#computer modelling

Lead the Follower

Computer modelling collective cell migration – such as occurs in wound healing, embryo development and cancer invasion – reveals the contributions to the speed of migration made by characteristics of the cells of the leader and follower rows

Read the published research article here

Video from work by Tien Comlekoglu and colleagues

Department of Cell Biology, University of Virginia, Charlottesville, VA, USA

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in Biology Open, September 2024

BIM Lesson today again. Also spent some time to work with the quick note jotted down during lessons.

How Tumours Grow

Compared with cells at the centre of a tumour, those on the surface are adjacent to healthy, blood-supplied tissues. This fact led to the hypothesis that cells divide rapidly at the surface of a tumour but rarely at its core. A recent spatial genomics analysis of hundreds of liver cancer samples from various positions and depths within tumours revealed, however, this isn’t the case. Liver cancer cells show uniform growth throughout the tumour mass. The analysis mapped cells bearing new mutations, finding their descendants were located in all directions, not just outward (as would occur with surface-only cell division). Validation was gained through computer models, like the one pictured, which shows mutations spreading uniformly through a tumour to a greater (red) or lesser (blue) extent. Since novel cancer mutations can confer resistance to drugs or immune detection, knowing how and where they arise will inform future tumour-tackling therapies.

Written by Ruth Williams

Image from work by Arman Angaji and colleagues

Institute for Biological Physics, University of Cologne, Cologne, Germany

Image contributed by the authors under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence

Published in eLife, November 2024

Powerful Model

Nothing stays still. Even at the atomic level – especially at the atomic level – forces between particles keep them wriggling, even when locked in a relatively 'stable' structure. In these computer simulations, researchers mimic tiny proteins in the conical outer shell or capsid of the human immunodeficiency virus. Each pentamer (green) or hexamer (cream) structure is built from smaller building blocks called monomers – the model traces their jostling movements over nanoseconds. Simulating so many moving parts at once is a huge challenge for computer power, so the research team uses new methods to balance the ‘granularity’ of the model – how abstracted the molecular details are from real life – with how faithfully they mimic the overall biological behaviour. New algorithms using a 'coarser' granularity require less computer power (and energy), opening up the power similar simulations to more research groups worldwide.

Written by John Ankers

Video from work by Alexander J. Bryer, Juan S. Rey & Juan R. Perilla

Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA

Video originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in Nature Communications, April 2023

Follow the Beat

Motile cilia keep things flowing. These cell projections, which line certain tissues, such as those in your nose, periodically beat to move fluid along. In dense carpets of cilia, they coordinate their beats in travelling movements called metachronal waves. How they do this isn’t clear, so researchers investigate in zebrafish noses. Fluorescence microscopy combined with spectral analysis revealed cilia only synchronised locally and the synchronisation area increased in size as the surrounding fluid became thicker. Although synchronisation was local, metachronal waves travelled across the entire multi-ciliated tissue. The direction of these wave patterns was the same across fish but different between left and right nose (pictured) where they were mirror reflections of each other. Computational modelling of wave patterns revealed that their synchronisation prevented cilia (magenta) colliding with each other and improved fluid movement but hardly affected the direction of flow. These waves, therefore, help cilia perform at their best.

Written by Lux Fatimathas

Image from work by Christa Ringers and colleagues

Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in eLife, January 2023

Bee Brained

Bee-lieve it or not, this image is the brain of a honeybee, with the coloured areas highlighting the parts that are involved in interpreting the signals coming from the insect’s antennae as it smells the world around it. Insects like bees are important subjects in neuroscience research, because they’re small enough to study their entire brains in detail but complex enough to show behaviours like sensing and learning. All around the world, researchers are collecting detailed images and datasets from a wide range of insects, from bees and butterflies to beetles and flies. But because all this information is stored in different places and formats, it’s hard to know what’s out there or make comparisons between different insects. The new InsectBrainDatabase (IBdb) gathers together all these datasets and makes them searchable and shareable, allowing researchers to compare brains of different insect species and gain new insights into how they work.

Written by Kat Arney

Image from work by Stanley Heinze and colleagues

Department of Biology, Lund University, Lund, Sweden

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in eLife, August 2021

A Little Perspective

Imagine strolling along the surface of a single cell from your body. Protruding structures tower over you like trees in a forest, helping you learn their biological form and function, like a child on a guided nature walk. Creating this experience, or a virtual version of it, is the goal of a new tool called Nanoscape. Our detailed understanding of structural cellular biology has enabled an explosion of digital renderings in recent years. But aligning scientific data with aesthetically functional and impactful images is not straightforward. This approach combines data from many sources to create as accurate a representation as possible without sacrificing the visualisations’ aesthetic appeal (pictured, well-known cell-surface markers above, then placed on a virtual sphere to approximate a cell surface environment). Immersive representations like this articulate intricate complexities of biology, both for education and for those seeking to answer fundamental questions about how microscopic dynamics underpin life.

Written by Anthony Lewis

Image adapted from work by Shereen R Kadir and colleagues

3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in eLife, June 2021