Abstract: An ellipsoid cell model for modeling cell and tissue organisms may enhance the quality of simulation of complex biological systems. Ellipsoid cell model may relate to the use of ellipsoid shapes to represent cells for modeling a biological system. This method may be capable of providing a more realistic representation of cells, for conducting computational experiments to study biological complexities at a large scale.

Abstract: A computing system for scalable computing on commodity hardware is provided. The computing system includes a first computing device communicatively connected to a second computing device. The first computing device includes a processor, a physical computer-readable medium, and program instructions stored on the physical computer-readable medium and executable by the processor to perform functions. The functions include determining a first task associated with the second computing device and a second task associated with the second computing device are to be executed, assigning execution of the first task and the second task to the processor of the first computing device, generating an aggregated message that includes (i) a first message including an indication corresponding to the execution of the first task and (ii) a second message including an indication corresponding to the execution of the second task, and sending the aggregated message to the second computing device.

Abstract: A method and system for allocating and de-allocating memory for threads of an application is provided. An allocation system provides a heap for tracking free tokens of memory that are available for allocation to threads of an application. A heap tracks collections of free tokens of the fixed token size. The allocation system receives memory requests from threads that specify an allocation type of allocate or de-allocate. When multiple memory requests are pending concurrently from multiple threads, then the allocation system attempts to combine memory requests of the same type and of the same token size that are received from different threads. One of the threads is responsible for updating the heap to effect the two memory requests. The allocation system combines multiple memory requests so that the heap need only be accessed once to allocate or de-allocate multiple tokens.

Abstract: A method and system for finding connected components of a graph using a parallel algorithm is provided. The connected nodes system performs a search algorithm in parallel to identify subgraphs of the graph in which the nodes of the subgraph are connected. The connected nodes system also identifies which subgraphs have at least one edge between their nodes. Thus, the connected nodes system effectively generates a hyper-graph with the subgraphs as hyper-nodes that are connected when subgraphs have at least one edge between their nodes. The connected nodes system may then perform a conventional connected component algorithm on the hyper-graph to identify the connected hyper-nodes, which effectively identifies the connected nodes of the underlying graphs.

Abstract: Various techniques for manipulating data using access states of memory, access control fields of pointers and operations, and exception raising and exception trapping in a multithreaded computer system. In particular, the techniques include synchronization support for a thread blocked in a word, demand evaluation of values, parallel access of multiple threads to a list, synchronized and unsynchronized access to a data buffer, use of forwarding to avoid checking for an end of a buffer, use of sentinel word to detect access past a data structure, concurrent access to a word of memory using different synchronization access modes, and use of trapping to detect access to restricted memory.