Browsing Biophysics by Title
Now showing items 1-20 of 31
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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 ... -
Active layer dynamics drives a transition to biofilm fingering
The emergence of spatial organization in biofilm growth is one of the most fundamental topics in biofilm biophysics and microbiology. Characterising distinct types of biofilm spatial structure, and understanding how they ... -
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 ... -
Complex small-world regulatory networks emerge from the 3D organisation of the human genome
The discovery that overexpressing one or a few critical transcription factors can switch cell state suggests that gene regulatory networks are relatively simple. In contrast, genome-wide association studies (GWAS) point ... -
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 ... -
Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-gamma-glutamic acid production
A hallmark of microbial biofilms is the self-production of extracellular matrix that encases the cells resident within the community. The matrix provides protection from the environment, while spatial heterogeneity 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 ... -
High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights on proto-oncogene deregulation
Simulation and experimental data and related scripts associated with the paper "High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights on proto-oncogene ... -
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 ... -
Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces
Understanding the interactions between viruses and surfaces or interfaces is important, as they provide the principles underpinning the cleaning and disinfection of contaminated surfaces. Yet, the physics of such interactions ... -
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 ...
