Tag Archives: quantum chemistry

Sonifying proteins to make music and brand new proteins

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Markus Buehler at the Massachusetts Institute of Technology (MIT) has been working with music and science for a number of years. My December 9, 2011 posting, Music, math, and spiderwebs, was the first one here featuring his work. My November 28, 2012 posting, Producing stronger silk musically, was a followup to Buehler’s previous work.

A June 28, 2019 news item on Azonano provides a recent update,

Composers string notes of different pitch and duration together to create music. Similarly, cells join amino acids with different characteristics together to make proteins.

Now, researchers have bridged these two seemingly disparate processes by translating protein sequences into musical compositions and then using artificial intelligence to convert the sounds into brand-new proteins. …

Caption: Researchers at MIT have developed a system for converting the molecular structures of proteins, the basic building blocks of all living beings, into audible sound that resembles musical passages. Then, reversing the process, they can introduce some variations into the music and convert it back into new proteins never before seen in nature. Credit: Zhao Qin and Francisco Martin-Martinez

A June 26, 2019 American Chemical Society (ACS) news release, which originated the news item, provides more detail and a video,

To make proteins, cellular structures called ribosomes add one of 20 different amino acids to a growing chain in combinations specified by the genetic blueprint. The properties of the amino acids and the complex shapes into which the resulting proteins fold determine how the molecule will work in the body. To better understand a protein’s architecture, and possibly design new ones with desired features, Markus Buehler and colleagues wanted to find a way to translate a protein’s amino acid sequence into music.

The researchers transposed the unique natural vibrational frequencies of each amino acid into sound frequencies that humans can hear. In this way, they generated a scale consisting of 20 unique tones. Unlike musical notes, however, each amino acid tone consisted of the overlay of many different frequencies –– similar to a chord. Buehler and colleagues then translated several proteins into audio compositions, with the duration of each tone specified by the different 3D structures that make up the molecule. Finally, the researchers used artificial intelligence to recognize specific musical patterns that corresponded to certain protein architectures. The computer then generated scores and translated them into new-to-nature proteins. In addition to being a tool for protein design and for investigating disease mutations, the method could be helpful for explaining protein structure to broad audiences, the researchers say. They even developed an Android app [Amino Acid Synthesizer] to allow people to create their own bio-based musical compositions.

Here’s the ACS video,

A June 26, 2019 MIT news release (also on EurekAlert) provides some specifics and the MIT news release includes two embedded audio files,

Want to create a brand new type of protein that might have useful properties? No problem. Just hum a few bars.

In a surprising marriage of science and art, researchers at MIT have developed a system for converting the molecular structures of proteins, the basic building blocks of all living beings, into audible sound that resembles musical passages. Then, reversing the process, they can introduce some variations into the music and convert it back into new proteins never before seen in nature.

Although it’s not quite as simple as humming a new protein into existence, the new system comes close. It provides a systematic way of translating a protein’s sequence of amino acids into a musical sequence, using the physical properties of the molecules to determine the sounds. Although the sounds are transposed in order to bring them within the audible range for humans, the tones and their relationships are based on the actual vibrational frequencies of each amino acid molecule itself, computed using theories from quantum chemistry.

The system was developed by Markus Buehler, the McAfee Professor of Engineering and head of the Department of Civil and Environmental Engineering at MIT, along with postdoc Chi Hua Yu and two others. As described in the journal ACS Nano, the system translates the 20 types of amino acids, the building blocks that join together in chains to form all proteins, into a 20-tone scale. Any protein’s long sequence of amino acids then becomes a sequence of notes.

While such a scale sounds unfamiliar to people accustomed to Western musical traditions, listeners can readily recognize the relationships and differences after familiarizing themselves with the sounds. Buehler says that after listening to the resulting melodies, he is now able to distinguish certain amino acid sequences that correspond to proteins with specific structural functions. “That’s a beta sheet,” he might say, or “that’s an alpha helix.”

Learning the language of proteins

The whole concept, Buehler explains, is to get a better handle on understanding proteins and their vast array of variations. Proteins make up the structural material of skin, bone, and muscle, but are also enzymes, signaling chemicals, molecular switches, and a host of other functional materials that make up the machinery of all living things. But their structures, including the way they fold themselves into the shapes that often determine their functions, are exceedingly complicated. “They have their own language, and we don’t know how it works,” he says. “We don’t know what makes a silk protein a silk protein or what patterns reflect the functions found in an enzyme. We don’t know the code.”

