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In December 1999, IBM announced the start of a five-year effort to build a massively parallel computer, to be applied to the study of biomolecular phenomena such as protein folding. The project has two main goals: to advance our understanding of the mechanisms behind protein folding via large-scale simulation, and to explore novel ideas in massively(More)
To meet the challenge of modeling the conformational dynamics of biological macromolecules over long time scales, much recent effort has been devoted to constructing stochastic kinetic models, often in the form of discrete-state Markov models, from short molecular dynamics simulations. To construct useful models that faithfully represent dynamics at the(More)
YORKTOWN HEIGHTS, NY, December 6, 1999-IBM today announced a new $100 million exploratory research initiative to build a supercomputer 500 times more powerful than the world's fastest computers today. The new computer-nicknamed "Blue Gene" by IBM researchers-will be capable of more than one quadrillion operations per second (one petaflop). This level of(More)
Protein folding involves physical timescales—microseconds to seconds—that are too long to be studied directly by straightforward molecular dynamics simulation, where the fundamental timestep is constrained to femtoseconds. Here we show how the long-time statistical dynamics of a simple solvated biomolecular system can be well described by a discrete-state(More)
A rigorous formalism for the extraction of state-to-state transition functions from a Boltzmann-weighted ensemble of microcanonical molecular dynamics simulations has been developed as a way to study the kinetics of protein folding in the context of a Markov chain. Analysis of these transition functions for signatures of Markovian behavior is described. The(More)
Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of(More)
The Blue Genet project involves the development of a highly parallel supercomputer, the coding of scalable applications to run on it, and the design of protein simulations that take advantage of the power provided by the new machine. This paper provides an overview of analysis techniques applied to scientific results obtained with Blue Matter, the software(More)