定量生物学
Diffusion models have achieved promising results for Structure-Based Drug Design (SBDD). Nevertheless, high-quality protein subpocket and ligand data are relatively scarce, which hinders the models' generation capabilities. Recently, Direct…
This article presents an artificial intelligence (AI) architecture intended to simulate the iterative updating of the human working memory system. It features several interconnected neural networks designed to emulate the specialized…
Redox biology underpins signalling, metabolism, immunity, and adaptation, yet lacks a unifying theoretical framework capable of formalising structure, function, and dynamics. Current interpretations rely on descriptive catalogues of…
Redox proteomics generates bounded biochemical measurements that are categorically mismatched to conventional linear algebraic formalisms. This work introduces Oxi-Shapes, a tropical geometric framework for the measurement-native analysis…
The crawling motility of many eukaryotic cells is driven by filamentous actin (F-actin), and regulated by a network of signaling proteins and lipids (including small GTPases). The tangle of positive and negative feedback loops gives rise to…
Human activity has an enormous impact on Earth, changing organisms, environments and landscapes, leading to the decline of original ecosystems and irreversible changes that create new combinations of living beings and materials. As a…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
The Great Filter hypothesis is an extension of the Fermi Paradox: "If life is so common in the universe, why don't we see it?" The Great Filter theory posits there are multiple obstacles or filters life must pass through which ultimately…
Traditional epidemiological models often fail to characterize the extreme volatility and heavy-tailed "Dragon King" events observed in real-world outbreaks. We propose a unified framework that bridges microscopic agent-based simulations…
In this work, we develop a stochastic multiscale model for glioma growth and invasion in the brain, incorporating the effects of therapeutic interventions. The model accounts for tumor cell migration influenced by brain tissue heterogeneity…
Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a critical analytical technique for molecular identification across metabolomics, environmental chemistry, and chemical forensics. A variety of computational methods have emerged…
Background and Objectives: Proximal catheter obstruction is the leading cause of ventriculoperitoneal shunt failure, yet the biological triggers of peri-catheter inflammation and tissue ingrowth remain poorly defined. Evidence of bacterial…
Recent work has shown that scaling large language models (LLMs) improves their alignment with human brain activity, yet it remains unclear what drives these gains and which representational properties are responsible. Although larger models…
How large language models (LLMs) align with the neural representation and computation of human language is a central question in cognitive science. Using representational geometry as a mechanistic lens, we addressed this by tracking…
Declarative memory, the memory that can be "declared" in words or languages, is made up of two dissociated parts: episodic memory and semantic memory. This dissociation has its neuroanatomical basis episodic memory is mostly associated with…
In vitro transcription (IVT) plays a critical role in the manufacture of mRNA vaccines and therapeutics. Optimizing mRNA yield and ensuring product quality, such as capping efficiency and integrity, are essential but mechanistically…
The release of Wolbachia-infected mosquitoes is a promising strategy for controlling Aedes aegypti populations, but exposure to high temperatures can induce temporary infection loss and compromise long-term persistence. In this work, we…
Physiological stress fundamentally alters disease susceptibility in aquatic environments. In this paper, we develop a stress-structured epidemiological model where host vulnerability is dynamically driven by water quality. Analytically, we…
A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that…
Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle…