Simulations document self-assembly of proteins and DNA

March 28, 2018, Springer

What makes particles self-assemble into complex biological structures? Often, this phenomenon is due to the competition between forces of attraction and repulsion, produced by electric charges in various sections of the particles. In nature, these phenomena often occur in particles that are suspended in a medium—referred to as colloidal particles—such as proteins, DNA and RNA. To facilitate self-assembly, it is possible to "decorate" various sites on the surface of such particles with different charges, called patches.

In a new study published in EPJE, physicists have developed an algorithm to simulate the molecular dynamics of these patchy . The findings published by Silvano Ferrari and colleagues from the TU Vienna and the Centre for Computational Materials Science (CMS), Austria, will improve our understanding of what makes self-assembly in biological systems possible.

In this study, the authors model charged patchy particles, which are made up of a rigid body with only two charged patches, located at opposite poles. They then develop the equations governing the dynamics of an ensemble of such colloidal patchy particles.

Based on an existing approach originally developed for molecular particles, their simulation includes additional constraints to guarantee that the electrical charge "decorations" are preserved over time. In this regard, they develop equations for describing the particles' motion; the solutions to these equations describe the trajectories of these colloidal particles. Such simulations lend themselves to being run in parallel on a huge number of particles.

With these findings, the authors complement the lessons learned from experimental observations of similar particles recently synthesised in the lab. Recent experiments have demonstrated that decorated at two interaction sites display a remarkable propensity for self-organising into highly unusual structures that remain stable over a broad temperature range.

Explore further: Solid and liquid at the same time

More information: Silvano Ferrari et al, Molecular dynamics simulations of inverse patchy colloids, The European Physical Journal E (2018). DOI: 10.1140/epje/i2018-11647-2

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