Nozzle Geometry Optimization of an MPD Thruster by Soft-Computing Approaches
NASA Astrophysics Data System (ADS)
Nakane, Masakatsu; Konno, Tomokazu; Iketani, Gen; Ishikawa, Yoshio; Funaki, Ikkoh; Toki, Kyoichiro
The optimization of flowfield of a self-field magnetoplasmadynamic (MPD) thruster was conducted by two soft-computing methods. Both the genetic algorithm (GA) and a new method to obtain a minimum/maximum based on the path integral were used to establish the optimum geometry that produces the highest thrust for specified operating conditions within a quasi-one-dimensional framework. The optimum geometry was found to be a quickly convergent and divergent geometry regardless of the method employed, and the optimized geometry was found to be the same that was obtained by the classical variational methods. This fact as well as their applicability to parallel computers assures that the soft computing methods are suitable for a more complicated multi-dimensional flowfield optimization problem.
A Computational Geometry Approach to Automated Pulmonary Fissure Segmentation in CT Examinations
Pu, Jiantao; Leader, Joseph K; Zheng, Bin; Knollmann, Friedrich; Fuhrman, Carl; Sciurba, Frank C; Gur, David
2010-01-01
Identification of pulmonary fissures, which form the boundaries between the lobes in the lungs, may be useful during clinical interpretation of CT examinations to assess the early presence and characterization of manifestation of several lung diseases. Motivated by the unique nature of the surface shape of pulmonary fissures in three-dimensional space, we developed a new automated scheme using computational geometry methods to detect and segment fissures depicted on CT images. After a geometric modeling of the lung volume using the Marching Cube Algorithm, Laplacian smoothing is applied iteratively to enhance pulmonary fissures by depressing non-fissure structures while smoothing the surfaces of lung fissures. Next, an Extended Gaussian Image based procedure is used to locate the fissures in a statistical manner that approximates the fissures using a set of plane “patches.” This approach has several advantages such as independence of anatomic knowledge of the lung structure except the surface shape of fissures, limited sensitivity to other lung structures, and ease of implementation. The scheme performance was evaluated by two experienced thoracic radiologists using a set of 100 images (slices) randomly selected from 10 screening CT examinations. In this preliminary evaluation 98.7% and 94.9% of scheme segmented fissure voxels are within 2 mm of the fissures marked independently by two radiologists in the testing image dataset. Using the scheme detected fissures as reference, 89.4% and 90.1% of manually marked fissure points have distance ≤ 2 mm to the reference suggesting a possible under-segmentation of the scheme. The case-based RMS (root-mean-square) distances (“errors”) between our scheme and the radiologist ranged from 1.48±0.92 to 2.04±3.88 mm. The discrepancy of fissure detection results between the automated scheme and either radiologist is smaller in this dataset than the inter-reader variability. PMID:19272987
A computational approach to continuum damping of Alfven waves in two and three-dimensional geometry
Koenies, Axel; Kleiber, Ralf
2012-12-15
While the usual way of calculating continuum damping of global Alfven modes is the introduction of a small artificial resistivity, we present a computational approach to the problem based on a suitable path of integration in the complex plane. This approach is implemented by the Riccati shooting method and it is shown that it can be transferred to the Galerkin method used in three-dimensional ideal magneto-hydrodynamics (MHD) codes. The new approach turns out to be less expensive with respect to resolution and computation time than the usual one. We present an application to large aspect ratio tokamak and stellarator equilibria retaining a few Fourier harmonics only and calculate eigenfunctions and continuum damping rates. These may serve as an input for kinetic MHD hybrid models making it possible to bypass the problem of having singularities on the path of integration on one hand and considering continuum damping on the other.
Computer-Aided Geometry Modeling
NASA Technical Reports Server (NTRS)
Shoosmith, J. N. (Compiler); Fulton, R. E. (Compiler)
1984-01-01
Techniques in computer-aided geometry modeling and their application are addressed. Mathematical modeling, solid geometry models, management of geometric data, development of geometry standards, and interactive and graphic procedures are discussed. The applications include aeronautical and aerospace structures design, fluid flow modeling, and gas turbine design.
An Automated Approach to Very High Order Aeroacoustic Computations in Complex Geometries
NASA Technical Reports Server (NTRS)
Dyson, Rodger W.; Goodrich, John W.
