Characterizing Optimality in Nonconvex Optimization: Addendum
Sanjo Zlobec (1992)
The Yugoslav Journal of Operations Research
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Sanjo Zlobec (1992)
The Yugoslav Journal of Operations Research
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Serafim Opricović, Lorenzo Eccher, Miodrag Isailovski (1992)
The Yugoslav Journal of Operations Research
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Ellis L. Johnson, George L. Nemhauser (1992)
The Yugoslav Journal of Operations Research
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Anatolly Anatolijevich Vatolin (1996)
The Yugoslav Journal of Operations Research
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Hannu Nurmi (1982)
Stochastica
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This paper deals with two ways in which uncertainty notions enter social science models: 1) They can be used in an effort to make intelligible some phenomena that would otherwise be difficult to comprehend, or 2) They can be use to generalize or modify the domain of validity of some theoretical results.
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....
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...
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.
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....
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...
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,...
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....
Chuan Li, Lin Li, Marharyta Petukh, Emil Alexov (2013)
Molecular Based Mathematical Biology
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This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nanoobjects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task...
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...