Oxford University, Structural Bioinformatics & Computational Biochemistry Unit
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A. Caroline E. Dahl


Structural Bioinformatics and Computational Biochemistry Unit
Dept. of Biochemistry
University of Oxford
South Parks Road
Oxford
OX1 3QU
UK

Telephone: +44 (0) 1865 613 304
Fax: +44 (0) 1865 613 238

e-mail: caroline.dahl AT dtc.ox.ac.uk
division line

Membrane protein mechanotransduction


Research

I use coarse-grained and atomistic GROMACS MD to investigate the conformational events that follow physiological membrane perturbation.

I am also interested in protein structure representation and analysis. Most recently I developed Bendix, a software for abstract display and quantification of helix geometry. I also coded collaboratively on the software projects Flows and Epock. Flows analyses the collective movement of molecules, while Epock provides rapid and customizable cavity analysis in molecules.

Following an internship at Microsoft Research in 2013, where I worked on the BioModelAnalyzer, a tool that uses software verification algorithms to analyse biological network dynamics, I was employed part-time throughout 2014.


Background

I left Sweden for a degree in Neuroscience, but quickly found that the real action takes place at the cell membrane. In the flexible undergraduate environment at the University of Edinburgh, I migrated from Neuroscience to Chemistry, completed internships in both Stockholm and Edinburgh stem cell labs, and was part of the Edinburgh University team at the MIT Genetically Engineered Machine competition, before landing in structural biochemistry. I graduated with Honours in Biochemistry in 2008, and entered Oxford University's Doctoral Training Centre on an EPSRC scholarship.

I joined the Sansom group as a D.Phil student in 2010 after completing three 10-week projects in physics, bioengineering/mathematics and optogenetics.


Research output

Laurent B, Chavent M, Cragnolini T, Dahl ACE, Pasquali S, Derreumaux P, Sansom MSP and Baaden M (2014) Epock: rapid analysis of protein pocket dynamics. Bioinformatics doi: 10.1093/bioinformatics/btu822. Preprint available here. See also the Epock website.

Chavent M, Reddy T, Goose J, Dahl ACE, Stone JE, Jobard B and Sansom MSP (2014) FD169: Methodologies for the Analysis of Instantaneous Lipid Diffusion in MD Simulations of Large Membrane Systems. Faraday Discussions 169 455-475. Full paper. See also the Flows website.

Dahl ACE, Aryal P, Tucker SJ, and Sansom MSP (2013) Ion channel mechanotransduction: lessons learned from bacteria, and application to human channels. Ion Channels in Health and Disease, University of Cambridge (poster presentation)

Dahl ACE (2012) Based on a true story - Adopting sequential art for science and technology communication. Transitions 3, Birkbeck, University of London (talk)

Dahl ACE, Chavent M and Sansom MSP (2012) Bendix: New software for intuitive helix geometry analysis and abstraction. OXION: Ion Channels and Disease Initiative Day (poster presentation)

Dahl ACE, Chavent M and Sansom MSP (2012) Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics 28 (16): 2193-2194. Abstract See also the Bendix website.

Dahl ACE (2012) Visualizing Molecular Data. GGM12 Tekniska Museet, Stockholm (invited talk)

Dahl ACE (2012) Code in Molecular Dynamics. GGM UK launch, Google Campus London (talk)

Dahl ACE, Chavent, M and Sansom, MSP (2012) Analysing helix flexibility in membrane proteins using Bendix. Annual US Biophysical Society conference, San Diego (poster presentation) Abstract

Dahl ACE, Chavent M and Sansom MSP (2011) Visualization and Analysis of Helix Flexibility Using Bendix. Young Modeller Forum, London (poster presentation)

Dahl ACE, Chavent M and Sansom MSP (2011) Bendix: a VMD plugin that cartoons proteins and characterizes helix conformation. OXION: Ion Channels and Disease Initiative Day (poster presentation)

Dahl ACE and Thompson MS (2011) 5.18 - Mechanobiology of Bone, In: Comprehensive Biotechnology (Second Edition) Volume editor Moo-Young M, Academic Press, Burlington, pp 217-236 Abstract

Dahl ACE (2011) Functional protein visualization. UK Systems Biology inter-DTC conference, University of Manchester (talk)

Dahl ACE and Thompson M (2010) Bone mechanosensation. Systems Biology InterDTC Conference 2010, University of Warwick (poster presentation)

Click below to download a Flash image overview of what happens to osteocytes upon mechanical impact (when you take a step) !
Mouse over molecule abbreviatons to view their full names, and toggle between pre-mechanical impact and during impact, which features suggested reaction pathways and changes to cell physiology in response to mechanical stimulus.
For more information, read the review here.

Download bone cell Flash file.

Dahl ACE (2008) A computational epigenetics study of nucleosome positioning with respect to CpG islands in the human and mouse genomes. Dissertation presented to University of Edinburgh in partial fulfillment of requirements for the degree of BSc (Hons Biochemistry).

Dahl ACE, Gerosa L, Hollingshead S, Marshall A, Ravindranath P, Rokicki J, Wang X, Yin D, Elfick A, French C and Ma H (2008) University of Edinburgh iGEM 2007 projects: A cell division detector, and self-flavouring yoghurt. BioSysBio 2008, Imperial College London (poster presentation)

Dahl ACE, Gerosa L, Hollingshead S, Marshall A, Ravindranath P, Rokicki J, Wang X, Yin D, Elfick A, French C and Ma H (2007) The Cell Division PoPper, and Self Flavouring Yoghurt. iGEM 2007, MIT Cambridge MA (poster presentation and talk). See the website for details.

Dahl ACE, Gerosa L, Hollingshead S, Marshall A, Ravindranath P, Rokicki J, Wang X, Yin D, Elfick A, French C and Ma H (2007) The 2007 Edinburgh iGEM team submissions. ESRC Genomics Policy and Research Forum, Edinburgh (talk)
Last updated January 2015