The resulting simulation describes how water molecules transition into solid ice with quantum accuracy. This level of accuracy, once thought unreachable due to the amount of computing power it would require, became possible when the researchers incorporated deep neural networks, a form of artificial intelligence, into their methods. The study was published in the journal Proceedings of the National Academy of Sciences.

“In a sense, this is like a dream come true,” said Roberto Car, Princeton’s Ralph W. *31 Dornte Professor in Chemistry, who co-pioneered the approach of simulating molecular behaviors based on the underlying quantum laws more than 35 years ago. “Our hope then was that eventually we would be able to study systems like this one, but it was not possible without further conceptual development, and that development came via a completely different field, that of artificial intelligence and data science.”

The ability to model the initial steps in freezing water, a process called ice nucleation, could improve accuracy of weather and climate modeling as well as other processing like flash-freezing food.

The new approach enables the researchers to track the activity of hundreds of thousands of atoms over time periods that are thousands of times longer, albeit still just fractions of a second, than in early studies.

Car co-invented the approach to using underlying quantum mechanical laws to predict the physical movements of atoms and molecules. Quantum mechanical laws dictate how atoms bind to each other to form molecules, and how molecules join with each other to form everyday objects.

Car and Michele Parrinello, a physicist now at the Istituto Italiano di Tecnologia in Italy, published their approach, known as “ab initio” (Latin for “from the beginning”) molecular dynamics, in a groundbreaking paper in 1985.

But quantum mechanical calculations are complex and take tremendous amounts of computing power. In the 1980’s, computers could simulate just a hundred atoms over spans of a few trillionths of a second. Subsequent advances in computing and the advent of modern supercomputers boosted the number of atoms and timespan of the simulation, but the result fell far short of the number of atoms needed to observe complex processes such as ice nucleation.

AI provided an attractive potential solution. Researchers train a neural network, named for its similarities to the workings of the human brain, to recognize a comparatively small number of selected quantum calculations. Once trained, the neural network can calculate the forces between atoms that it has never seen before with quantum mechanical accuracy. This “machine learning” approach is already in use in everyday applications such as voice recognition and self-driving automobiles.

In the case of AI applied to molecular modeling, a major contribution came in 2018 when Princeton graduate student Linfeng Zhang, working with Car and Princeton professor of mathematics Weinan E, found a way to apply deep neural networks to modeling quantum-mechanical interatomic forces. Zhang, who earned his Ph.D. in 2020 and is now a research scientist at the Beijing Institute of Big Data Research, called the approach “deep potential molecular dynamics.”

In the current paper, Car and postdoctoral researcher Pablo Piaggi along with colleagues applied these techniques to the challenge of simulating ice nucleation. Using deep potential molecular dynamics, they were able to run simulations of up to 300,000 atoms using significantly less computing power, for much longer timespans than were previously possible. They carried out the simulations on Summit, one of the world’s fastest supercomputers, located at Oak Ridge National Laboratory.

This work provides one of the best studies of ice nucleation, said Pablo Debenedetti, Princeton’s dean for research and the Class of 1950 Professor of Engineering and Applied Science, and a co-author of the new study.

“Ice nucleation is one of the major unknown quantities in weather prediction models,” Debenedetti said. “This is a quite significant step forward because we see very good agreement with experiments. We’ve been able to simulate very large systems, which was previously unthinkable for quantum calculations.”

Currently, climate models obtain estimates of how fast ice nucleates primarily from observations made in laboratory experiments, but these correlations are descriptive, not predictive, and are valid over a limited range of experimental conditions. In contrast, molecular simulations of the type done in this study can produce simulations that are predictive of future situations, and can estimate ice formation under extreme conditions of temperature and pressure, such as on other planets.

“The deep potential methodology used in our study will help realize the promise of ab initio molecular dynamics to produce valuable predictions of complex phenomena, such as chemical reactions and the design of new materials,” said Athanassios Panagiotopoulos, the Susan Dod Brown Professor of Chemical and Biological Engineering and a co-author of the study.

“The fact that we are studying very complex phenomena from the fundamental laws of nature, to me that is very exciting,” said Piaggi, the study’s first author and a postdoctoral research associate in chemistry at Princeton. Piaggi earned his Ph.D. working with Parrinello on the development of new techniques to study rare events, such as nucleation, using computer simulation. Rare events take place over timescales that are longer than the simulation times that can be afforded, even with the help of AI, and specialized techniques are needed to accelerate them.