By translating that language into a different form that humans are particularly well-attuned to, and that allows different aspects of the information to be encoded in different dimensions — pitch, volume, and duration — Buehler and his team hope to glean new insights into the relationships and differences between different families of proteins and their variations, and use this as a way of exploring the many possible tweaks and modifications of their structure and function. As with music, the structure of proteins is hierarchical, with different levels of structure at different scales of length or time.

The team then used an artificial intelligence system to study the catalog of melodies produced by a wide variety of different proteins. They had the AI system introduce slight changes in the musical sequence or create completely new sequences, and then translated the sounds back into proteins that correspond to the modified or newly designed versions. With this process they were able to create variations of existing proteins — for example of one found in spider silk, one of nature’s strongest materials — thus making new proteins unlike any produced by evolution.

Although the researchers themselves may not know the underlying rules, “the AI has learned the language of how proteins are designed,” and it can encode it to create variations of existing versions, or completely new protein designs, Buehler says. Given that there are “trillions and trillions” of potential combinations, he says, when it comes to creating new proteins “you wouldn’t be able to do it from scratch, but that’s what the AI can do.”

“Composing” new proteins

By using such a system, he says training the AI system with a set of data for a particular class of proteins might take a few days, but it can then produce a design for a new variant within microseconds. “No other method comes close,” he says. “The shortcoming is the model doesn’t tell us what’s really going on inside. We just know it works.

This way of encoding structure into music does reflect a deeper reality. “When you look at a molecule in a textbook, it’s static,” Buehler says. “But it’s not static at all. It’s moving and vibrating. Every bit of matter is a set of vibrations. And we can use this concept as a way of describing matter.”

The method does not yet allow for any kind of directed modifications — any changes in properties such as mechanical strength, elasticity, or chemical reactivity will be essentially random. “You still need to do the experiment,” he says. When a new protein variant is produced, “there’s no way to predict what it will do.”

The team also created musical compositions developed from the sounds of amino acids, which define this new 20-tone musical scale. The art pieces they constructed consist entirely of the sounds generated from amino acids. “There are no synthetic or natural instruments used, showing how this new source of sounds can be utilized as a creative platform,” Buehler says. Musical motifs derived from both naturally existing proteins and AI-generated proteins are used throughout the examples, and all the sounds, including some that resemble bass or snare drums, are also generated from the sounds of amino acids.

The researchers have created a free Android smartphone app, called Amino Acid Synthesizer, to play the sounds of amino acids and record protein sequences as musical compositions.

Here’s a link to and a citation for the paper,

A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence by Chi-Hua Yu, Zhao Qin, Francisco J. Martin-Martinez, Markus J. Buehler. ACS Nano 2019 XXXXXXXXXX-XXX DOI: https://doi.org/10.1021/acsnano.9b02180 Publication Date:June 26, 2019 Copyright © 2019 American Chemical Society

This paper is behind a paywall.

ETA October 23, 2019 1000 hours: Ooops! I almost forgot the link to the Aminot Acid Synthesizer.

Simulating elementary physics in a quantum simulation (particle zoo in a quantum computer?)

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Whoever wrote the news release used a very catchy title “Particle zoo in a quantum computer”; I just wish they’d explained it. Looking up the definition for a ‘particle zoo’ didn’t help as much as I’d hoped. From the particle zoo entry on Wikipedia (Note: Links have been removed),

In particle physics, the term particle zoo[1][2] is used colloquially to describe a relatively extensive list of the then known “elementary particles” that almost look like hundreds of species in the zoo.

In the history of particle physics, the situation was particularly confusing in the late 1960s. Before the discovery of quarks, hundreds of strongly interacting particles (hadrons) were known, and believed to be distinct elementary particles in their own right. It was later discovered that they were not elementary particles, but rather composites of the quarks. The set of particles believed today to be elementary is known as the Standard Model, and includes quarks, bosons and leptons.

I believe the writer used the term to indicate that the simulation undertaken involved elementary particles. If you have a better explanation, please feel free to add it to the comments for this post.

