Thursday, January 29, 2015

Quantum Chemistry Nanomedicine Theoretical and Computational Future Technologies






The absurd world of the electrons

The quantum chemical calculations solve the Schrödinger equation for molecules. This equation is fundamental to all chemistry and describes the whereabouts of all electrons within a molecule. But here we need to pay attention, for things are really rather more complicated than that. Your high school physics teacher will have told you that electrons circle the atom. Things are not that simple, though, in the world of quantum physics. Electrons are not only particles, but waves as well. The electrons can be in many places at the same time. It's impossible to keep track of their position. However, there is hope. Quantum chemical models describe the electrons' statistical positions. In other words, they can establish the probable location of each electron.

The results of a quantum chemical calculation are often more accurate than what is achievable experimentally.

Among other things, the quantum chemical calculations can be used to predict chemical reactions. This means that the chemists will no longer have to rely on guesstimates in the lab. It is also possible to use quantum chemical calculations in order to understand what happens in experiments.

Enormous calculations

The calculations are very demanding.

"The Schrödinger equation is a highly complicated, partial differential equation, which cannot be accurately solved. Instead, we need to make do with heavy simulations," says researcher Simen Kvaal.

The computations are so demanding that the scientists use one of the University's fastest supercomputers.

"We are constantly stretching the boundaries of what is possible. We are restricted by the available machine capacity," explains Helgaker.

Ten years ago it took two weeks to carry out the calculations for a molecule with 140 atoms. Now it can be done in two minutes.

"That's 20,000 times faster than ten years ago. The computation process is now running 200 times faster because the computers have been doubling their speed every eighteen months. And the process is a further 100 times faster because the software has been undergoing constant improvement," says senior engineer Simen Reine.

This year the research group has used 40 million CPU hours, of which twelve million were on the University's supercomputer, which is fitted with ten thousand parallel processors. This allows ten thousand CPU hours to be over and done with in 60 minutes.

"We will always fill the computer's free capacity. The higher the computational capacity, the bigger and more reliable the calculations."
Thanks to ever faster computers, the quantum chemists are able to study ever larger molecules.

Today, it's routine to carry out a quantum chemical calculation of what happens within a molecule of up to 400 atoms. By using simplified models it is possible to study molecules with several thousand atoms. This does, however, mean that some of the effects within the molecule are not being described in detail.
The researchers are now getting close to a level which enables them to study the quantum mechanics of living cells.

"This is exciting. The molecules of living cells may contain many hundred thousand atoms, but there is no need to describe the entire molecule using quantum mechanical principles. Consequently, we are already at a stage when we can help solve biological problems."







Hunting for the electrons of the insulin molecule

The chemists are thus able to combine sophisticated models with simpler ones. "This will always be a matter of what level of precision and detail you require. The optimal approach would have been to use the Schrödinger equation for everything."

By way of compromise they can give a detailed description of every electron in some parts of the model, while in other parts they are only looking at average numbers.

"We are always having to find a good balance between the details we need and those we don't need."

Simen Reine has been using the team's computer program, while working with Aarhus University, on a study of the insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons.

"All electrons repel each other, while at the same time being pulled towards the atom nuclei. The atom nuclei also repel each other. Nevertheless, the molecule remains stable. In order to study a molecule to a high level of precision, we therefore need to consider how all of the electrons move relative to one another. Such calculations are referred to as correlated equations and are very reliable."
A complete correlated equation of the insulin molecule takes nearly half a million CPU hours. If they were given the opportunity to run the program on the University's supercomputer, the calculations would theoretically take two days.
"In ten years, we'll be able to make these calculations in two minutes."

Medically important

Vice Rector Knut Fægri at the University of Oslo points out that quantum chemical calculations may become important to life sciences.
"Quantum chemical calculations can help describe phenomena at a level that may be difficult to access experimentally, but may also provide support for interpreting and planning experiments. Today, the calculations will be put to best use within the fields of molecular biology and biochemistry," says Knut Fægri.
Associate Professor Michele Cascella at the Centre for Theoretical and Computational Chemistry has recently been recruited from Italy to introduce quantum chemistry into life sciences.

"Quantum chemistry is a fundamental theory which is important for explaining molecular events, which is why it is essential to our understanding of biological systems," says Michele Cascella.

By way of an example, he refers to the analysis of enzymes. Enzymes are molecular catalysts that boost the chemical reactions within our cells.
Cascella also points to nanomedicines, which are drugs tasked with distributing medicine round our bodies in a much more accurate fashion.
"In nanomedicine we need to understand physical phenomena on a nano scale, forming as correct a picture as possible of molecular phenomena. In this context, quantum chemical calculations are important," explains Michele Cascella.




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