Displaying similar documents to “Simulation Software Selection 'Whys and Hows'”

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

Similarity:

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

Similarity:

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,...

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

Similarity:

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

Similarity:

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...

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

Similarity:

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...

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

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

Nanoscale Systems: Mathematical Modeling, Theory and Applications

Similarity:

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

Similarity:

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

Similarity:

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...

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

Similarity:

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...