Maxim V Fedorov | PubMed Health

PubMed2005

Structure and stability of chiral beta-tapes: a computational coarse-grained approach.

We present two coarse-grained models of different levels of detail for the description of beta-sheet tapes obtained from equilibrium self-assembly of short rationally designed oligopeptides in solution. Here we only consider the case of the homopolymer oligopeptides with the identical sidegroups attached, in which the tapes have a helicoid surface with two equivalent sides. The influence of the chirality parameter on the geometrical characteristics, namely the diameter, interstrand distance, and pitch, of the tapes has been investigated. The two models are found to produce equivalent results suggesting a considerable degree of universality in conformations of the tapes.

Computer Simulation↗

PubMed2004

Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model.

A new efficient method is developed for solving integral equations based on the reference interaction site model (RISM) of molecular liquids. The method proposes the expansion of site-site correlation functions into the wavelet series and further calculations of the approximating coefficients. To solve the integral equations we have applied the hybrid scheme in which the coarse part of the solution is calculated by wavelets with the use of the Newton-Raphson procedure, while the fine part is evaluated by the direct iterations. The Coifman 2 basis set is employed for the wavelet treatment of the coarse solution. This wavelet basis set provides compact and accurate approximation of site-site correlation functions so that the number of basis functions and the amplitude of the fine part of solution decrease sufficiently with respect to those obtained by the conventional scheme. The efficiency of the method is tested by calculations of SPC/E model of water. The results indicated that the total CPU time to obtain solution by the proposed procedure reduces to 20% of that required for the conventional hybrid method.

Journal Article↗