• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

• Structural Engineering and Mechanics
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• v.80 no.6
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• pp.749-765
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• 2021

Suspension bridges bear large eccentric live loads in rush hours when most vehicles travel in one direction on the left or right side of the bridge. With the increasing number and weight of vehicles and the girder widening, the eccentric live load effect on the bridge behavior, including bending and distortion of the main girder, gets more pronounced, even jeopardizing bridge safety. This study proposes an analytical algorithm based on multi-catenary theory for predicting the suspension bridge responses to eccentric live load via the nonlinear generalized reduced gradient method. A set of governing equations is derived to solve the following unknown values: the girder rigid-body displacement in the longitudinal direction; the horizontal projection lengths of main cable's segments; the parameters of catenary equations and horizontal forces of the side span cable segments and the leftmost segments of middle span cables; the suspender tensions and the bearing reactions. Then girder's responses, including rigid-body displacement in the longitudinal direction, deflections, and torsion angles; suspenders' responses, including the suspender tensions and the hanging point displacements; main cables' responses, including the horizontal forces of each segment; and the longitudinal displacement of the pylons' tower top under eccentric load can be calculated. The response of an exemplar suspension bridge with three spans of 168, 548, and 168 m is calculated by the proposed analytical method and the finite element method in two eccentric live load cases, and their results prove the former's feasibility. The nonuniform distribution of the live load in the lateral direction is shown to impose a greater threat to suspension bridge safety than that in the longitudinal direction, while some other specific features revealed by the proposed method are discussed in detail.