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Jacob Sanders edited sectionApplication_m.tex
over 9 years ago
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If we assume that a system has a finite range interaction between atoms, and since each atom has an approximately constant number of neighbors, irrespective of the total number of atoms in the molecule, the number of non-zero elements in a single column of the Hessian is constant. Hence, for large molecules, the sparsity \(S\) of the Hessian scales linearly with the number of atoms \(N\). Putting this result into \(O(S/N \log N) \times OE\) yields a best-case final scaling result of \(O\left(\log N \right)\times OE\), which is a significant improvement over the original \(O(N)\times OE\) in the absence of compressed sensing. {\color{red} However, we should note that eq.~\ref{eq:csscaling} is only valid for a random
sampling, and it is not necessarily valid for a column sampling.}
To study the validity of our scaling result we have performed numerical calculations...
Although for large systems the Hessian is expected to be sparse in the
molecular coordinate basis, for more moderately-sized molecules all
the atoms are relatively close to each other so we cannot rely on the
Hessian being sparse. Instead, we pursue an alternative strategy for
sparsifying the Hessian, namely guessing the basis of eigenvectors in
which the Hessian is diagonal. We believe this procedure of
estimating the eigenvectors and then recovering the sparse matrix in
this approximate eigenbasis via compressed sensing will generalize to
a wide range of scientific applications beyond molecular vibrations.
For a quantum mechanical Hessian, our method for cheaply estimating
the eigenvectors involves a simple molecular mechanics computation
which is essentially instantaneous for moderately-sized organic
molecules. Molecular mechanics computations approximate the
interactions between pairs of atoms via a force field, which is a set
of empirically-derived pair potentials between all pairs of atoms in
the molecule. The energy derivatives which appear in the Hessian may
be computed as analytical derivatives of these pair potentials, and
diagonalizing this molecular mechanics Hessian yields a cheap
approximation to eigenvectors of the true quantum mechanical Hessian.
Fig.~\ref{fig:HessianScheme} illustrates the viability of this procedure for anthracene (\(\textrm{C}_{14}\textrm{H}_{10}\)), an aromatic molecule consisting of three fused benzene rings. The left side depicts the quantum mechanical Hessian of anthracene in the basis of molecular coordinates (\(H\)), while the right side shows the same matrix in the approximate eigenbasis obtained via an auxiliary molecular mechanics computation (\(A\)). The matrix \(A\) is nearly diagonal and quite sparse, and is therefore well-suited to recovery via compressed sensing.