Domain Decomposition Algotithms and Comput , ation Fluid Dynamics

Parallel Domain-Decomposition Preconditioning for Computational Fluid Dynamics

An adaptive hierarchical domain decomposition method for parallel contact dynamics simulations of granular materials

A fully parallel version of the Contact dynamics (CD) method is presented in this paper. For large enough systems, 100% efficiency is reached for an arbitrary number of processors using hierarchical domain decomposition with dynamical load balancing. The iterative scheme to calculate the contact forces is left domain-wise sequential, with data exchange after each iteration step, which ensures i...

Designing a new tetrapeptide to inhibit the BIR3 domain of the XIAP protein via molecular dynamics simulations

The XIAP protein is a member of apoptosis proteins family. The XIAP protein plays a central role in the inhibition of apoptosis and consists of three Baculoviral IAP Repeat domains. The BIR3 domain binds directly to the N-terminal of caspase-9 and therefore it inhibits apoptosis. N-terminal tetrapeptide region of SMAC protein can bind to BIR3, inhibit it and subsequently induce apoptosis. In th...

Achieving Scalable Parallel Molecular Dynamics Using Dynamic Spatial Domain Decomposition Techniques

To achieve scalable parallel performance in Molecular Dynamics Simulations, we have modeled and implemented several dynamic spatial domain decomposition algorithms. The modeling is based upon the Bulk Synchronous Parallel architecture model (BSP), which describes supersteps of computation, communication, and synchronization. Using this model, we have developed prototypes that explore the differ...

Domain Decomposition Methods in Computational Fluid Dynamics

The divide-and-conquer paradigm of iterative domain decomposition or substructuring has become a practical tool in computational fluid dynamics applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards paralle...