Displaying similar documents to “Analyses of the Operational Performance of Maternal and Child Health (MCH) Services in Hong Kong”

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes

Tao Liao, Yongjie Zhang, Peter M. Kekenes-Huskey, Yuhui Cheng, Anushka Michailova, Andrew D. McCulloch, Michael Holst, J. Andrew McCammon (2013)

Molecular Based Mathematical Biology

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Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from atomic resolution data in the Protein Data Bank (PDB), which is accelerated by multi-core CPU and programmable Graphics Processing Units (GPU). A multi-level summation of Gaussian kernel functions is employed to generate implicit models for biomolecules....

A Stochastic Solver of the Generalized Born Model

Robert C. Harris, Travis Mackoy, Marcia O. Fenley (2013)

Molecular Based Mathematical Biology

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A stochastic generalized Born (GB) solver is presented which can give predictions of energies arbitrarily close to those that would be given by exact effective GB radii, and, unlike analytical GB solvers, these errors are Gaussian with estimates that can be easily obtained from the algorithm. This method was tested by computing the electrostatic solvation energies (ΔGsolv) and the electrostatic binding energies (ΔGbind) of a set of DNA-drug complexes, a set of protein-drug complexes,...

Reasoning with External Data

Vladan Devedžić, Dušan Velašević, Zoran Božović (1993)

The Yugoslav Journal of Operations Research

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High-order fractional partial differential equation transform for molecular surface construction

Langhua Hu, Duan Chen, Guo-Wei Wei (2013)

Molecular Based Mathematical Biology

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Fractional derivative or fractional calculus plays a significant role in theoretical modeling of scientific and engineering problems. However, only relatively low order fractional derivatives are used at present. In general, it is not obvious what role a high fractional derivative can play and how to make use of arbitrarily high-order fractional derivatives. This work introduces arbitrarily high-order fractional partial differential equations (PDEs) to describe fractional hyperdiffusions....

Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels

Nikolay A. Simakov, Maria G. Kurnikova (2013)

Molecular Based Mathematical Biology

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Poisson and Poisson-Boltzmann equations (PE and PBE) are widely used in molecular modeling to estimate the electrostatic contribution to the free energy of a system. In such applications, PE often needs to be solved multiple times for a large number of system configurations. This can rapidly become a highly demanding computational task. To accelerate such calculations we implemented a graphical processing unit (GPU) PE solver described in this work. The GPU solver performance is compared...

Nanonetworks: The graph theory framework for modeling nanoscale systems

Jelena Živkovic, Bosiljka Tadic (2013)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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Nanonetwork is defined as a mathematical model of nanosize objects with biological, physical and chemical attributes, which are interconnected within certain dynamical process. To demonstrate the potentials of this modeling approach for quantitative study of complexity at nanoscale, in this survey, we consider three kinds of nanonetworks: Genes of a yeast are connected by weighted links corresponding to their coexpression along the cell cycle; Gold nanoparticles, arranged on a substrate,...

Parallel Adaptive Finite Element Algorithms for Solving the Coupled Electro-diffusion Equations

Yan Xie, Jie Cheng, Benzhuo Lu, Linbo Zhang (2013)

Molecular Based Mathematical Biology

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rithms for solving the 3D electro-diffusion equations such as the Poisson-Nernst-Planck equations and the size-modified Poisson-Nernst-Planck equations in simulations of biomolecular systems in ionic liquid. A set of transformation methods based on the generalized Slotboom variables is used to solve the coupled equations. Calculations of the diffusion-reaction rate coefficients, electrostatic potential and ion concentrations for various systems verify the method’s validity and stability....

Vibrational properties of nanographene

Sandeep Kumar Singh, F.M. Peeters (2013)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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The eigenmodes and the vibrational density of states of the ground state configuration of graphene clusters are calculated using atomistic simulations. The modified Brenner potential is used to describe the carbon-carbon interaction and carbon-hydrogen interaction in case of H-passivated edges. For a given configuration of the C-atoms the eigenvectors and eigenfrequencies of the normal modes are obtained after diagonalisation of the dynamical matrix whose elements are the second derivative...