Murray Gell-Mann, who has died aged 89, was the leading figure in the study of elementary particle physics in the middle years of the 20th century. His work transformed the way that physicists conceive matter at the smallest length scales.

In 1950 the world of atomic and nuclear physics was relatively straightforward: atoms consisted of positively charged nuclei formed of protons and neutrons, with negatively charged electrons orbiting around them like planets round the sun, held together by photons, the quanta of quantum electrodynamics (QED). By 1975 the subject had changed beyond recognition, largely due to Murray’s work. Protons and neutrons were no longer elementary particles: instead they themselves were composite structures formed of three quarks held together by gluons, the quanta of quantum chromodynamics (QCD).

In 1964 Murray had introduced quarks as the basic building blocks of matter and five years later he received the Nobel prize in physics for the classification of elementary particles and their interactions.

The son of Pauline (nee Reichstein) and Arthur Gell-Mann, Murray was born in New York. His father had arrived from Czernowitz in Austria (now in Ukraine) 15 years earlier and had opened a language school in lower Manhattan. The school failed and the family were forced repeatedly to move, although Arthur eventually managed to find a job as a guard in a bank. Arthur, however, was fluent in several languages and was a self-taught mathematician.

It was soon clear that Murray was a child prodigy. At seven, he won a spelling bee set by a local radio station open to children under 12. When he was eight Columbia Grammar, a private school on the Upper West Side, gave him a full scholarship and at 14 he won a scholarship to Yale University. His father insisted that he study a subject that would be financially rewarding so suggested engineering. Murray refused and they compromised on physics. He received his bachelor’s degree at 18, moved to the Massachusetts Institute of Technology (MIT) and completed his doctoral dissertation two years later.

In 1951 he moved on to a post-doctoral position at the Institute for Advanced Study at Princeton with Robert Oppenheimer, and a year later to the University of Chicago with Enrico Fermi. During this period he studied the new particles that were being produced at particle accelerators and in cosmic rays. The new particles seemed to be produced in pairs in collisions of normal particles: if a lambda particle was seen then so was a K-meson or kaon. But then the lambda decayed into normal particles. So did the kaon.

Murray realised that the particles were being produced through the strong nuclear interaction but then decayed through a much weaker interaction. He concluded that there must be a new quantum number which he called “strangeness” to distinguish the normal particles from the new particles and that strangeness was conserved in strong interactions but not in weak interactions. So the proton and neutron were normal, with zero strangeness, while the lambda had strangeness of minus one unit and the kaon had strangeness of one unit.

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He moved to the California Institute of Technology (Caltech) in 1955, and the following year became their youngest full professor. He was soon appointed as professor of theoretical physics. Richard Feynman was also professor of theoretical physics, and the two men became both friends and rivals. Their styles were very different: Feynman was flamboyant, tieless, in shirtsleeves, and with a strong Brooklyn accent; Murray was always impeccably dressed and careful to enunciate every word according to received pronunciation, whether in English, French, German or Spanish.

In 1955 Murray married Margaret Dow, an English archaeologist who had been working at the Institute in Princeton. She was distinguished in her own right, having participated in 1952 in a dig at Mycenae where she had found Linear B tablets.

Feynman and Murray were both working on weak interactions, responsible for the radioactive decay of both particles and nuclei. They found that these decays could be understood in terms of weak currents, just as electromagnetism required an electromagnetic current. The crucial difference was that parity (left-right symmetry) was violated in the weak current, whereas it was conserved in the electromagnetic.

After a fruitful year as a visiting fellow in Paris, in the summer of 1960 Murray returned to Caltech, where I became one of his doctoral students. He still wanted to find a way of including all the strongly interacting particles in the same scheme, whether they were normal particles like the proton or strange particles. He encountered Richard Block, a mathematician at Caltech, who was an expert in the branch of mathematics called Lie group theory, and discovered that some of the physics problems he was considering involved examples of these groups: ie, the symmetry that physicists called isotopic spin that applied to nuclear forces was called the special unitary group in two dimensions SU(2) by mathematicians.

Murray discovered that the corresponding Lie group in three dimensions SU(3) included both isotopic spin and a quantum number that could well be strangeness.

