30,539 research outputs found
Evaluating force field accuracy with long-time simulations of a tryptophan zipper peptide
We have combined a custom implementation of the fast multiple-time-stepping
LN integrator with parallel tempering to explore folding properties of small
peptides in implicit solvent on the time scale of microseconds. We applied this
algorithm to the synthetic {\beta}-hairpin trpzip2 and one of its sequence
variants W2W9. Each simulation consisted of over 12 {\mu}s of aggregated
virtual time. Several measures of folding behavior showed convergence, allowing
comparison with experimental equilibrium properties. Our simulations suggest
that the electrostatic interaction of tryptophan sidechains is responsible for
much of the stability of the native fold. We conclude that the ff99 force field
combined with ff96 {\phi} and {\psi} dihedral energies and implicit solvent can
reproduce plausible folding behavior in both trpzip2 and W2W9.Comment: 10 pages, 11 figures, submitted to the Journal of Chemical Physics on
June 28, 201
Fluctuation-induced interactions between dielectrics in general geometries
We study thermal Casimir and quantum non-retarded Lifshitz interactions
between dielectrics in general geometries. We map the calculation of the
classical partition function onto a determinant which we discretize and
evaluate with the help of Cholesky factorization. The quantum partition
function is treated by path integral quantization of a set of interacting
dipoles and reduces to a product of determinants. We compare the approximations
of pairwise additivity and proximity force with our numerical methods. We
propose a ``factorization approximation'' which gives rather good numerical
results in the geometries that we study
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