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Quantum effects are only important at small distances (10-13 cms for the so called strong or nuclear forces, 10-8 cm for electromagnetically interacting particles).
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Often these short distance effects are unimportant and it is sufficient to treat physics classically. Then all matter is made up of particles - which are selected from set of atoms (electrons etc.).
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The most well known problems of this type come from biochemistry. Here we study biologically interesting proteins which are made up of some 10,000 to 100,000 atoms. We hope to understand the chemical basis of life or more practically find which proteins are potentially interesting drugs.
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Particles each obey Newton's Law and study of proteins generalizes the numerical formulation of the study of the solar system where the sun and planets are evolved in time as defined by Gravity's Force Law
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