Vincenzo Carnevale

Tightly Knotted Enzymes Inhibit Protein-Protein Aggregation

This study shows that knotted protein structures inhibit aggregation by limiting expanded states and suppressing liquid-liquid phase separation.

From Atoms to Neuronal Spikes: A Multi-Scale Simulation Framework

This paper presents a multi-scale simulation framework that links molecular events in ion channels to neuronal excitability by coupling molecular dynamics with neuronal simulations.

Lipid Dynamics and Organization Around Voltage-Gated Sodium Channels: A Coarse-Grained Perspective

This study uses coarse-grained simulations to show that hydrophobic mismatch drives lipid reorganization around voltage-gated sodium channels, favoring DIPC over DPPC and cholesterol.

TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization

TRUHiC enhances low-resolution Hi-C data using deep generative modeling to improve 3D chromatin structure characterization across cell lines and species.

Entrenchment and contingency in neutral protein evolution with epistasis

The paper shows that protein evolution with epistasis and purifying selection does not lead to entrenchment, and that rate variation is due to epistasis, not historical contingency.

Split-Transformer Impute (STI): A Transformer Framework for Genotype Imputation

STI is a transformer-based model for genome-scale genotype imputation that achieves high accuracy and handles multi-allelic variants effectively.

A consistent picture of TRPV1 activation emerges from molecular simulations and experiments

The paper proposes a molecular mechanism for TRPV1 activation through conformational changes and validates it with bioinformatics, structural analysis, and experimental data.

From Sequence to Function: Coevolving Amino Acids Encode Structural and Functional Domains

The paper introduces a co-evolutionary coupling analysis to identify structural and functional domains from protein sequences, showing that sequence-based methods can recover domain characteristics.