2000-01-01
Computational aeroacoustics requires efficient, high-resolution simulation tools. And for smooth problems, this is best accomplished with very high order in space and time methods on small stencils. But the complexity of highly accurate numerical methods can inhibit their practical application, especially in irregular geometries. This complexity is reduced by using a special form of Hermite divided-difference spatial interpolation on Cartesian grids, and a Cauchy-Kowalewslci recursion procedure for time advancement. In addition, a stencil constraint tree reduces the complexity of interpolating grid points that are located near wall boundaries. These procedures are used to automatically develop and implement very high order methods (>15) for solving the linearized Euler equations that can achieve less than one grid point per wavelength resolution away from boundaries by including spatial derivatives of the primitive variables at each grid point. The accuracy of stable surface treatments is currently limited to 11th order for grid aligned boundaries and to 2nd order for irregular boundaries.
Computer Environments for Learning Geometry.
ERIC Educational Resources Information Center
Clements, Douglas H.; Battista, Michael T.
1994-01-01
Reviews research describing computer functions of construction-oriented computer environments and evaluates their contributions to students' learning of geometry. Topics discussed include constructing geometric concepts; the use of LOGO in elementary school mathematics; software that focuses on geometric construction; and implications for the…
Geometry of discrete quantum computing
NASA Astrophysics Data System (ADS)
Hanson, Andrew J.; Ortiz, Gerardo; Sabry, Amr; Tai, Yu-Tsung
2013-05-01
Conventional quantum computing entails a geometry based on the description of an n-qubit state using 2n infinite precision complex numbers denoting a vector in a Hilbert space. Such numbers are in general uncomputable using any real-world resources, and, if we have the idea of physical law as some kind of computational algorithm of the universe, we would be compelled to alter our descriptions of physics to be consistent with computable numbers. Our purpose here is to examine the geometric implications of using finite fields Fp and finite complexified fields \\mathbf {F}_{p^2} (based on primes p congruent to 3 (mod4)) as the basis for computations in a theory of discrete quantum computing, which would therefore become a computable theory. Because the states of a discrete n-qubit system are in principle enumerable, we are able to determine the proportions of entangled and unentangled states. In particular, we extend the Hopf fibration that defines the irreducible state space of conventional continuous n-qubit theories (which is the complex projective space \\mathbf {CP}^{2^{n}-1}) to an analogous discrete geometry in which the Hopf circle for any n is found to be a discrete set of p + 1 points. The tally of unit-length n-qubit states is given, and reduced via the generalized Hopf fibration to \\mathbf {DCP}^{2^{n}-1}, the discrete analogue of the complex projective space, which has p^{2^{n}-1} (p-1)\\,\\prod _{k=1}^{n-1} ( p^{2^{k}}+1) irreducible states. Using a measure of entanglement, the purity, we explore the entanglement features of discrete quantum states and find that the n-qubit states based on the complexified field \\mathbf {F}_{p^2} have pn(p - 1)n unentangled states (the product of the tally for a single qubit) with purity 1, and they have pn + 1(p - 1)(p + 1)n - 1 maximally entangled states with purity zero.
A Whirlwind Tour of Computational Geometry.
ERIC Educational Resources Information Center
Graham, Ron; Yao, Frances
1990-01-01
Described is computational geometry which used concepts and results from classical geometry, topology, combinatorics, as well as standard algorithmic techniques such as sorting and searching, graph manipulations, and linear programing. Also included are special techniques and paradigms. (KR)
A computational approach to continuum damping of Alfvén waves in two and three-dimensional geometry
NASA Astrophysics Data System (ADS)
Könies, Axel; Kleiber, Ralf
2012-12-01
While the usual way of calculating continuum damping of global Alfvén modes is the introduction of a small artificial resistivity, we present a computational approach to the problem based on a suitable path of integration in the complex plane. This approach is implemented by the Riccati shooting method and it is shown that it can be transferred to the Galerkin method used in three-dimensional ideal magneto-hydrodynamics (MHD) codes. The new approach turns out to be less expensive with respect to resolution and computation time than the usual one. We present an application to large aspect ratio tokamak and stellarator equilibria retaining a few Fourier harmonics only and calculate eigenfunctions and continuum damping rates. These may serve as an input for kinetic MHD hybrid models making it possible to bypass the problem of having singularities on the path of integration on one hand and considering continuum damping on the other.
NASA Astrophysics Data System (ADS)
Sambasivan, Shiv Kumar; Shashkov, Mikhail J.; Burton, Donald E.
