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Displaying similar documents to “Theory, Experiment and Computation of Half Metals for Spintronics: Recent Progress in Si-based Materials”

Coulomb Interaction Effects on the Spin Polarization and Currents in Quantum Wires with Spin Orbit Interaction

Anton Heidar Thorolfsson, Andrei Manolescu, D.C. Marinescu, Vidar Gudmundsson (2012)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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We analyze the charge and spin distributions induced in an interacting electron system confined inside a semiconductor quantum wire with spin orbit interaction in the presence of an external magnetic field. The wire, assumed to be infinitely long, is obtained through lateral confinement in three different materials: GaAs, InAs, and InSb. The spin-orbit coupling, linear in the electron momentum is of both Rashba and Dresselhaus type. Within the Hartree-Fock approximation the many-body...

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 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...

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...

An inverse problem for adhesive contact and non-direct evaluation of material properties for nanomechanics applications

F.M. Borodich, B.A. Galanov, S.N. Gorb, M.Y. Prostov, Y.I. Prostov, M.M. Suarez-Alvarez (2012)

Nanoscale Systems: Mathematical Modeling, Theory and Applications

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We show how the values of the effective elastic modulus of contacting solids and the work of adhesion, that are the crucial material parameters for application of theories of adhesive contact to nanomechanics, may be quantified from a single test using a non-direct approach (the Borodich-Galanov (BG) method). Usually these characteristics are not determined from the same test, e.g. often sharp pyramidal indenters are used to determine the elastic modulus from a nanoindentation test,...

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....

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...

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...

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,...

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,...