2024

Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference

GB Brandani
Computational Methods for 3D Genome Analysis Protocol : 309

Can the AMOEBA forcefield be used for high pressure simulations? The extreme case of methane and water

M Kerr , GJ Ackland , D Marenduzzo , GB Brandani , CG Pruteanu
The Journal of Chemical Physics 161 : 054506

Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci

GB Brandani , C Gu , S Gopi , S Takada
PNAS Nexus 3 : pgae226

Combining contact frequency and histone modification data to tune a coarse-grained chromatin model

WS Chan , GB Brandani , S Takada , H Kono
Biophysical Journal 123 : 366a

2023

Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA

S Amaouteli , NC Bamford , GB Brandani , RJ Morris , M Schor , JT Carrington , L Hobley , DMF van Aalten , NR Stanley-Wall , CE MacPhee
Proceedings of the National Academy of Sciences 120 : e2312022120

Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning

S Park , GB Brandani , T Ha , GD Bowman
Nucleic Acids Research 51 : 10326

2022

Molecular dynamics simulations for the study of chromatin biology

GB Brandani , S Gopi , M Yamauchi , S Takada
Current Opinion in Structural Biology 77 : 102485

2021

The lane-switch mechanism for nucleosome repositioning by DNA translocase

F Nagae , GB Brandani , S Takada , T Terakawa
Nucleic acids research 49 : 9066

The kinetic landscape of nucleosome assembly: a coarse-grained molecular dynamics study

GB Brandani , C Tan , S Takada
PLoS computational biology 17 : e1009253

2020

Translational nucleosome positioning: A computational study

J Neipel , GB Brandani , H Schiessel
Physical Review E 101 : 022405

Nucleosomes as allosteric scaffolds for genetic regulation

S Takada , GB Brandani , C Tan
Current Opinion in Structural Biology 62 : 93

2019

Langmuir-Blodgett technique for anisotropic colloids: Young investigator perspective

T Li , K Lilja , RJ Morris , GB Brandani
Journal of Colloid and Interface Science 540 : 420

2018

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

GB Brandani , S Takada
PLoS computational biology 14 : e1006512

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

GB Brandani , T Niina , C Tan , S Takada
Nucleic acids research 46 : 2788

2017

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

T Niina , GB Brandani , C Tan , S Takada
PLoS computational biology 13 : e1005880

Adsorption of the natural protein surfactant Rsn-2 onto liquid interfaces

GB Brandani , SJ Vance , M Schor , A Cooper , MW Kennedy , BO Smith , CE MacPhee , DL Cheung
Physical Chemistry Chemical Physics 19 : 8584

2016

The Conformation of Interfacially Adsorbed Ranaspumin-2 Is an Arrested State on the Unfolding Pathway

RJ Morris , GB Brandani , V Desai , BO Smith , M Schor , CE MacPhee
Biophysical Journal 111 : 732

2015

The Bacterial Hydrophobin BslA is a Switchable Ellipsoidal Janus Nanocolloid

GB Brandani , M Schor , R Morris , N Stanley-Wall , CE MacPhee , D Marenduzzo , U Zachariae
Langmuir 31 : 11558

2013

Quantifying disorder through conditional entropy: an application to fluid mixing

GB Brandani , M Schor , CE Macphee , H Grubmuller , U Zachariae , D Marenduzzo
PLoS One 8 : e65617