Abstract and Keywords
This article describes quantum methods used to study proteins and nucleic acids: Hartree–Fock all-electron approaches, density-functional theory approaches, and hybrid quantum-mechanics/molecular-mechanics approaches. In addition to an analysis of the electronic structure, quantum-mechanical approaches for simulating proteins and nucleic acids can elucidate the cleavage and formation of chemical bonds in biochemical reactions. This presents a computational challenge, and a number of methods have been proposed to overcome this difficulty, including enhanced temperature methods such as high-temperature molecular dynamics, parallel tempering and replica exchange. Alternative methods not relying on the knowledge a priori of the final products make use of biasing potentials to push the initial system away from its local minimum and to enhance the sampling of the free-energy landscape. This article considers two of these biasing techniques, namely Blue Moon and metadynamics.
Keywords: quantum methods, proteins, nucleic acids, Hartree–Fock all-electron approaches, density-functional theory, quantum mechanics, molecular mechanics, biasing potentials, Blue Moon, metadynamics
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