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Given a protein, analyzing the geometric structure of protein is fundamental for the study of a protein folding, docking, interactions between proteins, and so on. One of the important geometric analyses is computing the molecular surface of protein. Discussed in this paper is an efficient algorithm to compute such a molecular surface of protein via the concept of blending operation among atoms...

Electrostatic interactions play a central role in biological processes. Development of fast computational methods to solve the underlying Poisson-Boltzmann equation (PBE) is vital for biomolecular modeling and simulation package. In this paper, we propose new methods for efficiently computing the electrostatic potentials for large molecules by using the geometry of the molecular shapes to guide...

MOTIVATION For a complex molecular system the delineation of atom-atom contacts, exposed surface and binding sites represents a fundamental step to predict its interaction with solvent, ligands and other molecules. Recently, atom depth has been also considered as an additional structural descriptor to correlate protein structure with folding and functional properties. The distance between an at...

The value of adjustable parameter C and the four-parameter potential U(r) = De [ 1−exp[−b(r−re)] 1−Cexp[−b(r−re)] ]2 has been expressed in terms of molecular parameters and its significance has been brought out. The potential so constructed, with C derived from the molecular parameters, has been applied to ten electronic states in addition to the states studied by Wei Hua. Average mean deviatio...

In [9] and [2] a formal model for molecular computing was proposed, which makes focused use of affinity purification. The use of PCR was suggested to expand the range of feasible computations, resulting in a second model. In this note, we give a precise characterization of these two models in terms of recognized computational complexity classes, namely branching programs (BP) and nondeterminist...

We have performed constant temperature two-dimensional molecular dynamicssimulations of a binary Lennard-Jones material, representing an idealized metallic alloy or amaterial containing a specified fraction of an additive atomic species. Differences in the interatomicpotentials between the atomic species can lead to clustering of the alloy atoms. An exponentialdistribution of cl...

Problems implementing DNA computers stem from the physical nature of molecules and their reactions. The present theory of computation requires assumptions that, at best, are extremely crude approximations of the physical chemistry. Here, I consider the hypothesis that discarding those assumptions in favor of more physically realistic descriptions would produce a more comprehensive theory of com...