Masataka Yamauchi

The paper extends a GPU-accelerated molecular dynamics simulator to support DNA models and improves efficiency for simulating chromatin interactions over long timescales.

This study uses molecular dynamics simulations to show that SMC complexes translocate DNA unidirectionally by capturing DNA segments and pumping them through an asymmetric kleisin path.

This study uses molecular dynamics simulations to show that transcription factors Nanog, Oct4, and Sox2 form phase-separated condensates with DNA, revealing a synergistic DNA deliverer-receiver mechanism.

This study uses molecular dynamics simulations to show how CMG helicase translocates directionally and navigates nucleosomes during DNA replication, with contributions from Csm3/Tof1 and RPA.

This study shows that an archaeal SMC complex forms TAD-like domains and is stalled by TrmBL2, with stalling efficiency linked to DNA structure.