Quantitative Biology
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Sensory information propagates through successive processing stages in the brain, where synaptic weight patterns between stations determine how downstream neurons decode information from upstream populations. Although optimized synaptic…
Deciphering brain function through non-invasive recordings requires synthesizing complementary high-frequency electromagnetic (EEG/MEG) and low-frequency metabolic (fMRI) signals. However, despite their shared neural origins, extreme…
Knee contact-stress hotspots are closely linked to meniscal/cartilage injury risk. Still, high-fidelity subject-specific FEA is too computationally expensive for large-cohort, multi-condition, near-real-time use. Existing MeshGraphNet-style…
Data-driven model discovery (DDMD) algorithms are powerful tools for extracting interpretable symbolic models from data. However, identifying the model that best balances goodness-of-fit and sparsity is often a laborious process requiring…
Dendritic keratitis is a form of eye infection caused by herpes simplex virus (HSV). The virus spreads via direct cell-to-cell infection among corneal epithelial cells. This leads to the formation of dendritic lesions characterized by…
Malignant tumors exhibit complex pathogenesis, yet classical oncological theories remain fragmented, failing to provide a unifying framework to address this complexity. This gap limits the utility and translational potential of the…
We examine the conceptual and ethical gaps in current representations of Superintelligence misalignment. We find throughout Superintelligence discourse an absent human subject, and an under-developed theorization of an "AI unconscious" that…
Mutualistic interactions, where individuals from different species can benefit from each other, are widespread across ecosystems. This study develops a general deterministic model of mutualism involving two populations, assuming that…
As numerical simulations grow in complexity, their demands on computing time and energy increase. Accelerators for numerical computation offer significant efficiency gains in many computationally-intensive scientific fields, but their use…
Biological systems like long-lived clonal organisms, holobionts and clades challenge traditional evolutionary thinking since they adapt without populations or reproduction. This paper aims to provide an overarching theoretical framework…
Tipping points are one of the hot topics in modern physics of complex systems. But what is a tipping point? A generic definition declares it as ``a state of the system where a small change in its parameters can lead to a significant change…
Integrating high-dimensional biological data into data-driven mechanistic modeling requires rigorous practical identifiability to ensure interpretability and generalizability. However, coordinate identifiability analysis often suffers from…
The discovery of novel proteins relies on sensitive protein identification, for which de novo peptide sequencing (DNPS) from mass spectra is a crucial approach. While deep learning has advanced DNPS, existing models inadequately enforce the…
Pro-inflammatory peptides (PIPs) play critical roles in immune signaling and inflammation but are difficult to identify experimentally due to costly and time-consuming assays. To address this challenge, we present KEMP-PIP, a hybrid machine…
Alzheimer's disease (AD) and Lewy body dementia (LBD) present overlapping clinical features yet require distinct diagnostic strategies. While neuroimaging-based brain network analysis is promising, atlas-based representations may obscure…
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling near-atomic-level visualization of biomolecular assemblies. However, the exponential growth in cryo-EM data throughput and complexity, coupled with diverse…
We present SeedProteo, a diffusion-based model for de novo all-atom protein design. We demonstrate how to repurpose a cutting-edge folding architecture into a powerful generative design framework by effectively integrating self-conditioning…
Valvular heart disease is prevalent and a major contributor to heart failure. Valve leaflet strain is a promising metric for evaluating the mechanics underlying the initiation and progression of valvular pathology. However, generalizable…
Multicellular tissues, such as the epithelium coating a developing embryo, often combine complex tissue shapes with heterogeneity in the spatial arrangement of individual cells. Discrete approximations, such as the cell vertex model, can…