Biophysics
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Data generated as part of research into the Physics of living matter, for example aqueous solutions of small bioactive molecules through proteins and DNA to single cells, cell-cell interactions, and collection of organisms in ecosystems, studying phenomena occurring at picoseconds to decades.
For example see:
- Physics of Living Matter Research Group
- Institute for Condensed Matter and Complex Systems
- Condensed Matter and Complex Systems at the University of Edinburgh
Image: Still (produced using Fiji distribution of ImageJ see https://imagej.net) from "Figure1_Ecoli-Flagella-Body-movie.tif" from Schwarz-Linek, Jana; Arlt, Jochen; Jepson, Alys; Dawson, Angela; Vissers, Teun; Miroli, Dario; Pilizota, Teuta; Martinez, Vincent A.; Poon, Wilson C. K.. (2015). Escherichia coli as a model active colloid: A practical introduction, [dataset]. University of Edinburgh. https://doi.org/10.7488/ds/290.
Items in this Collection
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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 ... -
Swimming suppresses correlations in dilute suspensions of pusher microorganisms
Active matter exhibits various forms of non-equilibrium states in the absence of external forcing, including macroscopic steady-state currents. Such states are often too complex to be modelled from first principles and our ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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. -
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 ... -
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 ... -
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 ... -
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 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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
What is the ‘minimum inhibitory concentration’ (MIC) of pexiganan acting on Escherichia coli? - A cautionary case study
We measured the minimum inhibitory concentration (MIC) of the antimicrobial peptide pexiganan acting on Escherichia coli, and report an intrinsic variability in such measurements. These results led to a detailed study of ...
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