Energy landscapes, complex, minima

Low lying saddle points of the LJ cluster, which can be reached directly from a minimum without passing through another minimum, are identified without any presumption of their characteristics, nor of the product states they lead to. The probabilities are computed for paths going from a given minimum to the surrounding saddle points. These probabilities are directly related to prefactors in the rate formula. This determination of the rate prefactors includes all anharmonicities, near or far from saddle points, which are pertinent in the very sophisticated energy landscape of LJ clusters and in many other complex systems. 

The dynamics can be complex in biophysics. The energy landscape is rough in the sense that it includes large number of barriers and local minima. Studies of minima and saddles of energy surfaces of peptides in vacuum illustrate this property [10,11]. For example, in protein activation, these barriers are rarely high and the motions are only moderately activated. By moderately activated we mean that the energy difference between the barrier and the minimum AU = (/bamer is of order of... 

Functional proteins in a biological organism are typically characterized by a unique three-dimensional molecular structure, which makes the protein selective for individual functions. In most cases, the free-energy landscape is believed to exhibit a rough shape with a large number of local minima and, for functional proteins, a deep, fuimel-like global minimum. This assumed complexity is the reason why it is difficult to understand how the random-coil conformation of covalently bonded amino acids spontaneously folds into a well-defined stable native conformation. Furthermore, it is expected that there are only... 

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