2013-03-01
A finite volume cell-centered Lagrangian formulation is presented for solving large deformation problems in cylindrical axisymmetric geometries. Since solid materials can sustain significant shear deformation, evolution equations for stress and strain fields are solved in addition to mass, momentum and energy conservation laws. The total strain-rate realized in the material is split into an elastic and plastic response. The elastic and plastic components in turn are modeled using hypo-elastic theory. In accordance with the hypo-elastic model, a predictor-corrector algorithm is employed for evolving the deviatoric component of the stress tensor. A trial elastic deviatoric stress state is obtained by integrating a rate equation, cast in the form of an objective (Jaumann) derivative, based on Hooke's law. The dilatational response of the material is modeled using an equation of state of the Mie-Grüneisen form. The plastic deformation is accounted for via an iterative radial return algorithm constructed from the J2 von Mises yield condition. Several benchmark example problems with non-linear strain hardening and thermal softening yield models are presented. Extensive comparisons with representative Eulerian and Lagrangian hydrocodes in addition to analytical and experimental results are made to validate the current approach.
Computing Bisectors in a Dynamic Geometry Environment
ERIC Educational Resources Information Center
Botana, Francisco
2013-01-01
In this note, an approach combining dynamic geometry and automated deduction techniques is used to study the bisectors between points and curves. Usual teacher constructions for bisectors are discussed, showing that inherent limitations in dynamic geometry software impede their thorough study. We show that the interactive sketching of bisectors…
Quadric solids and computational geometry
Emery, J.D.
1980-07-25
As part of the CAD-CAM development project, this report discusses the mathematics underlying the program QUADRIC, which does computations on objects modeled as Boolean combinations of quadric half-spaces. Topics considered include projective space, quadric surfaces, polars, affine transformations, the construction of solids, shaded image, the inertia tensor, moments, volume, surface integrals, Monte Carlo integration, and stratified sampling. 1 figure.
Classical versus Computer Algebra Methods in Elementary Geometry
ERIC Educational Resources Information Center
Pech, Pavel
2005-01-01
Computer algebra methods based on results of commutative algebra like Groebner bases of ideals and elimination of variables make it possible to solve complex, elementary and non elementary problems of geometry, which are difficult to solve using a classical approach. Computer algebra methods permit the proof of geometric theorems, automatic…
An approach for management of geometry data
NASA Technical Reports Server (NTRS)
Dube, R. P.; Herron, G. J.; Schweitzer, J. E.; Warkentine, E. R.
1980-01-01
The strategies for managing Integrated Programs for Aerospace Design (IPAD) computer-based geometry are described. The computer model of geometry is the basis for communication, manipulation, and analysis of shape information. IPAD's data base system makes this information available to all authorized departments in a company. A discussion of the data structures and algorithms required to support geometry in IPIP (IPAD's data base management system) is presented. Through the use of IPIP's data definition language, the structure of the geometry components is defined. The data manipulation language is the vehicle by which a user defines an instance of the geometry. The manipulation language also allows a user to edit, query, and manage the geometry. The selection of canonical forms is a very important part of the IPAD geometry. IPAD has a canonical form for each entity and provides transformations to alternate forms; in particular, IPAD will provide a transformation to the ANSI standard. The DBMS schemas required to support IPAD geometry are explained.
Geometry of Quantum Computation with Qudits
Luo, Ming-Xing; Chen, Xiu-Bo; Yang, Yi-Xian; Wang, Xiaojun
2014-01-01
The circuit complexity of quantum qubit system evolution as a primitive problem in quantum computation has been discussed widely. We investigate this problem in terms of qudit system. Using the Riemannian geometry the optimal quantum circuits are equivalent to the geodetic evolutions in specially curved parametrization of SU(dn). And the quantum circuit complexity is explicitly dependent of controllable approximation error bound. PMID:24509710
A computer program for analyzing channel geometry
Regan, R.S.; Schaffranek, R.W.
