Computational Microscope Brings Atomic and Subatomic World to Light

To streamline the process of atomic and subatomic simulations, researchers developed the computational microscope: a new hybrid method for molecular and quantum modeling.

The atomic and subatomic world is hard to access and experiment with using macroscopic simulation models.

To refine their understanding of matter at the atomic and subatomic scale, scientists use a set of computer simulation programs to model molecular mechanics.

Over the past few decades, the development of computational simulation techniques has helped advance research into several fields like chemistry, biochemistry, and condensed matter physics.

The Computational Microscope: Molecular and Quantum Modeling Made Easy

One of the computer simulation techniques used is Molecular Dynamics. This method is mainly used to study molecular and atomic movement and evolution over time

NAMD (Nanoscale Molecular-Dynamics) is a freeware molecular dynamics program that simulates the molecular mechanics of large atomic systems.

Developed at the University of Illinois at Urbana–Champaign, NAMD was introduced in 1995, and a stable version was released in 2016.

There are other visualization programs (like VMD, also developed at ULUC) that focus on the quantum dynamics of matter. These allow scientists to model the interactions between subatomic particles like electrons, neutrons, and protons.

However, molecular simulations at this very small scale require HPC (high-performance computing) resources.

To model a molecular system in efficient time, the computing environment has to meet certain requirements in terms of processing and storage capacities.

Now, researchers at the University of Illinois at Urbana–Champaign, with experts from the Max Planck Institute for Coal Research (Germany), and the Federal University of Paraiba (Brazil), have developed a new computer modeling method that combines two simulation techniques.

Referred to as a computational microscope, the new method is a hybrid between molecular dynamics (MM) and quantum dynamics. It also has the capabilities of both NAMD and VMD programs.

Basically, researchers took their NAMD program and updated it with quantum dynamics feature.

The new QM/MM interface, which is freely available, will streamline the work of preparing, running, and analyzing molecular simulations.

“We set it up so that researchers can easily choose how they will partition their own systems,” said Luthey-Schulten co-leader of the research and NAMD developer. “My own students are trying it out, and most of them are able to do it without much difficulty.”