Research works

sc P rofiterole : Clustering of Single-Cell Proteomic Data Using Graph Contrastive Learning via Spectral Filters

Novel technologies for the acquisition of protein expression data at the single cell level are emerging rapidly. Although there exists a substantial body of computational algorithms and tools for the analysis of single cell gene expression (scRNAseq) data, tools for even basic ta...

Magnetic granular matter: A review of phenomena and modeling approaches

Abstract Magnetic granular matter extends classical granular physics through the introduction of tunable, long-range dipolar interactions. These interactions give rise to a wide range of collective phenomena, including field-aligned chain formation, enhanced cohesion, anisotropic...

Beam-offset thermoreflectance with Bayesian optimization to measure the anisotropic thermal properties of semiconductor superlattices

The directional nature of heat conduction in semiconductor superlattices—marked by significant differences between in-plane and cross-plane pathways—poses substantial challenges for precise thermal property assessment. Conventional frequency-domain thermoreflectance (FDTR) techni...

Influence of the inhalation route on tracheal flow structures in patient-specific airways using 3D PTV

The tracheal flow field shapes particle transport into the lower airways and thus influences both the spread of inhaled pathogens and the effectiveness of aerosol-based therapies. Identifying how different inhalation routes modify the flow field is therefore crucial for understan...

Remarks on non-invertible symmetries on a tensor product Hilbert space in 1+1 dimensions

We propose an index of non-invertible symmetry operators in 1+1 dimensions and discuss its relation to the realizability of non-invertible symmetries on the tensor product of finite dimensional on-site Hilbert spaces on the lattice. Our index generalizes the Gross-Nesme-Vogts-Wer...

Enhanced Lifespan Bounds for 1D Quasilinear Klein–Gordon Flows

Abstract In this article we consider one-dimensional scalar quasilinear Klein–Gordon equations with general nonlinearities, on both $${\mathbb {R}}$$ R and $${\mathbb {T}}$$ T . By employing a refined modified-energy framework of Ifrim and Tataru, we investigate long time lifespa...

An integrated spatial-legal diagnosis of governance barriers to green corridor implementation in China’s Gan River Basin

Fragmentation of urban habitats necessitates governance that spatially aligns ecological requirements with legal structures. This study conducts a systematic diagnostic review of governance blockages to the establishment of a green corridor in China’s rapidly urbanising Gan River...

Drought responses of a Norway spruce forest on drained peat soil: combining sap-flow sensors, eddy-covariance, meteorological, soil and UAV data

Abstract. The summer of 2021 brought a severe drought to southern Finland. We explored how a drained boreal peatland forest responds to drought by combining a wide range of in situ monitoring and Unmanned Aerial Vehicle (UAV) remote sensing. A dataset combining eddy-covariance (E...

Rheologically tuned diffusion modulates quorum sensing in Vibrio fischeri

Understanding how the physical properties of a fluid influence bacterial behavior is essential for explaining how microorganisms interact with their environment and with animal hosts. Here, we examine how changes in fluid viscosity and rheological properties affect the locomotion...

The influence of lakes and reservoirs on estimated flood peaks at hourly vs. daily timescale in the Alps

Abstract. Water bodies such as lakes and reservoirs can play a crucial role in reducing flood peaks both on daily and hourly timescales. While the effect of water bodies on flood peaks at different time resolutions has been demonstrated in the past, it remains unclear how they af...

A Bayesian prevalence incidence cure model for estimating survival using electronic health records with incomplete baseline diagnoses

Retrospective cohorts can be extracted from electronic health records (EHRs) to study prevalence, time until disease or event occurrence, and cure proportion in real-world scenarios. However, EHRs are collected for patient care rather than research, and thus typically have comple...

Recurrence lacunarity of spatial data

Abstract Quantifying the structure and heterogeneity of complex spatial patterns remains a key challenge in spatial data analysis. Recurrence plots (RPs) offer a powerful method for visualizing the recurrent spatial patterns in such data. To quantify the structure of spatial recu...

Deeply nonlinear magnon-photon hybrid excitation

We investigate the microwave-power dependence of magnon-photon coupling in a yttrium iron garnet-sphere/split-ring resonator hybrid system at room temperature and demonstrate that nonlinear spin-wave interactions suppress the coupling through power-induced dissipation of magnetos...

Transcriptional responses of Solanum lycopersicum to three distinct parasites reveal host hubs and networks underlying parasitic successes

Abstract Crops face attacks from a wide range of pathogens and pests that deploy various parasitic strategies. All aggressors must manipulate major plant functions, such as immune signaling, hormone pathways, metabolism, and development, to successfully establish themselves and c...

Identification of optimal ERA5 model level for wind resource assessments in mountainous terrain

Abstract. Accurate estimation of hub-height wind speed is crucial for wind resources assessment at prospective sites. Traditionally, long-term wind speed series are derived from short-term site observations combined with reanalysis products, most commonly the ERA5 single-level da...

Light absorption properties and composition of water-soluble brown carbon in North China Plain: implication for an enhancing role of nitrogenous organic compounds

Abstract. Brown carbon (BrC), an efficiently light-absorbing carbonaceous aerosol, exerts significant impacts on the global energy budget and regional climate, attracting growing scientific attention. To advance understanding of the spatial variability of atmospheric BrC and its...

Asymptotic enumeration of constrained bipartite, directed and oriented graphs by degree sequence

In the sufficiently sparse case, we find the probability that a uniformly random bipartite graph with given degree sequence contains no edge from a specified set of edges. This enables us to enumerate loop-free digraphs and oriented graphs with given in-degree and out-degree sequ...

SSCHA-based evolutionary crystal structure prediction at finite temperatures with account for quantum nuclear motion

Abstract Reliable crystal structure prediction (CSP) at finite temperatures, including quantum anharmonic effects, remains challenging but is particularly important for systems containing light atoms such as superconducting hydrides. Here, we integrate machine-learned interatomic...

Process bigraphs and the architecture of compositional systems biology

Building multiscale biological models requires the integration of independently developed submodels, which means moving shared variables between them and coordinating when each submodel runs. Existing tools typically address isolated biological mechanisms with specific numerical...

Tree Rearrangement Graphs Admit Paths of Decreasing Robinson-Foulds Distance

Tree rearrangements such as Nearest Neighbor Interchange (NNI) and Subtree Prune and Regraft (SPR) are commonly used to explore phylogenetic treespace. Computing distances based on them, however, is often intractable, so the efficiently computable Robinson-Foulds (RF) distance is...