Abstract: A method for managing flow of particles into an array of pairwise-point-interaction-module includes receiving a first set of particles into a first queue. The first set is a proper subset of a second set of particles that comprises all particles that are to be passed into an array of pairwise-point-interaction-modules during a current time period. Prior to having received all particles from the second set, particles from the first set are allowed to pass from the first queue into the array.

Abstract: A method comprising causing a simulation machine for molecular dynamic simulation to determine that a topological distance that separates two particles is less than a threshold. The simulation machine includes nodes connected by a network. The nodes collectively representing a volume with each node corresponding to a portion of the simulation space. A topological relationship between the nodes corresponds to spatial relationship thereof in the simulation space. The simulation volume is occupied by particles that interact with each other. The two particles are among these particles. The simulation volume includes node boxes, each of which is handled by one of the nodes. Each of the nodes is implemented as an application specific integrated circuit that includes a combination of first and second hardware elements. The first hardware elements are especially designed to perform pairwise interactions. The second hardware elements operate to provide potentially interacting particles to the first hardware elements.

Abstract: A method for performing computations associated with bodies located in a computation region includes, for each subset of multiple subsets of the computations, performing the computations in that subset of computations, including accepting data of bodies located in each of a plurality of import regions associated with the subset of the computations, the import regions being parts of the computation region; for each combination of a predetermined plurality of combinations of multiple of the import regions, performing computations associated with sets of bodies, wherein for each of the sets of bodies, at least one body of the set is located in each import region of the combination.

Abstract: A method for managing flow of particles into an array of pairwise-point-interaction-module includes receiving a first set of particles into a first queue. The first set is a proper subset of a second set of particles that comprises all particles that are to be passed into an array of pairwise-point-interaction-modules during a current time period. Prior to having received all particles from the second set, particles from the first set are allowed to pass from the first queue into the array.

Abstract: A method comprising causing a computer to determine that a topological distance between two particles is less than a threshold.

Abstract: A method and a corresponding software and a system for processing a charge distribution according to a spreading function and a predefined operation are described.

Abstract: A generalized approach to particle interaction can confer advantages over previously described method in terms of one or more of communications bandwidth and latency and memory access characteristics. These generalizations can involve one or more of at least spatial decomposition, import region rounding, and multiple zone communication scheduling. An architecture for computation of particle interactions makes use various forms of parallelism. In one implementation, the parallelism involves using multiple computation nodes arranged according to a geometric partitioning of a simulation volume.

Abstract: A method and a corresponding software and a system for processing a charge distribution according to a spreading function and a predefined operation are described.