Saturn's moon Titan is a prime destination for investigating prebiotic chemistry beyond Earth, particularly at impact crater sites where transient liquid water may have enabled aqueous reactions between organic molecules. Selk crater represents one such environment and is a primary target of NASA's Dragonfly mission. Here, we present a thermodynamic assessment of nucleobases, ribose, and fatty acids formed from simple atmospheric precursors (HCN and C2H2) within a Selk-sized aqueous melt pool across varying ammonia (NH3) abundances. We find that ammonia acts as a chemical gatekeeper for molecular accessibility. In NH3-free systems, accessibility is restricted to adenine and butanoic acid. Once >=1% NH3 is introduced, all investigated molecular classes become thermodynamically accessible. Distinct molecular classes have different NH3 sensitivities: nucleobases, ribose, and C2-C6 fatty acids yield peaks at 1% NH3, and C7-C12 fatty acids yield peaks at 2% NH3. The modeled preference for pyrimidines vs. purines and monotonic decline of fatty acid abundance with chain length qualitatively mirror patterns observed in carbonaceous meteorites and returned asteroid samples. We show how molecular distributions and cross-class correlations may provide indirect constraints on Selk's past aqueous environment, help constrain past ammonia availability, and distinguish abiotic production from potential anomalies. By coupling thermodynamic predictions with an assessment of Dragonfly's mass spectrometer (DraMS) capabilities, we posit concrete, testable predictions for evaluating Selk's prebiotic potential in situ.

Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon a small perturbation. While such phase transitions have often been proposed in biology, connecting observed behavior to the underlying physics has remained challenging. We show how phase transitions naturally arise in microbial population dynamics and highlight their connection with genealogies. We rigorously demonstrate the existence of a first-order phase transition in a model of bacterial plasmid engineering and find a strict lower bound on the number of plasmids that can be stably maintained in a population.

Integrated information theory (IIT) starts from the existence of consciousness and characterizes its essential properties: every experience is intrinsic, specific, unitary, definite, and structured. IIT then formulates existence and its essential properties operationally in terms of cause-effect power of a substrate of units. Here we address IIT's operational requirements for existence by considering that, to have cause-effect power, to have it intrinsically, and to have it specifically, substrate units in their actual state must both (i) ensure the intrinsic availability of a repertoire of cause-effect states, and (ii) increase the probability of a specific cause-effect state. We showed previously that requirement (ii) can be assessed by the intrinsic difference of a state's probability from maximal differentiation. Here we show that requirement (i) can be assessed by the intrinsic difference from maximal specification. These points and their consequences for integrated information are illustrated using simple systems of micro units. When applied to macro units and systems of macro units such as neural systems, a tradeoff between differentiation and specification is a necessary condition for intrinsic existence, i.e., for consciousness.

Eukaryotic cells generally sense chemical gradients using the binding of chemical ligands to membrane receptors. In order to perform chemotaxis effectively in different environments, cells need to adapt to different concentrations. We present a model of gradient sensing where the affinity of receptor-ligand binding is increased when a protein binds to the receptor's cytosolic side. This interior protein (allosteric factor) alters the sensitivity of the cell, allowing the cell to adapt to different ligand concentrations. We propose a reaction scheme where the cell alters the allosteric factor's availability to adapt the average fraction of bound receptors to 1/2. We calculate bounds on the chemotactic accuracy of the cell, and find that the cell can reach near-optimal chemotaxis over a broad range of concentrations. We find that the accuracy of chemotaxis depends strongly on the diffusion of the allosteric compound relative to other reaction rates. From this, we also find a trade-off between adaptation time and gradient sensing accuracy.

High-throughput biological imaging is often constrained by a trade-off between acquisition speed and image quality. Fast imaging modalities, such as wide-field fluorescence microscopy, enable large-scale data acquisition but suffer from reduced contrast and resolution, whereas high-resolution techniques, including confocal microscopy or single-molecule localization microscopy-based super-resolution techniques, provide superior image quality at the cost of throughput and instrument time. Here, we present a deep learning-based approach for modality transfer across independent microscopes, enabling the transformation of low-quality images acquired on fast systems into high-quality representations comparable to those obtained using advanced imaging platforms. To achieve this, we employ a generative adversarial network (GAN)-based model trained on paired datasets acquired on physically separate wide-field and confocal microscopes, demonstrating that image quality can be reliably transferred between independent instruments. Quantitative evaluation shows substantial improvement in structural similarity and signal fidelity, with median SSIM and PSNR of 0.94 and 31.87, respectively, compared to 0.83 and 21.48 for the original wide-field images. These results indicate that key structural features can be recovered with high accuracy. Importantly, this approach enables a workflow in which high-throughput imaging can be performed on fast, accessible microscopy systems while preserving the ability to computationally recover high-quality structural information. High-resolution microscopy can then be reserved for targeted validation, reducing acquisition time and improving overall experimental efficiency. Together, our results establish deep learning-enabled modality transfer as a practical strategy for bridging independent microscopy systems and supporting scalable, high-content imaging workflows.

