Structure potential functions

Clearly, it is more desirable somehow to obtain detailed structural information on multilayer films so as perhaps to settle the problem of how properly to construct the potential function. Some attempts have been made to develop statistical mechanical other theoretical treatments of condensed layers in a potential field success has been reasonable (see Refs. 142, 143). 

Our work is targeted to biomolecular simulation applications, where the objective is to illuminate the structure and function of biological molecules (proteins, enzymes, etc) ranging in size from dozens of atoms to tens of thousands of atoms today, with the desire to increase this limit to millions of atoms in the near future. Such molecular dynamics (MD) simulations simply apply Newton s law to each atom in the system, with the force on each atom being determined by evaluating the gradient of the potential field at each atom s position. The potential includes contributions from bonding forces. 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Maiorov V N and G M Crippen 1994. Learning About Protein Folding via Potential Functions. Proteins Structure, Function and Genetics 20 167-173. 

In the chapter on vibrational spectroscopy (Chapter 6) 1 have expanded the discussions of inversion, ring-puckering and torsional vibrations, including some model potential functions. These types of vibration are very important in the determination of molecular structure. 

The photophysical properties of porphycenes make these structures potential sensitizers for an application in Photodynamic Tumor Therapy (PDT). To improve the photophysical properties and to modify possible biological activity it is necessary to have porphycenes with an extended chromophore and/or with additional functional groups for further modifications. The Diels-Alder reaction of a vinyl porphycene allows for the preparation of benzoporphycenes with an extended chromophore9 and additional functional groups (cf. Section 1.1.2.4.). 

The potential function for normal NO+, with a structure like that of the nitrogen molecule... 

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