Discover, rate, and verify biology preprints.

Heterogeneity in cilia patterning enables multiple flow functions in Paramecium

Paramecium tetraurelia partitions its ciliary array into a dense, fast-beating domain anterior to the oral apparatus that drives feeding flows and a sparser, slower domain that drives swimming.

Large scale prospective evaluation of co-folding across hundreds of Mac1-ligand complexes and three virtual screens

On 489 evaluable new Mac1 complexes, AlphaFold3, Chai-1 and Boltz-2 placed over half of ligands within 2 Å, but on docking hit-lists AF3 and Boltz-2 added little over docking.

Unraveling phenotypic variation in multiscale behavioral dynamics

Comparing coarse-grained dynamics across resolutions, weighted by sampling uncertainty, yields phenotypic spaces linking E. coli run speed to CheB and showing paramecia experience narrows zebrafish variability.

Structural Basis of Human Kinetochore-Microtubule Coupling by the Ndc80 and Ska Complexes

Cryo-EM shows human Ndc80 and Ska complexes bound to adjacent microtubule protofilaments, linked by a SKA3 tether that passes Ska's preference for GTP-like lattice and tip tracking to Ndc80.

The Central Coupler of ClpXP Controls Intersubunit Communication and Couples Intrasubunit Chemical Energy with Force Generation

Q208A mutations in up to four subunits of the ClpX central coupler barely slow unfolded-substrate translocation but raise ATP spent per step, weaken force generation and can abolish GFP unfolding.

Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models

A structure-conditioned nucleotide-level Potts model designs protein and coding sequences jointly, enabling tRNA adaptation and RNA motif embedding beyond synonymous codons with designability comparable to Caliby.

Physics and Morphology Constrained Quantitative Susceptibility Based Segmentation of Cerebral Veins

Dipole-field physics and Frangi vesselness losses lift QSM vein segmentation to centreline Dice 0.70 (U-Net 0.57); derived venous OEF tracks calibrated fMRI better than vessel filtering.

A water-pinning hotspot drives templated tau aggregation

In a minimal tau fibril model, residue 300/301 binds incoming peptide first and carries the most release-prone hydration water. Spin-labelling site 300 impairs locking and suppresses seeded growth.

QuantiTrack: A unified software to study protein dynamics in living cells

QuantiTrack, a MATLAB GUI, unifies single-molecule detection, tracking, quality control and mobility analyses; for glucocorticoid receptor, hormone washout cut bound fraction, dwell times and low-mobility occupancy.

On the effect of applied lateral tension on the deformation energetics of biological membranes and the lipid dynamics within

MARTINI 2.2 simulations show lateral tension changes the free energies of membrane bending and thickness deformations through a projected-area term (γΔΔA), while leaving lipid mixing, residence and exchange essentially unchanged.

Decoding Radiation-Induced Transcriptomic Signatures of Human Leukocytes using Long-Read RNA-Seq: Clinical and Biodosimetric Implications

Nanopore long-read RNA-seq of leukocytes from 4 Gy X-irradiated blood (three donors, 6 h) recovers p53 signaling and reveals isoform-level regulation plus candidate unannotated FBXO22/PHPT1 isoforms.

Spanning-Tree Thermostatistics of Protein Allostery: An Exact Kirchhoff Framework with Application to Oncogenic KRAS

Kirchhoff matrix-tree evaluation of residue-contact spanning-tree ensembles yields exact allosteric thermodynamics; KRAS G12D conserves global and channel heat capacity but reroutes paths via Q61 and F156.

DNA gyrase in live bacteria forms liquid condensates through weak multivalent bonding of excess GyrB

Live E. coli gyrase clusters hold excess GyrB (B:A 2.5:1), show hexanediol-sensitive liquid-like turnover, and docking suggests GyrB bridges heterotetramers.

Learning millisecond protein dynamics from what is missing in NMR spectra

Trained on missing NMR amide assignments in the Biological Magnetic Resonance Data Bank, Dyna-1 (ESM-3 layer 22 embeddings) predicts micro-to-millisecond conformational exchange seen in relaxation data.

Functional pocketomes and complete allosteric maps of five protein kinases

Energy-model maps of five human kinases show conserved distance-dependent decay of inhibitory allostery, but distal allosteric pockets and activating sites diverge between kinases.

Nuclear size and physical properties of the nucleoplasm are determined by colloid osmotic pressure at the nuclear envelope

Overexpressing mCherry-GST targeted to the nucleus or cytoplasm in fission yeast shifts the nuclear-to-cell volume ratio as a parameter-free colloid osmotic model predicts, retuning nucleoplasm diffusivity, condensates and heterochromatin.

Nonlinear Relationships of Fibrin Network Structure as a Function of Fibrinogen and Thrombin Concentrations for Purified Fibrinogen and Plasma Clots

Fibrin fiber diameter, segment length, density and pore size in plasma and purified clots follow fibrinogen-thrombin power laws; thrombin sets segment length, fibrinogen sets space filling.

AlphaFold as a Prior: Experimental StructureDetermination Conditioned on a Pretrained Neural Network

ROCKET refines AlphaFold2 predictions against crystallographic, cryo-EM and cryo-ET data by gradient descent on MSA cluster profiles, capturing loop flips and domain shifts without retraining.

Bringing the Genetically Minimal Cell to Life on a Computer in 4D

A hybrid 4D whole-cell simulation of the minimal bacterium JCVI-syn3A integrates spatial reaction-diffusion, metabolism, polymer chromosome dynamics, and division across a complete 105-minute cell cycle.

Computational design of conformation-biasing mutations to alter protein functions

Contrastive scoring of protein variants across alternative backbone structures with inverse folding models (Conformational Biasing) predicts mutations that shift conformational equilibria and tune effector binding, catalysis, and labeling specificity.