School of Natural Sciences

Using Protein Sequences to Predict Structure

By Lucy Colwell 

How do proteins self-assemble into functional molecules?

Proteins are typically cited as the molecules that enable life; the word protein stems from the Greek proteois meaning “primary,” “in the lead,” or “standing in front.” Living systems are made up of a vast array of different proteins. There are around 50,000 different proteins encoded in the human genome, and in a single cell there may be as many as 20,000,000 copies of a single protein.1

Each protein provides a fas­cinating example of a self-organ­izing system. The molecule is assembled as a chain of amino acid building blocks, which are bonded together by peptide bonds to form a linear polymer. Once synthesized, this polymer spontaneously self-assembles into the correct and highly ordered three-dimensional structure required for function. This ability to self-assemble is remarkable—each linear polypeptide chain is highly disorganized, and has the potential to adopt an array of conformations so vast that we cannot enumerate them, yet within less than a second a typical protein spontaneously assumes the correct, highly ordered three-dimensional structure required for function. The identity and order of the amino acids that make up this polypeptide, that is the protein sequence, typically contain all the information necessary to specify the folded functional molecule.2

What's Next?

New physics suggests a profound conceptual revolution that will change our view of the world.

The following excerpts are drawn from Professor Nathan Seiberg’s public lecture “What’s Next?” available at https://video.ias.edu/seiberg-2013/. 

I do not know what the future will bring. I guess nobody knows; and we do not know what will be discovered, either experimentally or theoretically, and that’s actually one of the reasons we perform experiments. If we knew for sure what the outcomes of the experiment would be, there would be no reason to perform the experiment. This is also the reason scientific research is exciting. It’s exciting because we’re constantly surprised either because an experiment has an unexpected outcome or theoretically someone comes up with a new insight. . . .

We are in an unusual and unprecedented situation in physics. We have two Standard Models. The Standard Model of particle physics describes the shortest distances and the Standard Model of cosmology describes the longest distances in the universe. These models work extremely well over the range of distances for which they were designed to work. However, there are excellent arguments that this story is not complete, and there must be new physics beyond these models. . . .

Entanglement and the Geometry of Spacetime

By Juan Maldacena 

Two papers written by Albert Einstein and Members at the Institute in 1935 on quantum mechanics and black holes initially seemed to be completely disconnected but recent research by Juan Maldacena suggests that they are closely connected.

Can the weird quantum mechanical property of entanglement give rise to wormholes connecting far away regions in space?

In 1935, Albert Einstein and collaborators wrote two papers at the Institute for Advanced Study. One was on quantum mechanics [1] and the other was on black holes [2]. The paper on quantum mechanics is very famous and influential. It pointed out a feature of quantum mechanics that deeply troubled Einstein. The paper on black holes pointed out an interesting aspect of a black hole solution with no matter, where the solution looks like a wormhole connecting regions of spacetime that are far away. Though these papers seemed to be on two completely disconnected subjects, recent research has suggested that they are closely connected.

Einstein’s theory of general relativity tells us that spacetime is dynamical. Spacetime is similar to a rubber sheet that can be deformed by the presence of matter. A very drastic deformation of spacetime is the formation of a black hole. When there is a large amount of matter concentrated in a small enough region of space, this can collapse in an irreversible fashion. For example, if we filled a sphere the size of the solar system with air, it would collapse into a black hole. When a black hole forms, we can define an imaginary surface called “the horizon”; it separates the region of spacetime that can send signals to the exterior from the region that cannot. If an astronaut crosses the horizon, she can never come back out. She does not feel anything special as she crosses the horizon. However, once she crosses, she will be inevitably crushed by the force of gravity into a region called “the singularity” (Figure 1a).

Infinite in All Directions

This original painting was created by Robbert Dijkgraaf, Director of the Institute and Leon Levy Professor, to commemorate the celebration in Freeman Dyson’s honor, “Dreams of Earth and Sky.” The title is taken from a book written in 1895 by Konstantin Tsiolkovsky, a Russian schoolteacher who worked out the mathematics of interplanetary rocketry in the nineteenth century. “The Earth is the cradle of the mind,” Tsiolkovsky wrote, “but we cannot live forever in a cradle.”

In 2013, Freeman Dyson celebrated his ninetieth birthday and also marked his sixtieth year as a Professor at the Institute for Advanced Study, the longest tenure of any Faculty member in the Institute’s history. When Dyson first arrived as a Member in 1948, the Institute was less than twenty years old. “Dreams of Earth and Sky,” a conference and celebration conceived by Dyson’s colleagues in the School of Natural Sciences and held September 27–28, provided a perspective on his work and impact across the sciences and humanities. The program featured a range of talks on mathematics, physics, astronomy, and public affairs that reflect both the diversity of Dyson’s interests and his ability to open new dialogues.

The son of composer Sir George Dyson and Mildred Atkey, Dyson was born in Crowthorne, England, on December 15, 1923. He worked as a civilian scientist for the Royal Air Force in World War II, and graduated from Cambridge University in 1945 with a B.A. degree in mathematics. He went on to Cornell University as a graduate student in 1947 and worked with Hans Bethe and Richard Feynman. One of Dyson’s most notable contributions to science was the unification of the three versions of quantum electrodynamics invented by Feynman, Julian Schwinger, and Sin-Itiro Tomonaga. Dyson then worked on nuclear reactors, solid state physics, ferromagnetism, astrophysics, and biology, looking for problems where mathematics could be usefully applied. Author of numerous articles and books about science for the general public, he has also been heavily invested in human issues, from arms control and space travel to climate studies. Dyson once remarked that he was “obsessed with the future.” His keen observations and sense of wonder, which have inspired generations here at the Institute and beyond, are powerful testaments to the freedom provided by the Institute to follow one’s future, wherever it may lead.

The Absolute Elsewhere

By Pia de Jong 

Punch cartoon inspired by seven-year-old Freeman Dyson
Immersed in Freeman Dyson’s World
 
In 1930, the British satirical magazine Punch published a cartoon of a boy, lying on his side on the lawn, reading a book on relativity. When asked where his sister is, he replies, “Somewhere in the absolute elsewhere.”

That boy was the seven-year-old Freeman Dyson. He did not understand why his father had sent his remark to Punch. It was after all technically correct. What was so funny about it?

Dyson grew up to be a world-famous mathematician, physicist, astronomer, and an elegant writer. For sixty years, he has worked at the Institute for Advanced Study. On December 15, he will be ninety. An elfin man with pointed ears and mischievous blue eyes, he still walks faithfully to his office every morning, invariably dressed as the British boarding school boy he once was—with a tweed jacket and tie.

To celebrate Dyson’s ninetieth birthday, a conference was held in his honor at the Institute. He himself gave it the title “Dreams of Earth and Sky.” The speakers, also all chosen by him, were just as exciting as the Jules Verne books he devoured as a child—until he realized that they lived only in science fiction.

Thus, I find myself immersed in his fascinating world. I hear the English Astronomer Royal, Martin Rees, talk about alternative universes. I see a map of the nearest stars where extraterrestrial life might really exist. Magic formulas, the interior of the Earth, climate change, nuclear disarmament, life on Mars—ideas that are often as controversial as those of Dyson himself. But also with an equally infectious enthusiasm about everything there is to discover. If I were a child, Dyson would be my hero, and I would want to be an astronomer. Happily, there are many children in the audience.

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