1985-01-01
The Channel Geometry Analysis Program (CGAP) provides the capability to process, analyze, and format cross-sectional data for input to flow/transport simulation models or other computational programs. CGAP allows for a variety of cross-sectional data input formats through use of variable format specification. The program accepts data from various computer media and provides for modification of machine-stored parameter values. CGAP has been devised to provide a rapid and efficient means of computing and analyzing the physical properties of an open-channel reach defined by a sequence of cross sections. CGAP 's 16 options provide a wide range of methods by which to analyze and depict a channel reach and its individual cross-sectional properties. The primary function of the program is to compute the area, width, wetted perimeter, and hydraulic radius of cross sections at successive increments of water surface elevation (stage) from data that consist of coordinate pairs of cross-channel distances and land surface or channel bottom elevations. Longitudinal rates-of-change of cross-sectional properties are also computed, as are the mean properties of a channel reach. Output products include tabular lists of cross-sectional area, channel width, wetted perimeter, hydraulic radius, average depth, and cross-sectional symmetry computed as functions of stage; plots of cross sections; plots of cross-sectional area and (or) channel width as functions of stage; tabular lists of cross-sectional area and channel width computed as functions of stage for subdivisions of a cross section; plots of cross sections in isometric projection; and plots of cross-sectional area at a fixed stage as a function of longitudinal distance along an open-channel reach. A Command Procedure Language program and Job Control Language procedure exist to facilitate program execution on the U.S. Geological Survey Prime and Amdahl computer systems respectively. (Lantz-PTT)
Computational algebraic geometry of epidemic models
NASA Astrophysics Data System (ADS)
Rodríguez Vega, Martín.
2014-06-01
Computational Algebraic Geometry is applied to the analysis of various epidemic models for Schistosomiasis and Dengue, both, for the case without control measures and for the case where control measures are applied. The models were analyzed using the mathematical software Maple. Explicitly the analysis is performed using Groebner basis, Hilbert dimension and Hilbert polynomials. These computational tools are included automatically in Maple. Each of these models is represented by a system of ordinary differential equations, and for each model the basic reproductive number (R0) is calculated. The effects of the control measures are observed by the changes in the algebraic structure of R0, the changes in Groebner basis, the changes in Hilbert dimension, and the changes in Hilbert polynomials. It is hoped that the results obtained in this paper become of importance for designing control measures against the epidemic diseases described. For future researches it is proposed the use of algebraic epidemiology to analyze models for airborne and waterborne diseases.
Computational field simulation of temporally deforming geometries
Boyalakuntla, K.; Soni, B.K.; Thornburg, H.J.
1996-12-31
A NURBS based moving grid generation technique is presented to simulate temporally deforming geometries. Grid generation for a complex configuration can be a time consuming process and temporally varying geometries necessitate the regeneration of such a grid for every time step. The Non Uniform Rational B Spline (NURBS) based control point information is used for geometry description. The parametric definition of the NURBS is utilized in the development of the methodology to generate well distributed grid in a timely manner. The numerical simulation involving temporally deforming geometry is accomplished by appropriately linking to a unsteady, multi-block, thin layer Navier-Stokes solver. The present method greatly reduces CPU requirements for time dependent remeshing, facilitating the simulation of more complex unsteady problems. This current effort is the first step towards multidisciplinary design optimization, which involves coupling aerodynamic heat transfer and structural analysis. Applications include simulation of temporally deforming bodies.
An Alternative Approach to Logo-Based Geometry
ERIC Educational Resources Information Center
Durmus, Soner; Karakirik, Erol
2005-01-01
Geometry is an important branch of mathematics. Geometry curriculum can be enriched by using different Technologies such as graphing calculators and computers. Logo-based different software packages aim to improve conceptual understanding in geometry. The goals of this paper are i) to present theoretical foundations of any computer software…
An Alternative Approach to Logo-Based Geometry
ERIC Educational Resources Information Center
Karakirik, Erol; Durmus, Soner
2005-01-01
Geometry is an important branch of mathematics. Geometry curriculum can be enriched by using different Technologies such as graphing calculators and computers. Logo-based different software packages aim to improve conceptual understanding in geometry. The goals of this paper are i) to present theoretical foundations of any compute software…
Teaching Geometry: An Experiential and Artistic Approach.
ERIC Educational Resources Information Center
Ogletree, Earl J.
