OpenNucleome

OpenNucleome performs GPU-accelerated molecular dynamics simulations of the human nucleus using particle-based representations of chromosomes at 100 KB resolution to investigate nuclear architecture and condensate formation.

Key Features:

• Particle-based chromosome representation: Models chromosomes at 100 KB resolution encompassing nuclear lamina, nucleoli, and speckles.
• GPU acceleration: Enables molecular dynamics simulations with computational acceleration on graphics processing units.
• Structural ensemble generation: Furnishes highly accurate structural models of nuclear architecture.
• Condensate dynamics simulation: Affords dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects.
• Nuclear zoning analysis: Supports investigation of genomic loci anchoring mechanisms and nuclear spatial organization principles.

Scientific Applications:

• Nuclear architecture investigation: Reconstructs high-resolution structural ensembles of the human nucleus to interpret experimental observations from high-throughput sequencing and microscopy.
• Condensate biology: Simulates formation and fusion of nuclear condensates including nucleoli and speckles.
• Genomic loci anchoring mechanism discovery: Uncovers mechanisms driving emergence of 'fixed points'—genomic loci robustly anchored near specific nuclear bodies for functional purposes.
• Non-equilibrium effects exploration: Investigates non-equilibrium phenomena in nuclear organization and dynamics.
• Nuclear zoning model validation: Supports a nuclear zoning model that elucidates genome functionality through analysis of chromosome radial positions and nuclear shape fluctuations.

Methodology:

Molecular dynamics simulations using GPU acceleration with particle-based representations of chromosomes at 100 KB resolution.