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Current spacecraft systems generally have monolithic structures, but a "fractionated" architecture is being considered for next generation spacecrafts. A fractionated spacecraft system is a cluster of independent modules that communicate wirelessly to maintain cluster flight formations and realize the functions usually performed by a monolithic satellite. The envisioned benefits of the fractionated approach include enhanced responsiveness, greater flexibility, robustness and co-existence of multiple missions from different sources with varying degree of trust. The fractionated architecture, however, introduces significant new challenges from the perspective of resource allocation and management. The mobile nature of the clusters and the modules within the cluster implies that the network topology is highly time-varying. A cluster with multiple missions can require messages to be transmitted across the network with varying degrees of QoS requirements such as timeliness and data delivery reliability. The system must determine the appropriate and timely resource allocation for these missions. In this paper, we address these resource allocation challenges by introducing an abstraction of dynamic graphs, and extending the QoS based Resource Allocation Model (Q-RAM) to operate on these dynamic graphs. We develop a mechanism to decompose a dynamic graph into multiple static sub-graphs using which the resource allocation problem is partitioned into multiple sub-problems within each of these static sub-graphs. We have experimentally evaluated our solution by building a simulation framework called SatSim, which can handle a variety of satellite configurations and mobility models. The proposed solution is shown to achieve a near-optimal solution for the resource allocation problem in time-varying networks, while reducing time complexity significantly.