Energy landscapes and properties of biomolecules.
Thermodynamic and dynamic properties of biomolecules can be calculated using a coarse-grained approach based upon sampling stationary points of the underlying potential energy surface. The superposition approximation provides an overall partition function as a sum of contributions from the local minima, and hence functions such as internal energy, entropy, free energy and the heat capacity. To obtain rates we must also sample transition states that link the local minima, and the discrete path sampling method provides a systematic means to achieve this goal. A coarse-grained picture is also helpful in locating the global minimum using the basin-hopping approach. Here we can exploit a fictitious dynamics between the basins of attraction of local minima, since the objective is to find the lowest minimum, rather than to reproduce the thermodynamics or dynamics.
Wales
David J
DJ
Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK. dw34@cam.ac.uk
D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D019295:Computational Biology; D004744:Enkephalin, Methionine / Q000737:chemistry; D019277:Entropy; D006358:Hot Temperature; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013696:Temperature; D013816:Thermodynamics
D010455:Peptides; D004744:Enkephalin, Methionine