Journal article

Absolute Versus Relative Entropy Parameter Estimation In A Coarse-Grain Model Of Dna

Maximum entropy procedures for estimating coarse-grain parameters from molecular dynamics (MD) simulation data are considered within the specific context of the sequence-dependent cgDNA rigid-base model of DNA. We describe a quite general approach that exploits a maximum absolute entropy principle to fit an observed matrix of covariances subject to the constraint of only allowing a prescribed sparsity pattern of nearest-neighbor interactions in the free energy. We also allow indefinite local stiffness-matrix parameter blocks that nevertheless always generate a positive-definite model stiffness matrix. Beginning from a database of atomic-resolution MD simulations of a library of short DNA oligomers in explicit solvent, these procedures deliver a complete parameter set for the cgDNA model. Due to the intrinsic linear structure of DNA and the convergence characteristics of the MD time series data, the maximum absolute entropy parameter set yields significantly improved predictions of persistence lengths, when compared to a previous parameter set that was fit to the same MD data, but using a maximum relative entropy fitting principle and local stiffness-matrix parameter blocks that were constrained to be semidefinite.


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