all temperatures 0  T  Tc up to the critical one, Tc, and show
that, in the limit of weak coupling, the ratio „.T /=Tc is given by a universal function of the relative temperature T =Tc. On the one hand, this recovers a recent result by Langmann and Triola
[Phys. Rev. B 108 (2023), no. 10, article no. 104503] on three-dimensional s-wave superconductors for temperatures bounded uniformly away from Tc. On the other hand, our result lifts these
restrictions, as we consider arbitrary spatial dimensions d 2 ¹1; 2; 3º, discuss superconductors
with non-zero angular momentum (primarily in two dimensions), and treat the perhaps physically most interesting (due to the occurrence of the superconducting phase transition) regime of
temperatures close to Tc.

​
 .},
  author       = {Henheik, Sven Joscha and Lauritsen, Asbjørn Bækgaard},
  issn         = {1664-0403},
  journal      = {Journal of Spectral Theory},
  number       = {1},
  pages        = {305–352},
  publisher    = {EMS Press},
  title        = {{Universal behavior of the BCS energy gap}},
  doi          = {10.4171/JST/540},
  volume       = {15},
  year         = {2025},
}

@unpublished{19552,
  abstract     = {Particle creation terms in quantum Hamiltonians are usually ultraviolet
divergent and thus mathematically ill defined. A rather novel way of solving
this problem is based on imposing so-called interior-boundary conditions on the
wave function. Previous papers showed that this approach works in the
non-relativistic regime, but particle creation is mostly relevant in the
relativistic case after all. In flat relativistic space-time (that is,
neglecting gravity), the approach was previously found to work only for certain
somewhat artificial cases. Here, as a way of taking gravity into account, we
consider curved space-time, specifically the super-critical
Reissner-Nordstr\"om space-time, which features a naked timelike singularity.
We find that the interior-boundary approach works fully in this setting; in
particular, we prove rigorously the existence of well-defined, self-adjoint
Hamiltonians with particle creation at the singularity, based on
interior-boundary conditions. We also non-rigorously analyze the asymptotic
behavior of the Bohmian trajectories and construct the corresponding Bohm-Bell
process of particle creation, motion, and annihilation. The upshot is that in
quantum physics, a naked space-time singularity need not lead to a breakdown of
physical laws, but on the contrary allows for boundary conditions governing
what comes out of the singularity and thereby removing the ultraviolet
divergence.},
  author       = {Henheik, Sven Joscha and Poudyal, Bipul and Tumulka, Roderich},
  booktitle    = {arXiv},
  title        = {{How a space-time singularity helps remove the ultraviolet divergence problem}},
  doi          = {10.48550/arXiv.2409.00677},
  year         = {2025},
}