Jack Weis, a graduate student in chemical and biological engineering, helped increase the likelihood of observing nucleation by “seeding” tiny ice crystals into the simulation. “The goal of seeding is to increase the likelihood that water will form ice crystals during the simulation, allowing us to measure the nucleation rate,” said Weis, who is advised by Debenedetti and Panagiotopoulos.

Water molecules consist of two hydrogen atoms and an oxygen atom. The electrons around each atom determine how atoms can bond with each other to form molecules.

“We start with the equation that describes how electrons behave,” Piaggi said. “Electrons determine how atoms interact, how they form chemical bonds, and virtually the whole of chemistry.”

The atoms can exist in literally millions of different arrangements, said Car, who is director of the Chemistry in Solution and at Interfaces center, funded by the U.S. Department of Energy Office of Science and including regional universities.

“The magic is that because of some physical principles, the machine is able to extrapolate what happens in a relatively small number of configurations of a small collection of atoms to the countless arrangements of a much bigger system,” Car said.

Although AI approaches have been available for some years, researchers have been cautious about applying them to calculations of physical systems, Piaggi said. “When machine learning algorithms started to become popular, a big part of the scientific community was skeptical, because these algorithms are a black box. Machine learning algorithms don’t know anything about the physics, so why would we use them?”

In the last couple of years, however, there has been a significant change in this attitude, Piaggi said, not only because the algorithms work but also because researchers are using their knowledge of physics to inform the machine learning models.

For Car, it is satisfying to see the work started three decades ago come to fruition. “The development came via something that was developed in a different field, that of data science and applied mathematics,” Car said. “Having this kind of cross interaction between different fields is very important.”

This work was supported by the U.S. Department of Energy (grant DE-731 SC0019394) and used resources of the Oak Ridge Leadership Computing Facility (grant DE-AC05-00OR22725) at the Oak Ridge National Laboratory. Simulations were substantially performed using the Princeton Research Computing resources at Princeton University. Pablo Piaggi was supported by an Early Postdoc.Mobility fellowship from the Swiss National Science Foundation.

The group’s Ikerbasque research fellow Irene de la Cruz-Pavía conducted a study in collaboration with the University of Padua researcher Judit Gervain and which was recently published in the journal PLOS ONE; it explores the ability of 7-month-old infants to perceive structural symmetry in abstract, mosaic-like visual patterns. This research was carried out at the University of Paris. “We examined the spontaneous looking patterns of almost 100 infants when presented with mosaic-like sequences displaying symmetrical and asymmetrical structures,” the researchers explained.

These mosaics comprised two categories of square tiles (A and B) that differed in terms of their colour scheme and internal shape. These tiles were arranged to create mosaics with symmetrical (e.g. ABA, ABABA) or asymmetrical (e.g. AAB, AABBA) structures. The study found that the infants “discriminated between structurally symmetrical and asymmetrical mosaics, and that the length of the sequence (3 or 5 tiles) or the level of symmetry did not significantly modulate their behaviour.” These results suggest that infants quickly detect structural symmetry in complex visual patterns: “Babies as young as 7 months have a robust, automatic ability to detect that a structure is symmetrical. This ability coincides with those found in studies we conducted using other stimuli, such as sign language or speech, demonstrating that babies are simply very good at detecting structures and regularities,” said the researcher in the UPV/EHU’s Department of Linguistics and Basque Studies.

Ability of babies to extract structure and rules from various media

As the Ikerbasque research fellow pointed out, “the grammar of a language consists of the set of structures and rules of a language. I want to understand to what extent infants’ abilities to extract structures, detect regularities and learn rules are specific to language or whether they are found in other areas.” “We conducted this study using information that is visual but which is not language. With these mosaics, we were able to see how babies were capable of extracting structure from different media.”

The researchers stress that this study allows them to better understand “these infants’ fundamental skills, which will enable them to start initially with some of the more accessible parts of grammar and gradually build up to something as complex as the grammar of a language. What we want to understand is this: what are the fundamental abilities of babies when it comes to detecting structure?”

“We have many more questions to answer,” they concluded. “In this study we were able to determine that babies are able to detect structures spontaneously and quickly. Now we want to understand when this ability begins, and the degree of detail with which they analyse that structure and what aspects of the mosaics allow them to detect its structure (the shape, the colour, both…).”

Additional information

This study was carried out in collaboration with the Integrative Neuroscience and Cognition Center (CNRS, University of Paris, France), the University of Vienna (Austria) and the University of Padua (Italy).

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While most fossils are ‘hard’ tissues, such as bone, shells or teeth, some rare sites around the world had unique conditions which allowed minerals to fossilise soft parts such skin, muscles and other organs — even the fragile eyeballs of some ancient creatures.

