The main goal of this research is to develop, analyze, and implement robust numerical upscaling algorithms for emerging multiphysics problems of flows in deformable porous media. The physical problem under consideration at the fine scale is the strongly coupled, nonlinear Fluid-Structure Interaction (FSI) problem subject to large pore-level deformations and/or a nonlinear hysteretic solid. Moreover, microstructures with a continuum distribution of poorly separated length scales will be considered. Novel iterative upscaling algorithms will be used to develop coarse scale models for such media. The research will result in a Multiscale Finite Element Method, which bypasses the explicit homogenization step by building fine-scale information directly into a coarse-scale computational grid. The approach allows accurate numerical simulations at several tightly coupled scales, with the fine scale physics being properly incorporated at the coarser scales. A highly efficient and scalable parallel implementation will be pursued that will allow numerical simulations of realistic problems. The proposed algorithms will be used for pilot numerical simulations of cutting edge problems in multiscale hydro-mechanical modeling of bone tissue and in automotive filter design. Moreover, design of novel temperature and pressure-controlled flow regulators with applications to filters, catalytic converters, and separators can only become possible with such advanced tools for multiscale simulations. The work will also have long term impact in development of upscaling methods for modeling and simulations of emerging multiphysics problems such as carbon sequestration, waste water management or unconventional oil recovery. It also fulfills the aim of reintegrating the researcher. It covers priority areas for the host and both sides have complementing experience. The host also has experience in EU level research and the work will lead to collaborations with US groups working in the area.