@article{22450,
  abstract     = {Background: Residential exposure to trees has been associated with reduced mortality risks. We hypothesise that in addition to tree canopy cover, tree canopy configuration also plays a role in exposure–mortality relationships. As there is limited evidence on this hypothesis, especially longitudinal evidence, we performed a nationwide study to investigate the residential tree canopy configuration–mortality associations in the Swiss population.
Methods: In this longitudinal study, the tree canopy cover and configuration metrics within 500 m of individuals’ residences were quantified using high-resolution tree canopy data (1 × 1 m) from 2010 to 2019. We developed single-exposure and multi-exposure time-varying Cox regression models to estimate the associations between the different exposure metrics and natural-cause and cause-specific mortality in Swiss adults (aged from 20 years to 90 years). Mortality and census data were taken from the Swiss National Cohort (SNC). We estimated the hazard ratios (HRs) and corresponding 95% CIs per IQR increase in the metrics adjusting for personal sociodemographic and contextual covariates. We also explored the effect modification by tree canopy cover, PM10, air temperature, urbanisation level, age, sex, and area-based local socioeconomic position.
Findings: Our analyses included 6 215 073 individuals from the SNC between 2010 and 2019. In the fully adjusted single-exposure models, we observed protective associations between natural-cause mortality risk and tree canopy cover (IQR 12·4%, HR 0·979 [95% CI 0·975–0·983]) and configuration metrics describing the aggregation (6·3%, 0·831 [0·823–0·840]), and connectedness (2·9%, 0·946 [0·938–0·953]); and detrimental associations with two metrics describing the fragmentation (211 patches per 100 ha, 1·073 [1·066–1·080]) and shape complexity (1·9, 1·094 [1·089–1·100]) of patches. The associations were generally preserved with other common causes of death. According to the multi-exposure models, the HR (95% CI) for the combination of one IQR decrease in aggregation and one IQR increase in fragmentation and shape complexity was 1·366 (1·343–1·390). Analyses on modification effects suggested a stronger association in people living in areas with a higher level of tree canopy cover, PM10 concentration, air temperature, and urbanisation level.
Interpretation: Aggregated, connected, and less fragmented forested greenspaces might offer stronger health benefits than isolated, fragmented ones, but are difficult to implement in cities. Our study provided valuable insights into optimising forested greenspaces and highlighted future directions for the planning and management of urban forests towards healthy and green cities.},
  author       = {Chi, Dengkai and Manoli, Gabriele and Lin, Brenda and Aerts, Raf and Yang, Jun and Hahs, Amy and Richards, Daniel and Meili, Naika and Zhu, Yue and Qiu, Yeshan and Wang, Jing and Burlando, Paolo and Fatichi, Simone and Tan, Puay Yok},
  issn         = {2542-5196},
  journal      = {The Lancet Planetary Health},
  number       = {3},
  pages        = {e186--e195},
  publisher    = {Elsevier},
  title        = {{Residential tree canopy configuration and mortality in 6 million Swiss adults: A longitudinal study}},
  doi          = {10.1016/s2542-5196(25)00022-1},
  volume       = {9},
  year         = {2025},
}

@article{22469,
  abstract     = {Accurate flood simulation remains a significant challenge in many flood-prone regions, particularly in developing countries and urban areas, where the availability of high-resolution topographic data is especially limited. While publicly available digital elevation model (DEM) datasets are increasingly accessible, their spatial resolution is often insufficient for reflecting fine-scaled elevation details, which hinders the ability to simulate pluvial floods in built environments. To address this issue, we implemented a deep-learning-based method, which efficiently enhances the spatial resolution of DEM data, and quantified the effect of the improved DEM on flood simulation. The method employs a tailored multi-source input module, enabling it to effectively integrate and learn from diverse data sources. By utilising publicly accessible global datasets, such as low-resolution DEM datasets (i.e. 30 m Shuttle Radar Topography Mission, SRTM) in conjunction with high-resolution multispectral imagery (e.g. Sentinel-2A), our approach allows us to produce a super-resolution DEM, which exhibits superior performance compared to conventional methods in reconstructing 10 m DEM data based on 30 m DEM data and 10 m multispectral satellite images. We evaluated the performance of the super-resolution DEM in flood simulations. Compared to conventional methods (e.g. bicubic interpolation), the simulation results demonstrated that our approach significantly improved the accuracy of flood simulations, with a reduction in the mean absolute error of floodwater depth of about 13.1 % and an increase in the intersection over union (IoU) for inundation area predictions of about 46 %. Accordingly, this study underscores the practical value of machine learning techniques that leverage publicly available global datasets to generate DEMs that allow for the enhancement of flood simulations.},
  author       = {Zhu, Yue and Burlando, Paolo and Tan, Puay Yok and Geiß, Christian and Fatichi, Simone},
  issn         = {1684-9981},
  journal      = {Natural Hazards and Earth System Sciences},
  number       = {7},
  pages        = {2271--2286},
  publisher    = {Copernicus Publications},
  title        = {{Improving pluvial flood simulations with a multi-source digital elevation model super-resolution method}},
  doi          = {10.5194/nhess-25-2271-2025},
  volume       = {25},
  year         = {2025},
}

