Efficiently Transplanting Potential Energy Interpolation Database between Two Systems: Bacteriochlorophyll Case with FMO and LH2 Complexes.

Generating a reliable potential energy surface (PES) is an important issue for studying the dynamics of any system with computational simulations. Interpolation mechanics/molecular mechanics (IM/MM) based on a PES interpolation scheme is a useful tool in that regard as it provides an accuracy of a quantum chemistry (QC) level while maintaining its computational cost comparable to conventional MM force fields. Despite this benefit, constructing the database for interpolation itself is still challenging and time-consuming. Here, we present a method with which we can construct the IM database of one system based on a preexisting data set for another related system. We adopt the case of constructing bacteriochlorophyll PESs for the light-harvesting 2 (LH2) complex by utilizing already available IM database for the BChls from the Fenna-Matthews-Olson (FMO) complex. In this method, the IM database from FMO is first transplanted to LH2 by considering BChl displacement vectors that take into account the geometry differences induced by the protein scaffolds. From this transplanted primitive database entries, a relatively small number of effective ones are selected by a survival process based on a genetic algorithm such that the IM energies evaluated at geometries in a conveniently collected prediction set can closely match with the reference QC energies. The selection process is expedited by using two different levels of basis sets for the QC calculations. To demonstrate the utility of the PES thus constructed, we carry out 1 ns of IM/MM dynamics simulations with the finally optimized BChl database for LH2. Indeed, the energy profiles of the snapshots are found to be closely matching with the reference QC calculation data, with only ∼0.07 eV of errors in the ground- and excited-state energies and ∼0.008 eV of errors in the transition energies. We also show that properly selecting data points is actually quite important for generating an IM PES toward performing molecular dynamics simulations.

Optimal scan timing and intravenous route for contrast-enhanced computed tomography in patients after Fontan operation.

PURPOSE: To determine the optimal scan timing and adequate intravenous route for patients having undergone the Fontan operation. MATERIALS AND METHODS: A total of 88 computed tomographic images in 49 consecutive patients who underwent the Fontan operation were retrospectively evaluated and divided into 7 groups: group 1, bolus-tracking method with either intravenous route (n = 20); group 2, 1-minute-delay scan with single antecubital route (n = 36); group 3, 1-minute-delay scan with both antecubital routes (n = 2); group 4, 1-minute-delay scan with foot vein route (n = 3); group 5, 1-minute-delay scan with simultaneous infusion via both antecubital and foot vein routes (n = 2); group 6, 3-minute-delay scan with single antecubital route (n = 22); and group 7, 3-minute-delay scan with foot vein route (n = 3). The presence of beam-hardening artifact, uniform enhancement, and optimal enhancement was evaluated at the right pulmonary artery (RPA), left pulmonary artery (LPA), and Fontan tract. Optimal enhancement was determined when evaluation of thrombus was possible. Standard deviation was measured at the RPA, LPA, and Fontan tract. RESULTS: Beam-hardening artifacts of the RPA, LPA, and Fontan tract were frequently present in groups 1, 4, and 5. The success rate of uniform and optimal enhancement was highest (100%) in groups 6 and 7, followed by group 2 (75%). An SD of less than 30 Hounsfield unit for the pulmonary artery and Fontan tract was found in groups 3, 6, and 7. CONCLUSIONS: The optimal enhancement of the pulmonary arteries and Fontan tract can be achieved by a 3-minute-delay scan irrespective of the intravenous route location.