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Section: Application Domains

Keywords : protein, enzyme reaction, membrane, drug design, biological simulation, molecular dynamics, quantum method, continuum method, crack propagation.

Molecular chemistry

Due to the increase of available computer power, new applications such as reaction paths, free energy computations, biomolecular dynamics simulations or failure material simulations are now commonly performed by chemists. These computations simulate systems up to several thousands of atoms, for large time scales up to several nanoseconds. The larger the simulation is, the smaller the computational cost of the potential driving the phenomena is, resulting in low precision results. To achieve realistic results, simulations need to include the environment surrounding the molecules, such as water and membranes, resulting in system sizes up to about several hundred thousands of atoms. Furthermore, simulating the aggregation of proteins, which is critical for biologists studying viruses, requires models of up to one million atoms, with a simulation time up to one millisecond. This implies that atomistic simulations must be speeded up by several orders of magnitude. To obtain this speed, numerical and parallel algorithms must be improved, as well as their implementations on distributed or parallel architectures.


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