@article{22463,
  abstract     = {Glacier retreat as a consequence of climate change creates new ice-free terrain and soil development that prompt plant colonization and ecological succession. These processes impact terrestrial ecosystems with profound ecological and societal consequences. However, quantification of how the carbon cycle evolves in deglaciated areas in response to these processes remains limited. We examined the impacts of forest expansion and soil development on the carbon cycle under climate change in a deglaciated area in the Swiss Alps. Using the mechanistic ecohydrological T&C model, we computed the changes in vegetation, soil, and carbon from 1981 to 2099 under climate change, revealing complex carbon cycle responses in deglaciating ecosystems. Vegetation growth, soil organic matter, and plant nutrient uptake are projected to increase by mid-century and then stabilize, indicating that plant growth is relatively limited by nutrient availability. The amount of carbon stored in plant biomass will increase toward the end of the century at a faster rate than that of carbon stored in soil and litter. The carbon cycle is projected to continue its current accelerating trend characterized by enhanced vegetation photosynthesis, increased plant and soil respiration, and higher net ecosystem production (NEP) by mid-century. Alpine ecosystems have already been serving as carbon sinks and have the potential to increase their carbon sink capacity, but at varying rates depending on how climate will evolve: NEP will stabilize around 24 gC m^−2 y^−1 in RCP4.5 or might elevate to 55 gC m^−2 y^−1 by end-century in RCP8.5. Even under the most extreme scenario, this increase in stored carbon in the proglacial areas of the Swiss Alps is still a drop in the ocean, as it represents only 0.9% of overall Swiss carbon emissions, thus highlighting the need for additional carbon management and mitigation efforts.},
  author       = {Jiang, Fuxiao and Fatichi, Simone and Losapio, Gianalberto and Peleg, Nadav},
  issn         = {1873-2240},
  journal      = {Agricultural and Forest Meteorology},
  publisher    = {Elsevier},
  title        = {{Future glacier retreat and forest expansion in the Swiss Alps provide limited benefits for carbon sinks}},
  doi          = {10.1016/j.agrformet.2025.110682},
  volume       = {372},
  year         = {2025},
}

@article{22462,
  abstract     = {Enhanced rock weathering (ERW) is an emerging carbon dioxide removal (CDR) strategy that can support net-zero emission targets. However, current ERW modelling efforts rely on assumptions that introduce substantial variation in CDR estimates across varying ecosystems and hydroclimatic conditions. They typically ignore or oversimplify plant–soil interactions and high-frequency hydrological dynamics, obscuring short-term weathering responses and biotic feedbacks to soil moisture dynamics. Here, we introduce an integrated, process-based modelling framework, T&C-SMEW, which represents ecohydrological and ERW dynamics, along with microbially explicit biogeochemical processes. We compared framework simulations against a controlled mesocosm experiment and long-term field observations, demonstrating its ability to reproduce feedstock cation release, soil pH dynamics, gross primary production, and CO2 fluxes. T&C-SMEW reveals hydrological constraints and vegetation effects on ERW-mediated CDR by quantifying impacts on ecosystem respiration, net ecosystem exchange, and alkalinity export, emphasising the importance of ecohydrological modelling for ecosystem-level CDR estimation. These advances provide a modelling framework for identifying optimal deployment scenarios to establish ERW as a viable and operationally feasible CDR approach.},
  author       = {Zhang, Ziyan and Jones, Gregory and Calabrese, Salvatore and Bertagni, Matteo and Fatichi, Simone and Waring, Bonnie and Paschalis, Athanasios},
  issn         = {1365-2486},
  journal      = {Global Change Biology},
  number       = {12},
  publisher    = {Wiley},
  title        = {{An integrated modelling framework to determine terrestrial carbon dioxide removal via enhanced rock weathering}},
  doi          = {10.1111/gcb.70650},
  volume       = {31},
  year         = {2025},
}

@article{22483,
  abstract     = {Agrivoltaic systems are characterized by the co‐existence of photovoltaic panels on agricultural land, allowing simultaneous solar energy and food production without need for further land. Agrivoltaic installations alter the local microclimatic conditions of the land surface, impacting the performance of the agricultural systems embedded in them. In this study we develop an ecohydrological modeling framework combining a module that simulates changes in micrometeorology due to photovoltaic panel installations with a state‐of‐the‐art model that resolves land surface water, energy, and vegetation dynamics (i.e., the terrestrial biosphere model T&C). We demonstrate that the modeling framework is capable of reproducing grassland dynamics across a broad range of climates and agrivoltaic architectures. With the use of the model we evaluated grassland performance across the Mediterranean for two most commonly used architectures, namely mixed mounted solar panels and rotating solar tracking panels. We found that C3 grassland yields can be significantly enhanced only in climates where annual potential evapotranspiration exceeds annual rainfall. Changes in grassland productivity were attributed primarily to changes in the light environment at the land surface, with changes in surface aerodynamic roughness and rainfall redistribution due to drainage on panels playing a smaller negative role of comparable magnitudes.},
  author       = {Paschalis, Athanasios and Bonetti, Sara and Fatichi, Simone},
  issn         = {2328-4277},
  journal      = {Earth's Future},
  number       = {3},
  publisher    = {American Geophysical Union},
  title        = {{Controls of ecohydrological grassland dynamics in agrivoltaic systems}},
  doi          = {10.1029/2024ef005183},
  volume       = {13},
  year         = {2025},
}

