DOI: 10.5061/dryad.g1jwstr4d
title: Gene loci fluctuations reveal bacterial chromosome dynamical organization

description: Chromosomal sites in rod-like bacteria move sub-diffusely, driven by the
 out-of-equilibrium nature of the viscoelastic, crowded intracellular
 environment. Furthermore, it has been shown that there is a pronounced
 dynamical asymmetry between longitudinal (long-axis) and transverse
 (radial) motions, manifested in different exponents in the mean square
 displacements, and respectively. Here, using polymer simulations and
 experimental observations of a locus in Bacillus subtilis, we substantiate
 the notion that asymmetric dynamics are a result of the asymmetric
 structure of the bacterial chromosome modelled as a bottlebrush polymer in
 a poor solvent. Our simulations recapitulate the observed asymmetry as
 well as the range of the observed exponent values that are related to
 scaling models of polymer dynamics, lending support to the notion that
 asymmetric dynamics is a consequence of the bottlebrush structure of the
 bacterial chromosome.
description: # Gene loci fluctuations reveal bacterial chromosome dynamical
 organization Dataset DOI:
 [10.5061/dryad.g1jwstr4d](10.5061/dryad.g1jwstr4d) ## Description of the
 data and file structure ### Description of the data and file structure
 Deposited data includes the following data files used to generate
 different figures in the main text, with their respective description (in
 Origin, Notepad and Excel files). ## File: Data_Fig1.opju
 **Description:** This dataset contains experimental raw data of the
 anisotropic mean square displacement (MSD) of a chromosomal locus as a
 function of time. The measurements were obtained from time-lapse
 microscopy tracking in the image plane. ##### File structure: The data are
 organized into three worksheets of an Origin file corresponding to
 different displacement components: * MSDX — Mean square displacement in
 the transversal (x) direction * MSDY — Mean square displacement in the
 longitudinal (y) direction * MSDr — Mean square displacement in the radial
 (r) direction Each worksheet contains: * Column 1: Time in seconds (s) *
 Columns 2–96: Individual MSD traces for separate trajectories in
 nano-meters square. ## File: Data_Fig4.zip **Description**: Simulation raw
 data of longitudinal (Data_Fig4a) and transverse (Data_Fig4b) mean square
 displacement (MSD) as a function of time for full regions, middle regions,
 and end regions of the chromosome chains. --- ##### **Folder Structure**
 The ZIP archive includes 10 folders, each corresponding to an individual
 simulation run. Each simulation folder contains three text files
 (Notepad), representing the MSD results for different regions along the
 chromosome chain: ##### File description: `full_region.txt, `MSD for the
 full region of the chromosome chain `middle_region.txt, `MSD for the
 middle region of the chromosome chain `end_region.txt, `MSD for the end
 region of the chromosome chain --- ##### **Data Format:** Each text file
 contains three columns: 1 Time (τ) 2 Longitudinal mean square displacement
 (MSD) 3 Transverse mean square displacement (MSD) **Units:** * Time (τ):
 simulation time units * MSD: simulation length units --- ## **File:
 Data_Fig5.zip** **Description:**  Simulation raw data of longitudinal MSD
 exponents 𝛼ℓ (Data_Fig5a, alpha_l), transverse MSD exponents α𝑟
 (Data_Fig5b, alpha_r), and the ratio of longitudinal to transverse
 exponents α𝑟/𝛼ℓ (Data_Fig5c) as functions of confinement radius and
 interaction strength. ##### **Folder Structure** The ZIP archive contains
 three sub-folders of data for panels Fig5a, Fig5b, with two Excel files
 each (allbeads representing 60-bead loops and topbeads representing beads
 25–35 of each 60-bead loop). Folder Fig5c contains two Excel files each,
 with the ratio α𝑟/𝛼ℓ.  ##### File description: Fig5a: 
 `alpha_l_allbeads.xlsx` `alpha_l_topbeads.xlsx` Fig5b:
 `alpha_r_allbeads.xlsx` `alpha_r_topbeads.xlsx` Fig5c:
 `alpha_ratio_allbeads.xlsx` `alpha_ratio_topbeads.xlsx` ##### **Data
 Format:** Each Excel file contains a table with columns corresponding to
 different values of the confinement radius R (units of beads) while rows
 correspond to the indicated values of epsilon (units of k~B~T) **Units:**
 * Simulation units * All beads: 60-bead loop * Top beads: 25–35 of each
 60-bead loop ### Code/software All custom analysis and visualization
 scripts developed for this study are included in the Zenodo repository
 ([https://doi.org/10.5281/zenodo.17307615](https://doi.org/10.5281/zenodo.17307615)). The molecular dynamics simulations were performed using LAMMPS (open-source, GPLv2 license), and data analysis was carried out using standard Python and MATLAB environments.