Here’s the news from a June 22, 2016 news item on ScienceDaily,

Elementary particles are the fundamental buildings blocks of matter, and their properties are described by the Standard Model of particle physics. The discovery of the Higgs boson at the CERN in 2012 constitutes a further step towards the confirmation of the Standard Model. However, many aspects of this theory are still not understood because their complexity makes it hard to investigate them with classical computers. Quantum computers may provide a way to overcome this obstacle as they can simulate certain aspects of elementary particle physics in a well-controlled quantum system. Physicists from the University of Innsbruck and the Institute for Quantum Optics and Quantum Information (IQOQI) at the Austrian Academy of Sciences have now done exactly that: In an international first, Rainer Blatt’s and Peter Zoller’s research teams have simulated lattice gauge theories in a quantum computer. …

A June 23, 2016 University of Innsbruck (Universität Innsbruck) press release, which seems  to have originated the news item, provides more detail,

Gauge theories describe the interaction between elementary particles, such as quarks and gluons, and they are the basis for our understanding of fundamental processes. “Dynamical processes, for example, the collision of elementary particles or the spontaneous creation of particle-antiparticle pairs, are extremely difficult to investigate,” explains Christine Muschik, theoretical physicist at the IQOQI. “However, scientists quickly reach a limit when processing numerical calculations on classical computers. For this reason, it has been proposed to simulate these processes by using a programmable quantum system.” In recent years, many interesting concepts have been proposed, but until now it was impossible to realize them. “We have now developed a new concept that allows us to simulate the spontaneous creation of electron-positron pairs out of the vacuum by using a quantum computer,” says Muschik. The quantum system consists of four electromagnetically trapped calcium ions that are controlled by laser pulses. “Each pair of ions represent a pair of a particle and an antiparticle,” explains experimental physicist Esteban A. Martinez. “We use laser pulses to simulate the electromagnetic field in a vacuum. Then we are able to observe how particle pairs are created by quantum fluctuations from the energy of this field. By looking at the ion’s fluorescence, we see whether particles and antiparticles were created. We are able to modify the parameters of the quantum system, which allows us to observe and study the dynamic process of pair creation.”

Combining different fields of physics

With this experiment, the physicists in Innsbruck have built a bridge between two different fields in physics: They have used atomic physics experiments to study questions in high-energy physics. While hundreds of theoretical physicists work on the highly complex theories of the Standard Model and experiments are carried out at extremely expensive facilities, such as the Large Hadron Collider at CERN, quantum simulations may be carried out by small groups in tabletop experiments. “These two approaches complement one another perfectly,” says theoretical physicist Peter Zoller. “We cannot replace the experiments that are done with particle colliders. However, by developing quantum simulators, we may be able to understand these experiments better one day.” Experimental physicist Rainer Blatt adds: “Moreover, we can study new processes by using quantum simulation. For example, in our experiment we also investigated particle entanglement produced during pair creation, which is not possible in a particle collider.” The physicists are convinced that future quantum simulators will potentially be able to solve important questions in high-energy physics that cannot be tackled by conventional methods.

Foundation for a new research field

It was only a few years ago that the idea to combine high-energy and atomic physics was proposed. With this work it has been implemented experimentally for the first time. “This approach is conceptually very different from previous quantum simulation experiments studying many-body physics or quantum chemistry. The simulation of elementary particle processes is theoretically very complex and, therefore, has to satisfy very specific requirements. For this reason it is difficult to develop a suitable protocol,” underlines Zoller. The conditions for the experimental physicists were equally demanding: “This is one of the most complex experiments that has ever been carried out in a trapped-ion quantum computer,” says Blatt. “We are still figuring out how these quantum simulations work and will only gradually be able to apply them to more challenging phenomena.” The great theoretical as well as experimental expertise of the physicists in Innsbruck was crucial for the breakthrough. Both Blatt and Zoller emphasize that they have been doing research on quantum computers for many years now and have gained a lot of experience in their implementation. Innsbruck has become one of the leading centers for research in quantum physics; here, the theoretical and experimental branches work together at an extremely high level, which enables them to gain novel insights into fundamental phenomena.

Here’s a link to and a citation for the paper,

Real-time dynamics of lattice gauge theories with a few-qubit quantum computer by Esteban A. Martinez, Christine A. Muschik, Philipp Schindler, Daniel Nigg, Alexander Erhard, Markus Heyl, Philipp Hauke, Marcello Dalmonte, Thomas Monz, Peter Zoller, & Rainer Blatt.  Nature 534, 516–519 (23 June 2016)  doi:10.1038/nature18318 Published online 22 June 2016

This paper is behind a paywall.

