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Replica-exchange (RE) algorithms are used to understand physical phenomena--ranging from protein folding dynamics to binding affinity calculations. They represent a class of algorithms that involve a large number of loosely coupled ensembles, and are thus amenable to using distributed resources. We develop a framework for RE that supports different replica(More)
Coupled Multi-Physics simulations, such as hybrid CFD-MD simulations, represent an increasingly important class of scientific applications. Often the physical problems of interest demand the use of high-end computers, such as TeraGrid resources, which are often accessible only via batch-queues. Batch-queue systems are not developed to natively support the(More)
The challenges facing biomolecular simulations are many-fold. In addition to long time simulations of a single large system, an important challenge is the ability to run a large number of identical copies (ensembles) of the same system. Ensemble-based simulations are important for effective sampling. Due to the low-level of coupling between them,(More)
The Indiana University (IU) Department of Chemistry's Martin F. Jarrold (MFJ) Research Group studies a specialized technique of mass spectrometry called Charge Detection Mass Spectrometry (CDMS). The goal of mass spectrometry is to determine the mass of chemical and biological compounds, and with CDMS, the MFJ Research Group is extending the upper limit of(More)
An increasing number of biologists' computational demands have outgrown the capacity of desktop workstations and they are turning to supercomputers to run their simulations and calculations. Many of today's computational problems, however, require larger resource commitments than even individual universities can provide. XSEDE is one of the first places(More)
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