G. B. Brandani

Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci

This paper introduces Hi-C metainference, a Bayesian method to model chromatin organization, revealing that gene loci in mouse embryonic stem cells are dynamically condensed and organized as crumpled globules.

DNA translocase repositions a nucleosome by the lane-switch mechanism

The paper identifies a lane-shift mechanism for downstream nucleosome repositioning by DNA translocases using simulations and experimental validation.

The Kinetic Landscape of Nucleosome Assembly: A Coarse-Grained Molecular Dynamics Study

This study uses molecular dynamics simulations to analyze the kinetic landscape of nucleosome assembly, revealing transition networks and the role of DNA bending and histone association in positioning sequences.

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

This study uses molecular dynamics simulations to show how ATP-dependent chromatin remodelers induce DNA sliding through twist defect formation during inchworm motion.

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

This study uses molecular simulations to show that nucleosome sliding depends on DNA sequence, with strong positioning sequences sliding in large jumps and uniform sequences sliding in a rotation-coupled manner.