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Viruses must remain infectious while in harsh extracellular environments. An important aspect of viral particle stability for double-stranded DNA viruses is the energetically unfavorable state of the tightly confined DNA chain within the virus capsid creating pressures of tens of atmospheres. Here, we study the influence of internal genome pressure on the thermal stability of viral particles. Using...
We present a performance analysis for a highly accurate, large-scale electromagnetic wave propagation model on two modern supercomputing platforms: the Cray XT5 and the IBM Blue Gene/L. The electromagnetic wave model is used to simulate the physical layer of a large-scale mobile ad-hoc network of radio devices. The model is based on the numerical technique called Transmission Line Matrix, and is implemented...
In this paper we illustrate scalable parallel performance for the TimeWarp synchronization protocol on the L and P variants of the IBM BlueGene supercomputer. Scalable Time Warp performance for models that communicate a large percentage of the event population over the network has not been shown on more than a handful of processors. We present our design for a robust performing Time Warp simulator...
The global health, threatened by emerging infectious diseases, pandemic influenza, and biological warfare, is becoming increasingly dependent on the rapid acquisition, processing, integration and interpretation of massive amounts of data. In response to these pressing needs, new information infrastructures are needed to support active, real time surveillance. Detection algorithms may have a high computational...
A major challenge in the field of Modeling & Simulation is providing efficient parallel computation for a variety of algorithms. Algorithms that are described easily and computed efficiently for continuous simulation, may be complex to describe and/or efficiently execute in a discrete event context, and vice-versa. Real-world models often employ multiple algorithms that are optimally defined in...
In this paper we describe a technique for efficient parallelization of digital wave guide network (DWN) models based on an interpretation of the finite difference time domain (FDTD) method for discrete event simulation. Modeling methodologies based on FDTD approaches are typically constrained in both the spatial and time domains. This interpretation for discrete event simulation allows us to investigate...
The traditional rollback mechanism deployed in optimistic simulation is state-saving. More recently, the method of reverse computation has been proposed to reduce the amount of memory consumed by state-saving. This method computes the reverse code for the model during rollback execution, rather than recalling saved state memory. In practice, this method has been shown to offer memory-efficiency without...
This paper introduces an algorithm for parallel simulation capable of executing the critical path without a priori knowledge of the model being executed. This algorithm is founded on the observation that each initial event in a model causes a stream of events to be generated for execution. By focusing on the parallelization of event streams, rather than logical processes, we have created a new simulation...
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