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If your computer freezes, users will naturally press the button to restart.
Researchers at Tel Aviv University (TAU) have discovered that this well-known IT practice can also be applied to chemistry – to enhance sampling in chemical simulations, simply stop and restart.
Team members explained that molecular dynamics simulations act like a virtual microscope, explaining the motion of all atoms in chemical, physical and biological systems such as proteins, liquids and crystals.
They provide insights into a variety of processes and have different technical applications, including drug design.
However, these simulations are limited to processes slower than a millionth of a second and therefore cannot describe slower processes such as protein folding and crystal nucleation. This limitation, known as the time scale problem, is a huge challenge in the field.
Research details
The research was led by PhD student Ofir Blumer in collaboration with Professor Shlomi Reuveni and Dr. Barak Hirshberg from Tel Aviv University’s School of Chemistry.The research was published in a prestigious journal nature communications Titled “Combining stochastic resets with metadynamics to accelerate molecular dynamics simulations.”
“In our new study, we show that the time scale problem can be overcome through stochastic (randomly decided) resets of the simulation. This may seem counterintuitive at first glance – how can a simulation end faster when restarted?” Bloomer explain.
“However, it turns out that reaction times vary widely between simulations. In some simulations, reactions happen very quickly, but other simulations get stuck in the middle for long periods of time. Resetting prevents simulations from getting stuck in such in-betweens and shortens Average simulation time.”
The researchers also combined stochastic resets with metadynamics, a popular method for speeding up simulations of slow chemical processes.
The combination can achieve greater acceleration than either method alone. Furthermore, metadynamics relies on a priori knowledge: the reaction coordinates must be known to speed up the simulation. The combination of metadynamics and reset significantly reduces the reliance on prior knowledge, saving time for practitioners of the method.
In the end, the researchers showed that this combination allowed for more accurate predictions of the rate of slow processes. This combined approach successfully enhanced simulations of protein folding in water and is expected to be applied to more systems in the future.
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