arXiv preprints from January 1, 2026 through July 21, 2026 — 21:24:27 EST
Recent advancements in single-cell multi-omics, particularly RNA-seq, have provided profound insights into cellular heterogeneity and gene regulation. While pre-trained language model (PLM) paradigm based single-cell foundation models have shown promise, they remain constrained by insufficient integration of in-depth individual...
The computational design of antibodies with high specificity and affinity is a cornerstone of modern therapeutic development. While deep generative models have demonstrated potential, they often struggle to balance high-fidelity geometric conditioning with the discrete nature of amino acid sequences. In this work, we present...
In order for epidemiological forecasts to be useful for decision-makers the forecasts need to be properly validated and evaluated. Although several metrics fore evaluation have been proposed and used none of them account for the potential costs and losses that the decision-maker faces. We have adapted a decision-theoretic framework to...
The brain is composed of billions of neurons with virtually endless morphologies and ion channel compositions, resulting in unique extracellular waveforms. Nevertheless, almost all neuronal morphologies can be reduced to a simple architecture made of three principal compartments: 1) the soma and nearby axonal hillock, 2) axonal...
Deep cognitive attention is characterized by heightened gamma oscillations and coordinated visual behavior. Despite the physiological importance of these mechanisms, computational studies rarely synthesize these modalities or identify the neural regions most responsible for sustained focus. To address this gap, this work introduces...
In stochastic population dynamics, stochastic wandering can produce transition to an absorbing state. In particular, under Allee effects, low densities amplify the possibility of population collapse. We investigate this in an Allee-Ornstein-Uhlenbeck (Allee-OU) model, that couples a bistable Allee growth equation, with demographic...
Light driven oxygen formation in Photosystem II protein is a fundamental process that sustains our biosphere and serves as a blue print to future clean energy solutions due to its high energy conversion efficiency. Last decade of intense research by advanced physical techniques delivered new insights on the structure and function of...
Examination of T-cell receptor (TCR) clonality has become a way of understanding immunologic response to cancer and its interventions in recent years. An aspect of these analyses is determining which receptors expand or contract statistically significantly as a function of an exogenous perturbation such as therapeutic intervention. We...
Synchronized rhythmic oscillatory activity in the beta frequency band in the basal ganglia (BG) is a hallmark of Parkinson's disease (PD). Recent experiments and theoretical studies have demonstrated the crucial roles of T-type and L-type calcium currents in shaping the activity patterns of subthalamic nucleus (STN) neurons. However,...
A highly diluted aqueous solution of histamine was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and hydrogen bonds and is practically independent of the choice of the water model. Dynamic analysis...
Bacteria seem masters of chemotaxis, yet recent work suggests otherwise. Henry Mattingly and colleagues (Nature Physics, 2026) argue that Escherichia coli uses only a small fraction of the sensory information available at its surface, challenging the long-held view that bacterial chemotaxis operates near physical sensing limits. This...
In this paper, we study the absorption and fixation times for evolutionary processes on graphs, under different updating rules. While in Moran process a single neighbour is randomly chosen to be replaced, in proliferation processes other neighbours can be replaced using Bernoulli or binomial draws depending on $0 < p \leq 1$. There is...
Living cells maintain size homeostasis by actively compensating for size fluctuations. Here, we present two stochastic maps that unify phenomenological models by integrating fluctuating single-cell growth rates and size-dependent noise mechanisms with cell size control. One map is applicable to mother machine lineages and the other to...
Estimating population-level prevalence and transmission dynamics of wildlife pathogens can be challenging, partly because surveillance data is sparse, detection-driven, and unevenly sequenced. Using highly pathogenic avian influenza A/H5 clade 2.3.4.4b as a case study, we develop zooNet, a graph-based epidemiological framework that...
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach for reducing computing time is to simulate populations that are much smaller than the natural...
Micronutrient deficiency in soils limits crop productivity and reduces the nutritional quality of cereals and pulses. Conventional fertilizer supplementation often suffers from low bioavailability and environmental losses. In this study, we investigate the use of Plasma Activated Water (PAW) enriched with divalent micronutrient ions...
As intelligent systems are developed across diverse substrates - from machine learning models and neuromorphic hardware to in vitro neural cultures - understanding what gives a system agency has become increasingly important. Existing definitions, however, tend to rely on top-down descriptions that are difficult to quantify. We...
Collective improvisation in dance provides a rich natural laboratory for studying emergent coordination in coupled neuro-motor systems. Here, we investigate how training shapes spontaneous synchronization patterns in both movement and brain signals during collaborative performance. Using a dual-recording protocol integrating 3D motion...
Fitness consequence of dispersal depends on property of the entire landscape, which patches are available and what are the cost of moving. These are information that are not available locally when an organism make the decision to disperse. This poses a problem to the organism, where it is unclear how an adaptive decision can be made....
Cooperation in large groups and one-shot interactions is often hindered by freeloading. Punishment can enforce cooperation, but it is usually regarded as wasteful because the costs of punishing offset its benefits. Here, we analyze an evolutionary game model that integrates upstream and downstream reciprocity with costly punishment:...
We present a data-driven framework to characterize large-scale brain dynamical states directly from correlation matrices at the single-subject level. By treating correlation thresholding as a percolation-like probe of connectivity, the approach tracks multiple cluster- and network-level observables and identifies a characteristic...
In the brain, neural activity undergoes directed flows between states, thus breaking time-reversal symmetry. At the same time, animals also exhibit irreversible flows between behavioral states. Yet it remains unclear whether -- and how -- irreversibility in the brain relates to irreversibility in behavior. Here, we explore this...
Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models for protein design may be attributed to; high experimental noise levels; the complex nature of...
A hallmark of aging is loss of information in gene regulatory networks. These networks are tightly connected, raising the question of whether information could be restored by perturbing single genes. We develop a simple theoretical framework for information transmission in gene regulatory networks that describes the information gained...
Differential gene expression (DGE) analysis is foundational to transcriptomic research, yet tool selection can substantially influence results. This study presents a comprehensive comparison of two widely used DGE tools, edgeR and DESeq2, using real and semi-simulated bulk RNA-Seq datasets spanning viral, bacterial, and fibrotic...