A vast amount of work has been done in recent years on the design, analysis, implementation and verification of special purpose parallel computing systems. This paper presents a survey of various aspects of this work. A long, but by no means complete, bibliography is given. 1. Introduction Turing [365] demonstrated that, in principle, a single general purpose sequential machine could be designed which would be capable of efficiently performing any computation which could be performed by a special purpose sequential machine. The importance of this universality result for subsequent practical developments in computing cannot be overstated. It showed that, for a given computational problem, the additional efficiency advantages which could be gained by designing a special purpose sequential machine for that problem would not be great. Around 1944, von Neumann produced a proposal [66, 389] for a general purpose storedprogram sequential computer which captured the fundamental principles of...

. This paper discusses the mathematical formulation of and solution attempts for the so-called protein folding problem. The static aspect is concerned with how to predict the folded (native, tertiary) structure of a protein, given its sequence of amino acids. The dynamic aspect asks about the possible pathways to folding and unfolding, including the stability of the folded protein. From a mathematical point of view, there are several main sides to the static problem: -- the selection of an appropriate potential energy function; -- the parameter identification by fitting to experimental data; and -- the global optimization of the potential. The dynamic problem entails, in addition, the solution of (because of multiple time scales very stiff) ordinary or stochastic differential equations (molecular dynamics simulation), or (in case of constrained molecular dynamics) of differential-algebraic equations. A theme connecting the static and dynamic aspect is the determination and formation of...

We present algorithms for kinematic manipulation of molecular chains subject to fixed bond lengths and bond angles. They are useful for calculating conformations of a molecule subject to geometric constraints, such as those derived from two-dimensional NMR experiments. Other applications include searching out the full range of conformations available to a molecule such as cyclic configurations. We make use of results from robot kinematics and recently developed algorithms for solving polynomial systems. In particular, we model the molecule as a serial chain using the Denavit-Hartenberg formulation and reduce these problems to inverse kinematics of a serial chain. We also highlight the relationship between molecular embedding problems and inverse kinematics. As compared to earlier methods, the main advantages of the kinematic formulation are its generality to all molecular chains without any restrictions on the geometry and efficiency in terms of performance. The algorithms give us real...

MOLGEN is a computer program system which is designed for generating molecular graphs fast, redundancy free and exhaustively. In the present paper we describe its basic features, new features of the current release MOLGEN 3.5, and future developments which provide considerable improvements and extensions. 1 Introduction MOLGEN [1--7] is a generator for molecular graphs (=connectivity isomers or constitutional formulae) allowing to generate all isomers that correspond to a given molecular formula and (optional) further conditions like prescribed and forbidden substructures, ring sizes etc. The input consists of ffl the empirical formula, together with ffl an optional list of macroatoms, which means prescribed substructures that must not overlap, ffl an optional goodlist, that consists of prescribed substructures which may overlap, ffl an optional badlist, containing forbidden substructures, ffl an optional interval for the minimal and maximal size of rings, ffl an optional num...