Sub-terahertz (THz) vibrational modes of the protein thioredoxin in a water environment were simulated using molecular dynamics (MD) in order to find the conditions needed for simulation convergence, improve the correlation between experimental and simulated absorption frequencies, and ultimately enhance the predictive capabilities of computational modeling. Thioredoxin from E. coli was used as a model molecule for protocol development and to optimize the simulation parameters. The empirically parameterized software packages Amber 8 and 10 were used in this work. Using atomic trajectories from the constant energy and volume MD simulations, thioredoxin's sub-THz vibrational spectra and absorption coefficients were calculated in a quasi-harmonic approximation. An optimal production run length ~100 ps was found, in agreement with experimental data on thioredoxin relaxation dynamics. At the same time, a new procedure was developed for averaging correlation matrices of atomic coordinates in MD simulations. In particular, the open source package ptraj was edited to improve a matrix-analyzing function. Averaging only six matrices gave much more consistent results, with absorption peak intensities exceeding those from the individual spectra and a rather good correlation between simulated vibrational frequencies and experimental data.
Abstract-Many useful scenarios involve allowing untrusted users to run queries against secret data, so long as the results do not leak too much information. This problem has been studied widely for statistical queries, but not for queries with more direct semantics. In this paper, we consider the problem of auditing queries where the result is a distance metric between the query input and some secret data. We develop an efficient technique for estimating a lower bound on the entropy remaining after a series of query-responses that applies to a class of distance functions including Hamming distance. We also present a technique for ensuring that no individual bits of the secret sequence is leaked. In this paper, we formalize the information leakage problem, describe our design for a query auditor, and report on experiments showing the feasibility and effectiveness of our approach for sensitive sequences up to thousands of bits.
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