Experimental evidence indicates that intracellular chloride concentration regulates the excitation and inhibition (EI) balance, yet the mechanisms by which activity-dependent chloride dynamics drive seizure evolution and stage transitions remain unclear. We present a conductance-based neuronal network in which EI balance emerges from chloride homeostasis via channel-mediated influx and transporter-mediated extrusion. We show that the fraction of inhibitory synaptic conductance contributing to channel-mediated influx acts as a control parameter that organizes seizure dynamics into distinct stages,pre-ictal, ictal-tonic, and ictal-clonic,distinguished by characteristic amplitude and frequency signatures. Decreasing this fraction shortens ictal activity and suppresses seizure initiation, whereas high fraction promotes the emergence of ictal-tonic and ictal-clonic stages and spiral-wave dynamics, rendering seizure dynamics largely insensitive to inhibition. At intermediate values, seizures bypass the ictal-tonic stage and emerge directly as the icta,clonic stage. Moreover, joint variation of fractions with synaptic strengths reveals that recurrent excitation expands the tonic-clonic seizure, while recurrent inhibition prolongs pre-ictal states and suppresses ictal-clonic activity.

Biochemical signalling cascades transduce extracellular stimuli into cellular responses through sequences of discrete, node-to-node activations. While signal fidelity depends critically on local interaction kinetics, the mechanisms governing information propagation in realistic, highly variable kinetic contexts remain poorly understood. In this paper, we develop a mathematical framework for travelling waves in canonical feed-forward pathways governed by nonlinear Michaelis-Menten-type kinetics. For uniform pathways, we characterise the complete steady-state landscape and demonstrate that activation bias (the contribution of the binary states of each node to downstream activation) between connected nodes acts as a key bifurcation parameter dictating wave existence. Extending this framework to heterogeneous networks, we show how parameter gradients and random kinetic variations distort wavefronts and induce heavy fluctuations in propagation speed. To recover predictable signal transmission, we introduce a novel reciprocal-velocity spatial rescaling technique. We demonstrate that this coordinate transformation inherently absorbs local kinetic variations, effectively smoothing wave velocities and preserving wavefront profiles without requiring bespoke parameter tuning or continuous limits. Finally, by testing the framework's limits against extreme parameter variability, we reveal how severe kinetic bottlenecks lead to functional pathway fragmentation, offering a mathematically justified basis for rational model reduction in complex biochemical networks.

We develop a kinetic theory of cohesin-driven loop extrusion on a disordered chromatin track with transient barriers. In the stationary state, the mean loop size is shown to obey a universal law determined by the bare processivity and a renormalized obstacle density. Beyond the mean, one-sided extrusion always yields a single-exponential loop-length distribution, whereas two-sided extrusion produces a finite sum of exponential modes and, generically, a peaked distribution. Experimental CTCF-anchored loop statistics exhibit such a peak, thereby providing a direct discriminator of extrusion symmetry. The theory therefore establishes a unified framework for disorder-limited loop extrusion and supports a scenario in which both cohesin arms actively operate in living cells.

Motivation: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce. Results: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors. Availability: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.

Detachment and fracture are central to many tissue-level processes, but they are challenging to simulate with Voronoi-type models that typically assume a confluent tissue. Here we analyze the finite Voronoi model, a nonconfluent extension of conventional Voronoi models, in which cell boundaries are composed of straight Voronoi edges and circular arcs of fixed radius $\ell$. When the line tension on cell-medium interfaces exceeds the tension on cell-cell contacts, we find that the model exhibits a strong time-step dependence in the fracture timescale of initially intact active clusters: decreasing $Δt$ can unphysically suppress cluster rupture events. We trace this behavior to a divergence of detachment forces in the finite Voronoi model and introduce a simple regularization. Finally, we calibrate the near-detachment mechanics against a deformable polygon model and examine how key physical parameters control the tissue fracture timescale under two different calibration strategies. Our results show that, for studies focused on fracture or intercellular adhesion in nonconfluent monolayers, a physically motivated calibration of near-detachment mechanics in the finite Voronoi model is essential.