The neutron and proton in the SU(3) scheme then had to be accompanied by six strange particles, and they were. But for the particles called mesons, the three normal pions or pi-mesons should have been accompanied by four strange kaons, and they were, but additionally by a normal meson to make up the eighth – however, this eighth was not known. Murray promptly predicted it, and it was found within 12 months. He playfully named this algebraic scheme where particles came in groups of eight the “eightfold way”, after the eightfold way of traditional Buddhism.

But why three dimensions? The mathematics suggested that the basic entity involved three states, not eight. So in 1964 Murray suggested that the elementary particles were not the proton and neutron, but these three entities, which he named quarks after a quote from Finnegans Wake, “Three quarks for Muster Mark”. The difficulty with quarks was that they had to be fractionally charged, and no such objects had ever been seen.

As the 1960s progressed Richard Dalitz and his co-workers at Oxford University showed that the particle spectrum that had been seen ex- perimentally was consistent with the quark model. Then experiments at much higher energies at Stanford in California showed that the scatter- ing of electrons from protons and neutrons was explained if the protons/neutrons consisted of pointlike quarks.

Why, however, were quarks not directly observable? And what held them together to form protons, neutrons and the other particles? These were the questions that Murray tried to understand in the early 70s. He was convinced that an invariance property of QED called gauge invariance could be based more generally on Lie groups and was the key to any understanding. This led to a theory similar to QED but where the quarks possessed another much stronger “colour” charge as well as their electric charge.

Murray and his collaborator Harald Fritzsch were leaders in developing what Murray called quantum chromodynamics (QCD), which is now accepted by physicists as being part of the standard model of elementary particle physics, which applies to all particle interactions other than gravity.

In 1980, just after Murray had turned 50, Margaret was diagnosed with cancer, and she died the following year. He became depressed: he had already won the Nobel prize and most other prizes and honours in physics, so he now turned to new fields to conquer.

From his childhood onwards he had been interested in birds, nature and sustainability. He had long wanted to apply the mathematical principles of theoretical physics to other fields, especially those that dealt with biological phenomena.

He was fascinated by language and its origins. Murray thought that future scientific development would involve the study of really complex phenomena: physics was not simple, but the origins of language or cognitive development were of a different order of complexity. With his wealth of contacts, he set about obtaining funds for the Santa Fe Institute, situated in the hills overlooking Santa Fe, which would study such problems. He left Caltech for the Santa Fe Institute in 1993 and settled in the city.

Murray always had wide interests. At the beginning of the 60s, with some of his physicist colleagues, he founded the Jason division of the Institute for Defense Analysis, which provided advice to the US military. He was chair of a Jason working group on anti-ballistic missile (ABM) defence in 1961 which realised that the installation of an ABM system reduced strategic stability since it made a pre-emptive nuclear strike by an opponent more likely.

He reported those conclusions to a Pugwash conference in India in 1964 to be greeted with ridicule by Soviet representatives at the conference. But the Soviet Union came to realise the logic of those arguments and an ABM treaty was eventually agreed between the US and Soviet Union in 1972. President George W Bush decided that the US should leave the treaty in 2002. Russia has responded recently by announcing the development of a series of technologically new missile systems.

He was appointed by Richard Nixon to the presidential science advisory committee in 1968 and served until 1972. Bill Clinton appointed him to his committee of advisers on science and technology from 1993 to 2000.

He was at various times a regent of the Smithsonian Institute, a director of the committee on world environment and resources of the MacArthur Foundation, a fellow of the American Physical Society and a foreign member of the Royal Society.

His knowledge of languages was remarkable. Once he was in London and I took him to the Gay Hussar, a Hungarian restaurant, for lunch. He looked at the menu, called the waiter and pointed to a dish. “This isn’t spelt correctly,” he said. The waiter apologised and said that they were waiting for a new menu.

When I last saw him in Santa Fe, he came to my home for dinner. I offered him a glass of Freixenet, the sparkling wine. Freixenet, he said: that’s Catalan for a grove of ash trees.

Murray is survived by a son, Nicholas, and daughter, Elizabeth, from his marriage to Margaret, and by a stepson, Nicholas, from his second marriage, in 1992, to Marcia Southwick, which ended in divorce.

• Murray Gell-Mann, physicist, born 15 September 1929; died 24 May 2019