Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD

DNA breathing dynamics—transient base-pair opening and closing due to thermal fluctuations—are vital for processes like transcription, replication, and repair. Traditional models, such as the Extended Peyrard-Bishop-Dauxois (EPBD), provide insights into these dynamics but are computationally limited for long sequences. We present JAX-EPBD , a high-throughput Langevin molecular dynamics framework leveraging JAX for GPU-accelerated simulations, achieving up to 30x speedup and superior scalability compared to the original C-based EPBD implementation. JAX-EPBD efficiently captures time-dependent behaviors, including bubble lifetimes and base flipping kinetics, enabling genome-scale analyses. Applying it to transcription factor (TF) binding affinity prediction using SELEX datasets, we observed consistent improvements in R ² values when incorporating breathing features with sequence data. Validating on the 77-bp AAV P5 promoter, JAX-EPBD revealed sequence-specific differences in bubble dynamics correlating with transcriptional activity. These findings establish JAX-EPBD as a powerful and scalable tool for understanding DNA breathing dynamics and their role in gene regulation and transcription factor binding.