Duc D. Nguyen

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Flexibility-rigidity index (FRI) has been developed as a robust, accurate, and efficient method for macromolecular thermal fluctuation analysis and B-factor prediction. The performance of FRI depends on its formulations of rigidity index and flexibility index. In this work, we introduce alternative rigidity and flexibility formulations. The structure of the(More)
It has been analytically proved that both MaxNet and SumNet can achieve m ax-min fair allocation in static networks. In SumNet networks, such as the TCP algorithm of the current Internet, the source rate is controlled by congestion signal which is the sum of signals from all of the congested links along the path from the source to the destination. In MaxNet(More)
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid(More)
This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a(More)
ax-min fair nternet, the ed links ngested link ects of both ent network ends on the network load. Within the stable ranges of operating points, SumNet's max-min fair allocation is obtained at e the stability of SumNet to meet the max-min fairness criterion. We have shown both analytically and by simulation that under stable conditions, Maxnet has faster(More)
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