There is a soundcloud audio file featuring an explanation of the work from the lead author, Esteban A. Martinez,

The quantum chemistry of nanomedicines

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A Jan. 29, 2015 news item on Nanowerk provides an overview of the impact quantum chemical reactions may have on nanomedicines. Intriguingly, this line of query started with computations of white dwarf stars,

Quantum chemical calculations have been used to solve big mysteries in space. Soon the same calculations may be used to produce tomorrow’s cancer drugs.

Some years ago research scientists at the University of Oslo in Norway were able to show that the chemical bonding in the magnetic fields of small, compact stars, so-called white dwarf stars, is different from that on Earth. Their calculations pointed to a completely new bonding mechanism between two hydrogen atoms. The news attracted great attention in the media. The discovery, which in fact was made before astrophysicists themselves observed the first hydrogen molecules in white dwarf stars, was made by UiO’s Centre for Theoretical and Computational Chemistry. They based their work on accurate quantum chemical calculations of what happens when atoms and molecules are exposed to extreme conditions.

A Jan. 29, 2015 University of Oslo press release by Yngve Vogt, which originated the news item, offers a substantive description of molecules, electrons, and more for those of us whose last chemistry class is lost in the mists of time,

The research team is headed by Professor Trygve Helgaker, who for the last thirty years has taken the international lead on the design of a computer system for calculating quantum chemical reactions in molecules.

Quantum chemical calculations are needed to explain what happens to the electrons’ trajectories within a molecule.

Consider what happens when UV radiation sends energy-rich photons into your cells. This increases the energy level of the molecules. The outcome may well be that some of the molecules break up. This is exactly what happens when you sun-bathe.

“The extra energy will affect the behaviour of electrons and can destroy the chemical bonding within the molecule. This can only be explained by quantum chemistry. The quantum chemical models are used to produce a picture of the forces and tensions at play between the atoms and the electrons of a molecule, and of what is required for a molecule to dissociate,” says Trygve Helgaker.

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.”

There’s more from the press release which describes how this work could be applied in the future,

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.

…

Simen Reine has been using the team’s computer program, while working with Aarhus University [Finland], 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 atomic nuclei. The 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 and are very reliable.”

A complete correlated calculation of the insulin molecule takes nearly half a million CPU hours. If they were given the opportunity to run the program on the entire 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

…

“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 [vice-rector at the University of Oslo].

…

“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 [Associate Professor] 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.

Proteins and enzymes

Professor K. Kristoffer Andersson at the Department of Biosciences uses the simpler form of quantum chemical calculations to study the details of protein structures and the chemical atomic and electronic functions of enzymes.

“It is important to understand the chemical reaction mechanism, and how enzymes and proteins work. Quantum chemical calculations will teach us more about how proteins go about their tasks, step by step. We can also use the calculations to look at activation energy, i.e. how much energy is required to reach a certain state. It is therefore important to understand the chemical reaction patterns in biological molecules in order to develop new drugs,” says Andersson.

His research will also be useful in the search for cancer drugs. He studies radicals, which may be important to cancer. Among other things, he is looking at the metal ions function in proteins. These are ions with a large number of protons, neutrons and electrons.

Photosynthesis

Professor Einar Uggerud at the Department of Chemistry has uncovered an entirely new form of chemical bonding through sophisticated experiments and quantum chemical calculations.

Working with research fellow Glenn Miller, Professor Uggerud has found an unusually fragile key molecule, in a kite-shaped structure, consisting of magnesium, carbon and oxygen. The molecule may provide a new understanding of photosynthesis. Photosynthesis, which forms the basis for all life, converts CO2 into sugar molecules.

The molecule reacts so fast with water and other molecules that it has only been possible to study in isolation from other molecules, in a vacuum chamber.

“Time will tell whether the molecule really has an important connection with photosynthesis,” says Einar Uggerud.

I’m delighted with this explanation as it corrects my understanding of chemical bonds and helps me to better understand computational chemistry. Thank you University of Oslo and Yngve Vogt.

Finally, here’s a representation of an insulin molecule as understood by quantum computation,

QuantumInsulinMolecule

INSULIN: Working with Aarhus University, Simen Reine has calculated the tensions between the electrons and atoms of an insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons. Illustration: Simen Reine-UiO