Genomics has become a research area where high performance computing (HPC) applications are in the highest demand. Two new gene-prediction algorithms developed in the lab of Mark Borodovsky at Georgia Tech are ***-ES ...
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Genomics has become a research area where high performance computing (HPC) applications are in the highest demand. Two new gene-prediction algorithms developed in the lab of Mark Borodovsky at Georgia Tech are ***-ES and GeneMark-ES+. Borodovsky and his fellow Georgia Tech researchers are hoping to address the problems posed by 20 GB genome of Norway spruce by developing new algorithms that will delineate large swaths of surely noncoding regions, prior to pinpointing exact locations of protein-coding genes. Research funded by the American Recovery and Reinvestment Act of 2009 aims to develop computational tools that will utilize next-generation petascale computers to understand genomic evolution. The researchers are developing a new high performance software package called Comparing Orders of Genes using Novel Algorithms and high-performance Computers (COGNAC) and will test the performance of their new algorithms by analyzing a collection of fruit fly (Drosophilia) genomes.
Bistable structures associated with nonlinear deformation behavior, exemplified by the Venus flytrap and slap bracelet, can switch between different functional shapes upon actuation. Despite numerous efforts in modeli...
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Bistable structures associated with nonlinear deformation behavior, exemplified by the Venus flytrap and slap bracelet, can switch between different functional shapes upon actuation. Despite numerous efforts in modeling such large deformation behavior of shells, the roles of mechanical and nonlinear geometric effects on bistability remain elusive. We demonstrate, through both theoretical analysis and tabletop experiments, that two dimensionless parameters control bistability. Our work classifies the conditions for bistability, and extends the large deformation theory of plates and shells.
Waveform inversion of crosshole data based on acoustic wave equation is investigated in this paper. The inversion is set as an optimization problem with the Lagrange multiplier function. The Tikhonov regularization is...
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作者：
Huajie ChenXingao GongLianhua HeAihui ZhouLSEC
Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China Department of Physics
Fudan UniversityShanghai 200433China
In this paper,we study an adaptive finite element method for a class of nonlinear eigenvalue problems resulting from quantum physics that may have a nonconvex energy *** prove the convergence of adaptive finite elemen...
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In this paper,we study an adaptive finite element method for a class of nonlinear eigenvalue problems resulting from quantum physics that may have a nonconvex energy *** prove the convergence of adaptive finite element approximations and present several numerical examples of micro-structure of matter calculations that support our theory.
A conservative modification to the ghost fluid method(GFM)is developed for compressible multiphase *** motivation is to eliminate or reduce the conservation error of the GFM without affecting its *** track the conserv...
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A conservative modification to the ghost fluid method(GFM)is developed for compressible multiphase *** motivation is to eliminate or reduce the conservation error of the GFM without affecting its *** track the conservative variables near the material interface and use this information to modify the numerical solution for an interfacing cell when the interface has passed the *** modification procedure can be used on the GFM with any base *** this paper we use the fifth order finite difference WENO scheme for the spatial discretization and the third order TVD Runge-Kutta method for the time *** level set method is used to capture the *** experiments show that the method is at least mass and momentum conservative and is in general comparable in numerical resolution with the original GFM.
A 3D dynamic programming approach to first-arrival traveltime computation is extended to anisotropic velocity models with rugged topography, which is necessary for 3D kirchhoff integral migration or near-surface tomog...
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作者：
M. Alper TungaMetin DemiralpBahçeşehir University
Faculty of Engineering Department of Software Engineering Beşiktaş 34349 İstanbul Turkey İstanbul Technical University
Informatics Institute Computational Science and Engineering Program Group for Science and Methods of Computing Maslak 34469 İstanbul Turkey
High Dimensional Model Representation (HDMR) method does not have the random data partitioning capability because of its nature. This paper focuses on how we can bring the random data partitioning feature to the HDMR ...
High Dimensional Model Representation (HDMR) method does not have the random data partitioning capability because of its nature. This paper focuses on how we can bring the random data partitioning feature to the HDMR method by virtue of the fluctuation free approximation method for the multivariate interpolation problems. The main aim of this work is to construct the universal fluctuation free matrix and to determine the best eigenvalues and the corresponding eigenvectors needed in our new method for partitioning the given multivariate random data through the HDMR method.
In this work, we propose an hN adaptive algorithm for optimal control problems whose space discretization is based on the spectral element method. We focus on a special class of problems described by quadratic cost fu...
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作者：
Liqun CaoLei ZhangLSEC
Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China
In this talk, we discuss the multiscale computation for Schr(")odinger-Poisson system arising from the electronic properties of semiconductors such as quantum wells, wires and dots, and CMOS *** first introdu...
In this talk, we discuss the multiscale computation for Schr(")odinger-Poisson system arising from the electronic properties of semiconductors such as quantum wells, wires and dots, and CMOS *** first introduce the Schr(o)dinger equations with the effective mass approximation which has been particularly successful in the case of *** Allaire's work (cf.[?]) and our result (cf.[?, ?]), we give a interpretation why the effective mass approximation is very successful for calculating the band structures of semiconductor nanostructures in the vicinity of Γ point, from the viewpoint of ***, we analyze the relationship between microscopic Maxwell's equations and macroscopic Maxwell's ***, we discuss mathematical modeling of electromagnetics at nano-scale and offer an explanation as to why Schr(o)dinger-Poisson equations and Maxwell-Schr(o)dinger equations have been widely used to semiconductor ***, the multiscale method or Schr(o)dinger-Poisson system in heterogeneous materials is *** simulations are carried out to validate the theoretical ***, some unsolved problems are advanced.
Waveform inversion of crosshole data based on acoustic wave equation is investigated in this paper. The inversion is set as an optimization problem with the Lagrange multiplier function. The Tikhonov regularization is...
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Waveform inversion of crosshole data based on acoustic wave equation is investigated in this paper. The inversion is set as an optimization problem with the Lagrange multiplier function. The Tikhonov regularization is adopted in objective function. The gradient of the objective function is generated by solving the adjoint equation of the forward problem with the finite difference method. In order to prevent the quasi-Newton method to trap in local optimal value, a suitable initial model is required. For comparison, the traveltime inversion or tomography is implemented which provide smooth features of the velocity model. Numerical computations are given which show the good ability of the new velocity inversion method.
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