Biological agents navigate complex environments by combining long-term memory of successful actions with short-term suppression of recently visited locations-a capability that remains difficult to replicate in artificial systems, especially under partial observability. Inspired by the complementary timescales of neural and astrocytic dynamics, we introduce a spiking neuron-astrocyte network (SNAN) where spike-timing-dependent plasticity (STDP) reinforces successful action sequences on a distant time scale, while astrocytic calcium transients suppress recently visited states on a short-term time scale, effectively blocking locations already explored. This dual-timescale memory mechanism biases the agent toward unexplored regions, accelerating goal finding without requiring explicit global statistics. We show that in grid-world navigation tasks with extreme partial observability, SNAN reduces median path length by up to sixfold and drastically improves goal completion rates compared to baseline agents. The astrocytic modulation inherently mitigates the exploration-exploitation trade-off as an emergent consequence of local state suppression. This kind of local sensory data modulation can be considered as a new type of working memory referred to as a "Topological-Context Memory". To validate hardware feasibility using neuromorphic approaches, we map STDP to a memristive VTEAM model and implement a subset of the network on a crossbar array, achieving order-of-magnitude gains in speed per area and energy per decision over CPU implementations. Our results establish astrocyte-inspired dual-timescale memory as a scalable, hardware-realizable principle for neuromorphic robotics and edge-AI systems.

Recent progress in visual brain decoding from fMRI has been enabled by large-scale datasets such as the Natural Scenes Dataset (NSD) and powerful diffusion-based generative models. While current pipelines are primarily optimized for perception, their performance under mental-imagery remains less well understood. In this work, we study how a state-of-the-art (SOTA) perception decoder (DynaDiff) can be adapted to reconstruct imagined content from the Imagery-NSD benchmark. We propose a latent functional alignment approach that maps imagery-evoked activity into the pretrained model's conditioning space, while keeping the remaining components frozen. To mitigate the limited amount of matched imagery-perception supervision, we further introduce a retrieval-based augmentation strategy that selects semantically related NSD perception trials. Across four subjects, latent functional alignment consistently improves high-level semantic reconstruction metrics relative to the frozen pretrained baseline and a voxel-space ridge alignment baseline, and enables above-chance decoding from multiple cortical regions. These results suggest that semantic structure learned from perception can be leveraged to stabilize and improve visual imagery decoding under out-of-distribution conditions.

Motivated behaviour relies on the brain's capacity to evaluate effort and reward. Dysregulation within these processes contributes to a spectrum of conditions, from hyperactivity in attention-deficit/hyperactivity disorder (ADHD) to diminished goal-directed behaviour in apathy. This thesis investigates the neural mechanisms underlying ADHD using electroencephalography (EEG) and examines individual differences in effort and reward sensitivity using neuroimaging, applying machine learning approaches through three main studies. In Study 1, task-based and resting-state EEG were employed with machine learning models to classify adult individuals with ADHD and healthy controls. Machine learning classifiers trained on task-based EEG during a stop signal task outperformed those trained on resting-state EEG, with the strongest predictive features arising from gamma-band spectral power over fronto-central and parietal regions. In Study 2, diffusion MRI and whole-brain permutation-based analyses identified associations between white matter integrity and computationally modelled parameters reflecting effort and reward sensitivity, with SMA-connected tracts emerging as a central hub. In Study 3, grey matter volumes from structural T1-weighted MRI were used to examine correlates of effort sensitivity, reward sensitivity, and subclinical apathy, with machine learning confirming robust decoding of reward sensitivity and apathy levels. Across studies, fronto-parietal circuits emerged as central to effort valuation and reward processing. These findings may serve as neural biomarkers for improving diagnostic accuracy in ADHD and motivational impairments, and for guiding personalised neurotechnological interventions.

Gradient saliency from deep sequence models surfaces candidate biomarkers efficiently, but the resulting gene lists can be contaminated by tissue-composition confounders that degrade downstream classifiers. We study whether LLM chain-of-thought (CoT) reasoning can filter these confounders, and whether reasoning quality is associated with downstream performance. We train a Mamba SSM on TCGA-BRCA RNA-seq and extract the top-50 genes by gradient saliency; DeepSeek-R1 evaluates every candidate with structured CoT to produce a final 17-gene set. On the held-out test split, the raw 50-gene saliency set (no LLM) performs worse than a 5,000-gene variance baseline (AUC 0.832 vs. 0.903), while the LLM-filtered set surpasses it (AUC 0.927), using 294x fewer features. A faithfulness audit (COSMIC CGC, OncoKB, PAM50) shows that 6 of 17 selected genes (35.3%) are validated BRCA biomarkers, while 10 of 16 known BRCA genes present in the input were missed - including FOXA1. This divergence between downstream performance and reasoning faithfulness suggests selective faithfulness in this setting: targeted confounder removal can improve predictive performance without comprehensive recall.

