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Firstly, the macroscopic solver is chosen to reduce the number of required iterations to a minimum.
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A default direct problem solver is RNAfold.
Rerunning the solver is still necessary.
GLPK: the CPLEX solver is used in the simulation.
In additional file 1: supplementary materials in section C examples of fitting of experimental data by means of ODE Solver, Explicit Solver and Implicit Solver are presented.
Two concurrent executions of the ABAQUS solver were performed.
The Tomlab mixed-integer linear programming solver was used.
For convex hull calculation, the MATLAB convhull solver was used.
A puzzle-solver is not entering completely uncharted territory.
The macroscopic constraints on the individual molecular solvers are artificial body-force distributions, used in conjunction with standard periodicity.
Recently, the finite element heterogeneous multiscale method (FE-HMM) has been proposed for such problems, based on a macroscopic solver with effective data recovered from the solution of micro problems on sampling domains at quadrature points of a macroscopic mesh.
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