The knotty problem of DNA tangling

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This article is a little different from the fare you’re used to getting from me: it’s for SIAM News, which is the magazine for members of the Society for Industrial and Applied Mathematics (SIAM). The audience for this magazine, in other words, is professional mathematicians and related researchers working in a wide variety of fields. While the article contains equations, I wrote it to be understandable even if you skip over the math.

I will also have you know, I only included one of the many knot-theory puns I came up with while writing the piece. Professionalism, people. Professionalism.

Untangling DNA with Knot Theory

For SIAM News:

Long before there were sailors, nature learned to tie—and untie—knots. Certain DNA types, proteins, magnetic fields, fluid vortices, and other diverse phenomena can manifest in the form of loops, which sometimes end up tangled. But knots, kinks, and tangles are often undesirable for the system in which they occur; for instance, knotted DNA can kill its cell. In such cases, nature finds ways to restore order.

Mariel Vazquez of the University of California, Davis, uses topology to understand the knotting and unknotting of real-world molecules. Specifically, she and her colleagues employ topological concepts from knot theory to demonstrate that cells detangle DNA with optimal efficiency.

During her talk at the 2018 SIAM Annual Meeting, held in Portland, Ore., this July, Vazquez emphasized her work’s multidisciplinary nature; although she focuses on DNA, her research has applications beyond molecular biology.

[Read the rest at SIAM News]


How physics and biology work together to understand cell organization

[ This blog is dedicated to tracking my most recent publications. Subscribe to the feed to keep up with all the science stories I write! ]

Cells get organized

How researchers probe the physics of motion, communication and organization in cell networks, and how understanding these systems could help us tackle serious issues in medicine and biology

self-organized bacterial community

A colony of bacteria organize with each other under certain conditions to maximize nutrient intake. [Credit: Eshel Ben-Jacob]

From Physics World:

Consider this scenario: in your haste to grab the latest issue of Physics World, you scrape your hand on your postbox. It’s nothing severe, just a little scratch, but if your immune system is functioning as it should, your body will perform an amazing feat of microscopic organization. Your body assesses the level of damage and threat from infection, sending security cells to the site to hoover up intrusive bacteria and seal the wound. Within a few days you’d hardly know the scrape was ever there: your skin and blood vessels repair themselves.

Except of course there’s no mind behind this repair. Your brain isn’t required to heal a wound: there’s no local oversight from any intelligent agent, and the cells involved don’t think. Instead, cells interact with their neighbours, and a larger pattern emerges from those small-scale interactions. That’s the key to “self-organization”, whether it occurs in the human immune system, swarms of locusts, water molecules in a snowflake or electrons in a magnetic material.

For that reason, researchers studying biological self-organization draw heavily on physics. Some directly investigate the physical interactions between cells and their environments; others use theoretical models drawn or adapted from physics to understand emergent behaviours in biological systems. It’s an interdisciplinary field, involving physicists, computer scientists, biologists, mathematicians and medical doctors.

The rest of this story is in the print edition of Physics World, which you can subscribe to through membership in the Institute of Physics, which costs £15, €20, or $25 per year. You can join by clicking here. You can also get a nice mobile- and tablet-formatted version of the story using the Physics World app, available in the Google Play and iTunes stores. However, if you just want to read the rest of this article, Physics World has kindly allowed me to offer it to you as a PDF download, which looks exactly like the printed version!