Displaying similar documents to “Characterizing Optimality in Nonconvex Optimization: Addendum”

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,...

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...

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....

An overview of some recent developments on the Invariant Subspace Problem

Isabelle Chalendar, Jonathan R. Partington (2013)

Concrete Operators

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This paper presents an account of some recent approaches to the Invariant Subspace Problem. It contains a brief historical account of the problem, and some more detailed discussions of specific topics, namely, universal operators, the Bishop operators, and Read’s Banach space counter-example involving a finitely strictly singular operator.

Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Amelia B. Kreienkamp, Lucy Y. Liu, Mona S. Minkara, Matthew G. Knepley, Jaydeep P. Bardhan, Mala L. Radhakrishnan (2013)

Molecular Based Mathematical Biology

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We analyze and suggest improvements to a recently developed approximate continuum-electrostatic model for proteins. The model, called BIBEE/I (boundary-integral based electrostatics estimation with interpolation), was able to estimate electrostatic solvation free energies to within a mean unsigned error of 4% on a test set of more than 600 proteins¶a significant improvement over previous BIBEE models. In this work, we tested the BIBEE/I model for its capability to predict residue-by-residue...

Efficient simulation of unidirectional pulse propagation in high-contrast nonlinear nanowaveguides

Jonathan Andreasen, Miroslav Kolesik (2013)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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This work demonstrates an improved method to simulate long-distance femtosecond pulse propagation in highcontrast nanowaveguides. Different from typical beam propagation methods, the foundational tool here is capable of simulating strong spatiotemporal waveform reshaping and extreme spectral dynamics. Meanwhile, the ability to fully capture effects due to index contrast in the transverse direction is retained, without requiring a decomposition of the electric field in terms of waveguide...

A numerically efficient approach to the modelling of double-Qdot channels

A. Shamloo, A.P. Sowa (2013)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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We consider the electronic properties of a system consisting of two quantum dots in physical proximity, which we will refer to as the double-Qdot. Double-Qdots are attractive in light of their potential application to spin-based quantum computing and other electronic applications, e.g. as specialized sensors. Our main goal is to derive the essential properties of the double-Qdot from a model that is rigorous yet numerically tractable, and largely circumvents the complexities of an ab...

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....

Theory, Experiment and Computation of Half Metals for Spintronics: Recent Progress in Si-based Materials

C. Y. Fong, M. Shaughnessy, L. Damewood, L. H. Yang (2012)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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Since the term “spintronics” was conceived in 1996, there have been several directions taken to develop new semiconductor-based magnetic materials for device applications using spin, or spin and charge, as the operational paradigm. Anticipating their integration into mature semiconductor technologies, one direction is to make use of materials involving Si. In this review, we focus on the progress made, since 2005, in Si-based half metallic spintronic materials. In addition to commenting...

Quantum optimal control using the adjoint method

Alfio Borzì (2012)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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Control of quantum systems is central in a variety of present and perspective applications ranging from quantum optics and quantum chemistry to semiconductor nanostructures, including the emerging fields of quantum computation and quantum communication. In this paper, a review of recent developments in the field of optimal control of quantum systems is given with a focus on adjoint methods and their numerical implementation. In addition, the issues of exact controllability and optimal...