@article{22431,
  abstract     = {The snow and glaciers of the Peruvian Andes provide vital water supplies in a region facing water scarcity and substantial glacier change. However, there remains a lack of understanding of snow processes and quantification of the contribution of melt to runoff. Here we apply a distributed glacio-hydrological model over the Rio Santa basin to disentangle the role of the cryosphere in the Andean water cycle. Only at the highest elevations (>5000 m a.s.l.) is the snow cover continuous; at lower elevations, the snowpack is thin and ephemeral, with rapid cycles of snowfall and melt. Due to the large catchment area affected by ephemeral snow, its contribution to catchment inputs is substantial (23% and 38% in the wet and dry season, respectively). Ice melt is crucial in the mid-dry season (up to 44% of inputs). Our results improve estimates of water fluxes and call for further process-based modelling across the Andes.},
  author       = {Fyffe, Catriona L. and Potter, Emily and Miles, Evan and Shaw, Thomas E. and McCarthy, Michael and Orr, Andrew and Loarte, Edwin and Medina, Katy and Fatichi, Simone and Hellström, Rob and Baraer, Michel and Mateo, Emilio and Cochachin, Alejo and Westoby, Matthew and Pellicciotti, Francesca},
  issn         = {2662-4435},
  journal      = {Communications Earth & Environment},
  publisher    = {Springer Nature},
  title        = {{Thin and ephemeral snow shapes melt and runoff dynamics in the Peruvian Andes}},
  doi          = {10.1038/s43247-025-02379-x},
  volume       = {6},
  year         = {2025},
}

@article{22438,
  abstract     = {The topography of a landscape regulates the spatial distribution of water and energy fluxes, which are main drivers of vegetation and soil carbon and nutrient dynamics. Despite the recognized role of topography in mediating such processes, quantifying and predicting the spatial distribution of carbon and nutrient fluxes and stocks in highly heterogeneous landscapes remains challenging. The main limitations stem from the prevalence of largely decoupled modeling approaches which fail to concurrently account for ecohydrological and biogeochemical processes as well as the lack of adequate frameworks describing the links among topography, water and energy balances, and soil biogeochemical dynamics. Here, we extend the capabilities of the mechanistic ecohydrological model Tethys-Chloris-Biogeochemistry (T&C-BG) by including a soil carbon and nutrient routing module in the distributed model version. The newly developed T&C-BG-2D model is validated against long-term hydrological and biogeochemical measurements from the Hafren catchment in Wales (UK) and the Erlenbach catchment in the Swiss pre-Alps. The model successfully captures carbon and nutrient concentrations and dynamics in these catchments, with relative differences between simulated and observed median values of between −4% and −0.3% for dissolved organic carbon, and between 1% and 20% for ammonia. A sensitivity analysis in the Erlenbach basin suggests that elevation explains over 80% of the observed spatial patterns, followed by topographic wetness index (12.6%), aspect (2.9%), and curvature (2.1%). These findings underscore topography's critical role in shaping water, carbon, and nutrient dynamics, which cannot be reflected in plot-scale simulations neglecting spatial interactions and topographic effects.},
  author       = {Lian, Taiqi and Fatichi, Simone and Stähli, Manfred and Bonetti, Sara},
  issn         = {1944-7973},
  journal      = {Water Resources Research},
  number       = {10},
  publisher    = {American Geophysical Union},
  title        = {{Assessing spatial patterns of carbon and nutrient dynamics in catchments of complex topography}},
  doi          = {10.1029/2025wr040260},
  volume       = {61},
  year         = {2025},
}

