Discrete molecular dynamics studies of the folding of a protein-like model

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical properties of the proteins (lattice models), while others are computationally heavy (traditional MD). Results: We use a recently-proposed approach of Zhou and Karplus to study the folding of the protein model based on the discrete time molecular dynamics algorithm. We show that this algorithm resolves with respect to time the folding --- unfolding transition. In addition, we demonstrate the ability to study the coreof the model protein. Conclusion: The algorithm along with the model of inter-residue interactions can serve as a tool to study the thermodynamics and kinetics of protein models.Comment: 15 pages including 20 figures (Folding & Design in press

Aerospace Medicine and Biology: a Continuing Bibliography with Indexes (Supplement 328)

This bibliography lists 104 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during September, 1989. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

How Models Fail. A Critical Look at the History of Computer Simulations of the Evolution of Cooperation

Simulation models of the Reiterated Prisoner's Dilemma have been popular for studying the evolution of cooperation since more than 30 years now. However, there have been practically no successful instances of empirical application of any of these models. At the same time this lack of empirical testing and confirmation has almost entirely been ignored by the modelers community. In this paper, I examine some of the typical narratives and standard arguments with which these models are justified by their authors despite the lack of empirical validation. I find that most of the narratives and arguments are not at all compelling. None the less they seem to serve an important function in keeping the simulation business running despite its empirical shortcomings

Tarski's influence on computer science

The influence of Alfred Tarski on computer science was indirect but significant in a number of directions and was in certain respects fundamental. Here surveyed is the work of Tarski on the decision procedure for algebra and geometry, the method of elimination of quantifiers, the semantics of formal languages, modeltheoretic preservation theorems, and algebraic logic; various connections of each with computer science are taken up