Joseph A. Bank

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Java offers the real possibility that most programs can be written in a type-safe language. However, for Java to be broadly useful, it needs additional expressive power. This paper extends Java in one area where more power is needed: support for parametric polymorphism, which allows the definition and implementation of generic abstractions. We discuss both(More)
Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of(More)
Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first time the simulation of biological molecules at an atomic level of detail for periods on the order of a(More)
Anton, a massively parallel special-purpose machine for molecular dynamics simulations, performs a 32x32x32 FFT in 3.7 microseconds and a 64x64x64 FFT in 13.3 microseconds on a configuration with 512 nodes---an order of magnitude faster than all other FFT implementations of which we are aware. Achieving this FFT performance requires a coordinated(More)
Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics simulations that achieves significant gains in performance, programmability, and capacity compared to its predecessor, Anton 1. The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of(More)
Java offers the real possibility that most programs can be written in a type-safe language. However, for Java to be broadly useful, it needs additional expressive power. This paper extends Java in one area where more power is needed: support for parametric polymorphism, which allows the definition and implementation of generic abstractions. The paper(More)
Strong scaling of scientific applications on parallel architectures is increasingly limited by communication latency. This paper describes the techniques used to mitigate latency in Anton, a massively parallel special-purpose machine that accelerates molecular dynamics (MD) simulations by orders of magnitude compared with the previous state of the art.(More)
Exploiting parallelism to accelerate a computation typically involves dividing it into many small tasks that can be assigned to different processing elements. An efficient execution schedule for these tasks can be difficult or impossible to determine in advance, however, if there is uncertainty as to when each task's input data will be available. Ideally,(More)
Special-purpose computing hardware can provide significantly better performance and power efficiency for certain applications than general-purpose processors. Even within a single application area, however, a special-purpose machine can be far more valuable if it is capable of efficiently supporting a number of different computational methods that, taken(More)
Cascade is a cycle-based C++ simulation infrastructure used in the design and verification of two successive versions of Anton, a specialized machine designed for high-speed molecular dynamics computation. Cascade was engineered to address the size and speed challenges inherent in simulating massively parallel special-purpose machines. It provides a(More)