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Protein folding problem: Is it possible to predict the secondary, tertiary and quaternary structure of a polypeptide sequence based solely on the sequence and environmental information? Inverse protein-folding problem: Is it possible to design a polypeptide sequence which will adopt a given structure under certain environmental conditions?
This problem was studied in detail by Joseph Louis Lagrange, who laid out most of the methods for solving it. [1] The simplest approach is to define new generalized coordinates that are unconstrained; this approach eliminates the algebraic equations and reduces the problem once again to solving an ordinary differential equation.
The resulting equations are a set of non-linear equations, which are solved in an iterative manner. Standard quantum-chemistry packages (GAMESS (US), NWChem, ACES II, etc.) solve the coupled-cluster equations using the Jacobi method and direct inversion of the iterative subspace extrapolation of the t-amplitudes to accelerate convergence.
Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems. [1] It uses methods of theoretical chemistry incorporated into computer programs to calculate the structures and properties of molecules , groups of molecules, and solids. [ 2 ]
Since the Hartree term and V XC depend on n(r), which depends on the φ i, which in turn depend on V s, the problem of solving the Kohn–Sham equation has to be done in a self-consistent (i.e., iterative) way. Usually one starts with an initial guess for n(r), then calculates the corresponding V s and solves the Kohn–Sham equations for the ...
The many-electron function is generally a linear combination of many simpler electron functions with the dominant function being the Hartree-Fock function. Each of these simple functions are then approximated using only one-electron functions. The one-electron functions are then expanded as a linear combination of a finite set of basis functions.
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