Background: Human-to-human transmission of pathogens fundamentally depends on interactions among infectious and susceptible individuals, yet traditional population-scale models often overlook the stochastic, behaviour-driven, and highly heterogeneous nature of these interactions. Methods: Here, we develop a large-scale actor-based model capturing early epidemic dynamics of a novel respiratory pathogen on dynamic contact networks. We build these networks upon explicitly integrating detailed demographic and residential registry data from the Netherlands. The model simulates the Dutch population characterised by age, residency and mobility patterns, with actors interacting stochastically across households, workplaces and schools. Results: We show how the geographic and demographic profiles of initial cases impact transmission trajectories, with densely populated municipalities in the country's western core acting as key hubs driving epidemic spread. The framework enables rigorous assessment of intervention strategies incorporating behavioural adaptations. As case studies, we quantify the effects of symptomatic self-isolation and travel restrictions to and from major urban centres, highlighting their potential to modulate epidemic outcomes. Conclusions: Our findings underscore the necessity of integrating fine-scale human-to-human contact realism and population scale in epidemic forecasting and control.

(Im)balance indices can be used to quantify the (im)balance of trees by assigning numerical scores to them. An easy way to generate a new index is to construct a compound index, e.g., a linear combination of established indices. Two of the most prominent and widely used imbalance indices are the Sackin index and the Colless index. In this study, we show that these classic indices are themselves compound in nature: they can be decomposed into more elementary components that independently satisfy the defining properties of a tree (im)balance index. We further show that the difference Colless minus Sackin results in another imbalance index that is minimized (amongst others) by all Colless minimal trees. Conversely, the difference Sackin minus Colless forms a balance index. Finally, we compare the building blocks of which the Sackin and the Colless indices consist to these indices as well as to the stairs2 index, which is another index from the literature. Our results suggest that the elementary building blocks we identify are not only foundational to established indices but also valuable tools for analyzing disagreement among indices when comparing the balance of different trees. Along the way, we investigate the so-called echelon tree, which plays an important role for several (im)balance indices, and present the first non-recursive algorithm to construct it.

Modelling the evolution of a continuous trait in a biological population is one of the oldest problems in evolutionary biology, which led to the birth of quantitative genetics. With the recent development of GWAS methods, it has become essential to link the evolution of the trait distribution to the underlying evolution of allelic frequencies at many loci, co-contributing to the trait value. The way most articles go about this is to make assumptions on the trait distribution, and use Wright's formula to model how the evolution of the trait translates on each individual locus. Here, we take a gene's eye-view of the system, starting from an explicit finite-loci model with selection, drift, recombination and mutation, in which the trait value is a direct product of the genome. We let the number of loci go to infinity under the assumption of strong recombination, and characterize the limit behavior of a given locus with a McKean-Vlasov SDE and the corresponding Fokker-Planck IPDE. In words, the selection on a typical locus depends on the mean behaviour of the other loci which can be approximated with the law of the focal locus. Results include the independence of two loci and explicit stationary distribution for allelic frequencies at a given locus (under some assumptions on the fitness function).

Living cells inherently reorganize their intracellular structures in response to mechanical cues from their environment. Among these responses, the formation of actin-based stress fibers exhibits a series of structural transitions depending on substrate stiffness: from disordered states on soft substrates, to partial alignment, and eventually to bundled formations as stiffness increases. While these transformations have been well documented in many cell types, the physical principles underlying their emergence remain elusive. Here, we observe identical stiffness-dependent actin reorganizations in senescent fibroblasts despite their diminished biochemical and metabolic activities, suggesting that physical constraints play a dominant role in the phenomenon. We then develop a statistical-mechanical framework to demonstrate that these changes arise through a hierarchy of threshold-dependent phase transitions dictated by energy-entropy competition. This formulation provides a thermodynamic basis for understanding how distinct cytoskeletal orders become favored under different mechanical regimes. We propose that these transitions serve as mechanical checkpoints that coordinate intracellular organization during G1-phase spreading. These findings reveal how mechanical cues guide distinct intracellular orders through a physically constrained hierarchy of transitions.