Annotation
Computational models are invaluable for visualisation in molecular biology, as they employ our best quantitative physical understanding of biomolecules and their interactions. Modelling and simulation can help us to assemble experimental information from different sources, and can generate insightful new research questions that inspire new experiments. I will highlight the challenges for simulations and how these intersect with experiments, and comment on how these reflect the bigger questions in structural and integrative biology. I will use our work on DNA supercoiling and molecular motors to show how we have used computation to address mechanistic questions in molecular biology.
References:
[1] Solernou A., Hanson B. S., Richardson R. A., Welch R., Read D. J., Harlen O. G. & Harris S. A. “Fluctuating Finite Element Analysis (FFEA): A Continuum Mechanics Software Tool for Mesoscale Simulation of Biomolecules” PLoS Comp. Bio. (Software Paper) (2018), 14, e1005897
[2] Leng J., Shoura M., McLeish T. C. B., Real A. N., Hardey M., McCafferty J., Ranson N. A. & Harris S. A. “Securing the future of Research Computing in the biosciences”, Plos Comp. Bio. (2019), 15, e1006958.
[3] Pyne, A.L.B., et al., “Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.” Nat Commun. (2021). 12: p. 1053.
Language
English
Tutor
Sarah Harris, University of Sheffield, United Kingdom
Sarah Anne Harris is a computational biophysicist and Chair of Biological and Materials Physics in the School of Mathematical and Physical Sciences in Sheffield. Her research uses high performance computer simulations to provide physical insight into biological mechanisms from the atomistic up to the cellular level. She has developed new theoretical physics tools to understand molecular biology at the mesoscale (https://ffea.bitbucket.io/), with a focus on modelling molecular motors such as dynein and myosin. Sarah is a strong advocate for the use of computation in the biological sciences, and is the current Chair of the Collaborative Computational Project in Biomolecular simulation (CCPBioSim) which supports UK researchers using simulations to understand biomolecular interactions and processes. CCPBioSim provides both beginners and expert workshops, and meetings identifying new cutting edge topics (https://www.ccpbiosim.ac.uk/).
This course was supported by the Ministry of Education, Youth and Sports of the Czech Republic through the e-INFRA CZ (ID:90254).
All presentations and educational materials of this course are provided under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license.
