Browsing Biophysics by Title
Now showing items 1-20 of 22
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A 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNA
The first level of folding of DNA in eukaryotes is provided by the so-called “10-nm chromatin fibre”, where DNA wraps around histone proteins (∼10 nm in size) to form nucleosomes, which go on to create a zig-zagging ... -
Bacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion
This dataset contains data corresponding to the figures in the main text of the manuscript "Bacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion" (Science Advances, 4, 4, eaao1170, 2018). Data ... -
Data accompanying "Shaping the Growth Behaviour of Biofilms Initiated from Bacterial Aggregates, 2013-2016" (Submitted paper).
Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural ... -
Data accompanying 'A growing bacterial colony in two dimensions as an active nematic'
How a single bacterium becomes a colony of many thousand cells is important in biomedicine and food safety. Much is known about the molecular and genetic bases of this process, but less about the underlying physical ... -
Data accompanying the manuscript "Mechanical interactions in bacterial colonies and the surfing probability of beneficial mutations"
Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed cultures routinely used in microbial research, bacteria in ... -
Data and movies accompanying 'Kinetic theory of pattern formation in mixtures of microtubules and molecular motors'
In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous ... -
Dataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy"
Dataset supporting the manuscript "High-throughput characterisation of bull semen motility using differential dynamic microscopy" published in PLOSone. -
Degradation of beta-lactams in bacterial growth media
The dataset contains growth curves of E. coli RJA002 in various growth media in the presence of beta-lactam antibiotics. These growth curves were used to determine the degradation rate of these antibiotics in a range of ... -
Dynamical analysis of bacteria in microscopy movies
This repository contains data and code related to the manuscript "Dynamical analysis of bacteria in microscopy movies", PloS One, 14, 6, e0217823, 2019 (https://doi.org/10.1371/journal.pone.0217823). Please find more ... -
Escherichia coli as a model active colloid: A practical introduction
The flagellated bacterium Escherichia coli is increasingly used experimentally as a self-propelled swimmer. To obtain meaningful, quantitative results that are comparable between different laboratories, reproducible protocols ... -
Experimental data for the article "Predictable Properties of Fitness Landscapes Induced by Adaptational Tradeoffs"
We used strains from Marcusson et al. (2009) (courtesy of Douglas Huseby and Diarmaid Hughes). The strains are isogenic derivatives of MG1655, a K12 strain of the bacterium E. coli, with specific point mutations or gene ... -
The long term epidemic predictions from Imperial College CovidSim Report 9
A single tarball containing several directories, corresponding to the figures and tables in our paper. Raw simulation output is provided alongside python scripts to process it, and scripts to reproduce it from the original ... -
Nonequilibrium chromosome looping via molecular slip links
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of cohesinlike molecules, which, along with the CTCF protein, stabilize loops which ... -
Nucleosome positions alone can be used to predict domains in yeast chromosomes
Simulation data related to the project "Nucleosome positions alone can be used to predict domains in yeast chromosomes". DNA is packaged into chromosomes, which are further organized into domains: Regions of the genome ... -
A Phenomenological Description of BslA Assemblies Across Multiple Length Scales
Intrinsically interfacially active proteins have garnered considerable interest recently due to their potential use in a range of materials applications. Notably, the fungal hydrophobins are known to form robust and well ... -
Polymer Modelling Predicts Chromosome Reorganisation in Senescence
This dataset contains the data related to the figures and supplemental figures in the manuscript "Polymer Modelling Predicts Chromosome Reorganisation in Senescence". Lamina-associated domains (LADs) cover a large part of ... -
Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci
This dataset contains data corresponding to the figures and supplemental figures of the manuscript "Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci". Data sets from next ... -
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms ... -
The role of correlations in the collective behaviour of microswimmer suspensions
In this work, we study the collective behaviour of a large number of self-propelled microswimmers immersed in a fluid. Using unprecedently large-scale lattice Boltzmann simulations, we reproduce the transition to bacterial ... -
Supplementary data for the manuscript "Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic"
Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription ...