@article{19785,
  abstract     = {We consider a family of totally asymmetric simple exclusion processes (TASEPs), consisting of particles on a lattice that require binding by a “token” in various physical configurations to advance over the lattice. Using a combination of theory and simulations, we address the following questions: (i) How does token binding kinetics affect the current-density relation on the lattice? (ii) How does this current-density relation depend on the scarcity of tokens? (iii) How do tokens propagate the effects of the locally imposed disorder (such as a slow site) over the entire lattice? (iv) How does a shared pool of tokens couple concurrent TASEPs running on multiple lattices? and (v) How do our results translate to TASEPs with open boundaries that exchange particles with the reservoir? Since real particle motion (including in biological systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations.},
  author       = {Kavcic, Bor and Tkačik, Gašper},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Token-driven totally asymmetric simple exclusion processes}},
  doi          = {10.1103/physreve.111.054122},
  volume       = {111},
  year         = {2025},
}

@misc{20641,
  abstract     = {Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. },
  author       = {Becker, Lea Marie and Schanda, Paul},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes"}},
  doi          = {10.15479/AT-ISTA-20641},
  year         = {2025},
}

@article{18820,
  abstract     = {Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy.},
  author       = {Wild, Romina and Wodaczek, Felix and Del Tatto, Vittorio and Cheng, Bingqing and Laio, Alessandro},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance}},
  doi          = {10.1038/s41467-024-55449-7},
  volume       = {16},
  year         = {2025},
}

@article{20926,
  abstract     = {Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which infers electrostatic interactions, polarization, and Born effective charges (BECs), just by learning from energy and force training data. Here, we present LES as a standalone library, compatible with any short-range MLIP, and demonstrate its integration with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark LES-enhanced models on distinct systems, including bulk water, polar dipeptides, and gold dimer adsorption on defective substrates, and show that LES not only captures correct electrostatics but also improves accuracy. Additionally, we scale LES to large and chemically diverse data by training MACELES-OFF on the SPICE set containing molecules and clusters, making a universal MLIP with electrostatics for organic systems, including biomolecules. MACELES-OFF is more accurate than its short-range counterpart (MACE-OFF) trained on the same data set, predicts dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling efficient long-range electrostatics without directly training on electrical properties, LES paves the way for electrostatic foundation MLIPs.},
  author       = {Kim, Dongjin and Wang, Xiaoyu and Vargas, Santiago and Zhong, Peichen and King, Daniel S. and Inizan, Theo Jaffrelot and Cheng, Bingqing},
  issn         = {1549-9626},
  journal      = {Journal of Chemical Theory and Computation},
  number       = {24},
  pages        = {12709--12724},
  publisher    = {American Chemical Society},
  title        = {{A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials}},
  doi          = {10.1021/acs.jctc.5c01400},
  volume       = {21},
  year         = {2025},
}

@article{20990,
  abstract     = {Modeling the response of material and chemical systems to electric fields remains a longstanding challenge. Machine learning interatomic potentials (MLIPs) offer an efficient and scalable alternative to quantum mechanical methods, but do not by themselves incorporate electrical response. Here, we show that polarization and Born effective charge (BEC) tensors can be directly extracted from long-range MLIPs within the Latent Ewald Summation (LES) framework, solely by learning from energy and force data. Using this approach, we predict the infrared spectra of bulk water under zero or finite external electric fields, ionic conductivities of high-pressure superionic ice, and the phase transition and hysteresis in ferroelectric PbTiO3 perovskite. This work thus extends the capability of MLIPs to predict electrical response –without training on charges or polarization or BECs– and enables accurate modeling of electric-field-driven processes in diverse systems at scale.},
  author       = {Zhong, Peichen and Kim, Dongjin and King, Daniel S. and Cheng, Bingqing},
  issn         = {2057-3960},
  journal      = {npj Computational Materials},
  publisher    = {Springer Nature},
  title        = {{Machine learning interatomic potential can infer electrical response}},
  doi          = {10.1038/s41524-025-01911-z},
  volume       = {11},
  year         = {2025},
}