Anton, a special-purpose machine for molecular dynamics simulation

Abstract

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond-several orders of magnitude beyond the duration of the longest current MD simulations. We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized highspeed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.

Towards personalized computational oncology: from spatial models of tumour spheroids, to organoids, to tissues

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Automatic Algorithm Selection for Complex Simulation Problems

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