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Scientific workflows are a powerful programming technique for specifying complex computations using a number of otherwise independent components. When used in a Grid environment, it is possible to build powerful "virtual applications" across multiple distributed and heterogeneous resources. Whilst toolkits such as Globus virtualize many system attributes, and thus make it easier to span different organizations, inconsistent security policies and resource heterogeneity can limit the applicability of workflow techniques. In earlier work, we have described a novel run time environment, GriddLeS, that supports flexible communication patterns between workflow components. GriddLeS abstracts IO operations, such that applications are given the illusion of operating on a local file system, whilst in fact they send and receive data between components. In this paper, we describe how GriddLeS assists in resolving some of the issues that arise due to heterogeneity in security policies and system architectures in a Grid environment. We illustrate the solution using a real world scientific workflow for climate modeling, and demonstrate a system that spans multiple conflicting security domains with heterogeneous resources.