Shoji Takada

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 shows that disrupting CaMKII's liquid-liquid phase separation with synaptic partners causes ADHD-like behaviors and memory deficits in mice, mirroring a human patient with a similar mutation.

This paper introduces a physics-based model to simulate chromatin domain dynamics driven by epigenetic factors, revealing that nucleosome-nucleosome interactions shape genomic organization.

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 combines optical tweezers with high-speed AFM to visualize DNA folding dynamics, revealing reversible structural changes and metastable intermediates.

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.

The paper investigates multiphase separation in postsynaptic density components, showing that membrane geometry and CaMKII valency and volume drive morphology reversal between solution and membrane environments.

The paper introduces OpenCafeMol, a GPU-accelerated MD simulator for biomolecules, showing speedups over CPU and applying it to vesicle fusion studies.

This study shows that tension in the neck linker of kinesin-1 suppresses premature binding of the detached head, explaining coordinated stepping through allosteric regulation.

This study uses molecular dynamics simulations to analyze the heterogeneous behavior of condensates formed by four master transcription factors in embryonic stem cells, revealing distinct roles for each factor in condensate formation.

The paper develops a multiscale modeling pipeline to simulate chromatin organization and transcription regulation in mouse embryonic stem cells, revealing how sequence-regulated accessibility facilitates enhancer-promoter communication.

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

This study uses AFM imaging and molecular modeling to investigate how ATP hydrolysis affects the structural changes in yeast condensin.

This study uses computational modeling and molecular dynamics simulations to elucidate the proton-transfer coupled rotation mechanism of MotAB in bacterial flagellar motors.

The paper develops a kinetic model of cytoplasmic dynein's bipedal stepping motions, showing how different stepping patterns arise from ATP hydrolysis and conformational changes.