Legacy of a Molecular Dynamics Pioneer – ScienceDaily


life is movement So to understand how living organisms work, one must understand the movement and reorganization of the atoms and molecules that make them up. Dubbed “molecular dynamics simulation,” the approach allows scientists to use computer programs to simulate the dynamic motion of all atoms in a molecular system as a function of time.

In a new newspaper in EPJ Historical Perspectives on Contemporary PhysicsDaniele Macuglia from Peking University in Beijing, China, Benoît Roux from the University of Chicago in Chicago, USA, and Giovanni Ciccotti from the University of Rome in Rome, Italy, explain how theoretical chemist Martin Karplus and his team carried out the first have molecular dynamics simulation of a large biological molecule, a protein that has revolutionized biology and science in the 20th centuryth and 21St centuries. Currently, machine learning researchers are using biomolecular simulations to better understand their time-dependent movements and the function that governs the forces between them.

In the early 1970s, physicists and physical chemists began using molecular dynamics simulations to study the behavior of simple substances such as water and liquids formed from noble gases. Martin Karplus and his team have further developed this method by applying it for the first time to a large biological molecule – a protein.

Proteins can be thought of as miniature machines, functioning in part as a result of how they fold and deform into different shapes over time. Due to their complexity, simulating their changes over time was a particular challenge. Karplus first published this approach in 1977 with a paper showing the first molecular dynamics simulation of a protein. More recently, the great influence of his contribution to the accurate modeling of chemical reactions was recognized by being awarded the 2013 Nobel Prize in Chemistry, along with Arieh Warshel and Michael Levitt.

The authors conclude that Karplus’ 1977 paper opened the door to pursue a line of research that led him to successfully merge computational statistical mechanics with biochemistry.

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