But one aspect of this rare preservation that has troubled scientists is why some internal organs seem to fossilise more commonly that others.

Researchers in Leicester’s Centre for Palaeobiology developed an experiment to study the chemistry inside a decaying fish and map the pH levels of its internal organs over the course of the carcass decaying for two-and-a-half months.

Their findings, published today (Monday) in Palaeontology, show that each organ’s specific tissue chemistry governs its likelihood to be replaced by minerals.

This result explains why some tissues are more easily turned into the calcium phosphate fossils which capture high-resolution detail of a creature’s most fragile material, while other organs are seemingly lost to time.

Dr Thomas Clements, now of the University of Birmingham, led the study during his time as a PhD researcher at Leicester. He said:

“One of the best ways that soft tissue can turn into rock is when they are replaced by a mineral called calcium phosphate (sometimes called apatite). Scientists have been studying calcium phosphate for decades trying to understand how this process happens — but one question we just don’t understand is why some internal organs seem more likely to be preserved than others.

“We designed an experiment observing rotting fish which was disgusting and smelly, but we made an interesting discovery.

“The organs don’t generate special microenvironments — they all rot in a kind of ‘soup’ together. This means that it is the specific tissue chemistry of the organs that governs their likelihood to turn into fossils.”

In order for a tissue to phosphatize, its pH must fall below about pH 6.4. At this acidity, if the fossil is buried quickly, calcium phosphate and other minerals can begin the fossilisation process which preserves the exquisite detail of some soft tissues.

One of the finest examples of such fossils includes a Cretaceous-era octopus of the extinct genus Keuppia unearthed in Lebanon, estimated to be at least 94 million years old.

Sarah Gabbott is a Professor of Palaeobiology and co-author of the paper. Professor Gabbott added:

“Watching and recording (and smelling) how a fish rots may not be most people’s idea of science, but for palaeontologists understanding the process of decay is crucial to revealing which anatomical features of an animal are likely to become a fossil, and what they will look like.

“We were really pleased with the results because we can now explain, for example, why fossils often preserve an animal’s gut but never preserve their liver.”

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The pioneering research project, led by Newcastle University’s School of Natural and Environmental Sciences and published today in Nature Communications, uncovered a mechanism that can generate hydrogen peroxide from rocks during the movement of geological faults.

While in high concentrations hydrogen peroxide can be harmful to life, it can also provide a useful source of oxygen to microbes. This additional source of oxygen may have influenced the early evolution, and feasibly even origin, of life in hot environments on the early Earth prior to the evolution of photosynthesis.

In tectonically active regions, the movement of the Earth’s crust not only generates earthquakes but riddles the subsurface with cracks and fractures lined with highly reactive rock surfaces containing many imperfections, or defects. Water can then filter down and react with these defects on the newly fractured rock.

In the laboratory, Masters student Jordan Stone simulated these conditions by crushing granite, basalt and peridotite — rock types that would have been present in the early Earth’s crust. These were then added to water under well controlled oxygen-free conditions at varying temperatures.

The experiments demonstrated that substantial amounts of hydrogen peroxide — and as a result, potentially oxygen — was only generated at temperatures close to the boiling point of water. Importantly, the temperature of hydrogen peroxide formation overlaps the growth ranges of some of the most heat-loving microbes on Earth called hyperthermophiles, including evolutionary ancient oxygen-using microbes near the root of the Universal Tree of Life.

Lead author Jordan Stone, who conducted this research as part of his MRes in Environmental Geoscience, said: “While previous research has suggested that small amounts of hydrogen peroxide and other oxidants can be formed by stressing or crushing of rocks in the absence of oxygen, this is the first study to show the vital importance of hot temperatures in maximising hydrogen peroxide generation.”

Principal Investigator Dr Jon Telling, Senior Lecturer, added: “This research shows that defects on crushed rock and minerals can behave very differently to how you would expect more ‘perfect’ mineral surfaces to react. All these mechanochemical reactions need to generate hydrogen peroxide, and therefore oxygen, is water, crushed rocks, and high temperatures, which were all present on the early Earth before the evolution of photosynthesis and which could have influenced the chemistry and microbiology in hot, seismically active regions where life may have first evolved.”

The work was supported through grants from the Natural Environmental Research Council (NERC) and the UK Space Agency. A major new follow-up project led by Dr Jon Telling, funded by NERC, is underway to determine the significance of this mechanism for supporting life in the Earth’s subsurface.

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