Computers Math

With a big assist from artificial intelligence and a heavy dose of human touch, Tim Cernak’s lab at the University of Michigan made a discovery that dramatically speeds up the time-consuming chemical process of building molecules that will be tomorrow’s medicines, agrichemicals or materials.
The discovery, published in the Feb. 3 issue of Science, is the culmination of years of chemical synthesis and data science research by the Cernak Lab in the College of Pharmacy and Department of Chemistry.
The goal of the research was to identify key reactions in the synthesis of a molecule, ultimately reducing the process to as few steps as possible. In the end, Cernak and his team achieved the synthesis of a complex alkaloid found in nature in just three steps. Previous syntheses took between seven and 26 steps.
“Making a chemical structure that has atoms in just the right place to give you efficacious and nontoxic medicines, for instance, is tricky,” said Cernak, assistant professor of medicinal chemistry and chemistry. “It requires a chemical synthesis strategy grounded in the chemical building blocks you can actually buy and then stitch together using chemical reactions.”
The accomplishment has powerful implications for speeding up the development of medicines.
Cernak compared the construction of these complex molecules to playing chess. You need to orchestrate a series of moves to get to the end of the game. While there’s a near infinite number of possible moves, there’s a logic that can be followed.
“We developed a logic here, based in graph theory, to get to the end as quickly as possible,” he said.
Cernak and colleagues used SYNTHIA Retrosynthesis Software, which provides scientists with a database of pathways, or steps, and formulas for millions of molecular structures. This gave the team an enormous amount of computational synthesis data to play with.
Using an algorithm they developed to curate the data, the researchers identified the steps along the pathway that were high impact, or key steps, and the steps that were making progress toward completing the synthesis but ultimately inefficient for the whole process.
“We hope this research can lead to better medicines,” Cernak said. “So far, we have been limited in the molecular structures we can quickly access with chemical synthesis.”
Co-authors include Yingfu Lin, senior research fellow in pharmacy; Rui (Sam) Zhang, doctoral student in chemistry; and Di Wang, doctoral student in pharmacy. More

An exciting prospect in modern optics is to exploit “patterns of light,” how the light looks in its many degrees of freedom, often referred to as structured light.
Each pattern could form an encoding alphabet for optical communication or might be used in manufacturing to enhance performance and productivity. Unfortunately, patterns of light get distorted when they pass through noisy channels, for instance, stressed optical fiber, aberrated optics, turbid living tissue, and perhaps a very severe example, atmospheric turbulence in air.
In all these examples, the distorted pattern can deteriorate to the point that the output pattern looks nothing like the input, negating the benefit. Now researchers from the University of the Witwatersrand (Wits University) in South Africa have shown how it is possible to find distortion-free forms of light that come out of a noisy channel exactly the same as they were put in.
Using atmospheric turbulence as an example, they showed that these special forms of light, called eigenmodes, can be found for even very complex channels, emerging undistorted, while other forms of structured light would be unrecognisable. Their research has been published in the journal, Advanced Photonics — the flagship journal of SPIE, the international society for optics and photonics.
“Passing light through the atmosphere is crucial in many applications, such as free-space optics, sensing and energy delivery, but finding how best to do this has proved challenging,” says Professor Andrew Forbes, head of the Structured Light Laboratory at Wits University.
Traditionally a trial-and-error approach has been used to find the most robust forms of light to some particular noisy channel, but to date all forms of familiar structured light have shown to be distorted as the medium become progressively more noisy. The reason is that we “see” the distortion.
To establish whether it is possible to create light that doesn’t “see” the distortion, passing through as if it wasn’t there the researchers treated the noisy channel as a mathematical operator and asked a simple question: “what forms of light would be invariant to this operator?.” In other words, what forms of light appear as the natural mode of the channel that it is in, so that it don’t see the distortion. This can also be called the true eigenmodes of the channel.
The example tackled was the severe case of distortions due to atmospheric turbulence. The answer to the problem revealed unrecognizable forms of light — in other words, light that is not in any well-known structured light family, but nevertheless completely robust to the medium. This fact was confirmed experimentally and theoretically for weak and strong turbulence conditions.
“What is exciting about the work is that it opens up a new approach to studying complex light in complex systems, for instance, in transporting classical and quantum light through optical fiber, underwater channels, living tissue and other highly aberrated systems,” says Forbes.
Because of the nature of eigenmodes, it doesn’t matter how long this medium is, nor how strong the perturbation, so that it should work well even in regimes where traditional corrective procedures, such as adaptive optics, fail.
“Maintaining the integrity of structured light in complex media will pave the way to future work in imaging and communicating through noisy channels, particularly relevant when the structured forms of light are fragile quantum states.” More