Category Archives: simulation

Quantum computers could excel in modeling chemical reactions

Quantum computers would likely outperform conventional computers in simulating chemical reactions involving more than four atoms, according to scientists at Harvard University, the Massachusetts Institute of Technology, and Haverford College. Such improved ability to model and predict complex chemical reactions could revolutionize drug design and materials science, among other fields.

Writing in the Proceedings of the National Academy of Sciences, the researchers describe “software” that could simulate chemical reactions on quantum computers, an ultra-modern technology that relies on quantum mechanical phenomena, such as entanglement, interference, and superposition. Quantum computing has been heralded for its potential to solve certain types of problems that are impossible for conventional computers to crack.

“There is a fundamental problem with simulating quantum systems — such as chemical reactions — on conventional computers,” says Alán Aspuru-Guzik, assistant professor of chemistry and chemical biology in Harvard’s Faculty of Arts and Sciences. “As the size of a system grows, the computational resources required to simulate it grow exponentially. For example, it might take one day to simulate a reaction involving 10 atoms, two days for 11 atoms, four days for 12 atoms, eight days for 13 atoms, and so on. Before long, this would exhaust the world’s computational power.”

Unlike a conventional computer, Aspuru-Guzik and his colleagues say, a quantum computer could complete the steps necessary to simulate a chemical reaction in a time that doesn’t increase exponentially with the reaction’s complexity.


The future of biomedicine: virtual humans

The future of biomedicine: virtual humans

This is your brain on a chip. This is your liver on a slide. This is your body in a supercomputer. Any questions?

It’s a bit more complicated than that, but recently scientists have provided a sneak preview of the future of biomedicine with a range of projects seeking to assemble virtual humans — or parts of them — on computers and “labs on a chip.” Someday, the descendants of these sophisticated new programs and devices could serve as our stand-ins for clinical tests on drugs, cosmetics and toxic compounds.

“I would predict that this century is going to be dominated by our ability to handle biomedical problems in a computational domain,” said Peter Coveney, director of the Centre for Computational Science at University College London.

Researchers Simulate Photosynthesis, Design Better Leaf

Researchers successfully simulate photosynthesis and design a better leaf

University of Illinois researchers have built a better plant, one that produces more leaves and fruit without needing extra fertilizer. The researchers accomplished the feat using a computer model that mimics the process of evolution. Theirs is the first model to simulate every step of the photosynthetic process.

Photosynthesis converts light energy into chemical energy in plants, algae, phytoplankton and some species of bacteria and archaea. Photosynthesis in plants involves an elaborate array of chemical reactions requiring dozens of protein enzymes and other chemical components. Most photosynthesis occurs in a plant’s leaves.

It wasn’t feasible to tackle this question with experiments on actual plants, Long said. With more than 100 proteins involved in photosynthesis, testing one protein at a time would require an enormous investment of time and money.

“But now that we have the photosynthetic process ‘in silico,’ we can test all possible permutations on the supercomputer,” he said.

Using “evolutionary algorithms,” which mimic evolution by selecting for desirable traits, the model hunted for enzymes that – if increased – would enhance plant productivity. If higher concentrations of an enzyme relative to others improved photosynthetic efficiency, the model used the results of that experiment as a parent for the next generation of tests.

This process identified several proteins that could, if present in higher concentrations relative to others, greatly enhance the productivity of the plant. The new findings are consistent with results from other researchers, who found that increases in one of these proteins in transgenic plants increased productivity.

“By rearranging the investment of nitrogen, we could almost double efficiency,” Long said.

Virtual Model of Human Metabolism

Human metabolism recreated in lab

US researchers say they have created a “virtual” model of all the biochemical reactions that occur in human cells.They hope the computer model will allow scientists to tinker with metabolic processes to find new treatments for conditions such as high cholesterol.

It could also be used to individually tailor diet for weight control, the University of California team claimed.

A team of six bioengineering researchers at the University of California analysed the human genome to see what genes corresponded to metabolic processes, such as those responsible for the production of enzymes.

They spent a year manually going through 1,500 books, review papers and scientific reports from the past 50 years before constructing a database of 3,300 metabolic reactions.

The information was then used to create a network of metabolic processes in the cell, similar to a traffic network.