For example, the biologically active structure of the protein can be a rare fluctuation that is not observed in the average experimental structure. These fluctuations can be studied with the method of Molecular Dynamics. Elber develops theoretical approaches and algorithms to extend the scope of the Molecular Dynamics method and applies them to a variety of biophysical problems. Protein dynamics 1. Mechanisms and dynamics of peptide folding.
Peptides are short polymers of amino acids.
They serve as model systems for nucleation sites in protein folding. It is believed that protein folding proceeds via a time sequence of nuclei of structures. The identity and the physical forces that hold the initiators of structure are a topic of intense investigations by theorists and experimentalists. The results indicate that long-range electrostatic attraction and the local propensity of the proline are the prime initiators of the folding process. Algorithms for long time dynamics.