The view that geometry should be taught at every grade level is promoted. Primary and elementary school children are thought to rarely have any direct experience with geometry, except on an incidental basis. Children are supposed to be able to learn geometry rather easily, so long as the method and content are adapted to their development and…
Heuristic Approach to the Schwarzschild Geometry
NASA Astrophysics Data System (ADS)
Visser, Matt
In this article I present a simple Newtonian heuristic for motivating a weak-field approximation for the spacetime geometry of a point particle. The heuristic is based on Newtonian gravity, the notion of local inertial frames (the Einstein equivalence principle), plus the use of Galilean coordinate transformations to connect the freely falling local inertial frames back to the "fixed stars." Because of the heuristic and quasi-Newtonian manner in which the specific choice of spacetime geometry is motivated, we are at best justified in expecting it to be a weak-field approximation to the true spacetime geometry. However, in the case of a spherically symmetric point mass the result is coincidentally an exact solution of the full vacuum Einstein field equations — it is the Schwarzschild geometry in Painlevé-Gullstrand coordinates. This result is much stronger than the well-known result of Michell and Laplace whereby a Newtonian argument correctly estimates the value of the Schwarzschild radius — using the heuristic presented in this article one obtains the entire Schwarzschild geometry. The heuristic also gives sensible results — a Riemann flat geometry — when applied to a constant gravitational field. Furthermore, a subtle extension of the heuristic correctly reproduces the Reissner-Nordström geometry and even the de Sitter geometry. Unfortunately the heuristic construction is not truly generic. For instance, it is incapable of generating the Kerr geometry or anti-de Sitter space. Despite this limitation, the heuristic does have useful pedagogical value in that it provides a simple and direct plausibility argument (not a derivation) for the Schwarzschild geometry — suitable for classroom use in situations where the full power and technical machinery of general relativity might be inappropriate. The extended heuristic provides more challenging problems — suitable for use at the graduate level.
Computers in geology, geometry, planning, training, communications
Anderson, D.
1996-07-01
The Pittsburgh Research Center (PRC), in partnership with Carnegie Mellon University, is developing a mapping system to obtain two- and three-dimensional geometric information about the mine environment and produce two-dimensional (2-D) mine maps and three-dimensional (3-D) geometric models of mine areas. It is also developing mine visualization systems. In its current stage of development, the sensor and computer hardware can gather 2-D and 3-D data as it is transported about the mine environment. The driver transporting the sensor through the mine need only stop for seconds during each scan, to allow the gimballed mount of the sensor to settle, thereby eliminating errors due to sensor tilt. Post-processing software can compile the geometrical data and construct an extensive 2-D map. The final map is similar to mine maps generated by hand measurements today. However, the resolution and rate at which data are acquired result in maps that are more representative of the true shape of coal pillars, intersections, and corners. The 3-D geometric models are of sufficient resolution to support accurate volumetric calculations, navigation information, and assessment of structural size and conditions.
Grid generation and inviscid flow computation about aircraft geometries
NASA Technical Reports Server (NTRS)
Smith, Robert E.
1989-01-01
Grid generation and Euler flow about fighter aircraft are described. A fighter aircraft geometry is specified by an area ruled fuselage with an internal duct, cranked delta wing or strake/wing combinations, canard and/or horizontal tail surfaces, and vertical tail surfaces. The initial step before grid generation and flow computation is the determination of a suitable grid topology. The external grid topology that has been applied is called a dual-block topology which is a patched C (exp 1) continuous multiple-block system where inner blocks cover the highly-swept part of a cranked wing or strake, rearward inner-part of the wing, and tail components. Outer-blocks cover the remainder of the fuselage, outer-part of the wing, canards and extend to the far field boundaries. The grid generation is based on transfinite interpolation with Lagrangian blending functions. This procedure has been applied to the Langley experimental fighter configuration and a modified F-18 configuration. Supersonic flow between Mach 1.3 and 2.5 and angles of attack between 0 degrees and 10 degrees have been computed with associated Euler solvers based on the finite-volume approach. When coupling geometric details such as boundary layer diverter regions, duct regions with inlets and outlets, or slots with the general external grid, imposing C (exp 1) continuity can be extremely tedious. The approach taken here is to patch blocks together at common interfaces where there is no grid continuity, but enforce conservation in the finite-volume solution. The key to this technique is how to obtain the information required for a conservative interface. The Ramshaw technique which automates the computation of proportional areas of two overlapping grids on a planar surface and is suitable for coding was used. Researchers generated internal duct grids for the Langley experimental fighter configuration independent of the external grid topology, with a conservative interface at the inlet and outlet.
Measurement of Fracture Geometry for Accurate Computation of Hydraulic Conductivity
NASA Astrophysics Data System (ADS)
Chae, B.; Ichikawa, Y.; Kim, Y.
2003-12-01
Fluid flow in rock mass is controlled by geometry of fractures which is mainly characterized by roughness, aperture and orientation. Fracture roughness and aperture was observed by a new confocal laser scanning microscope (CLSM; Olympus OLS1100). The wavelength of laser is 488nm, and the laser scanning is managed by a light polarization method using two galvano-meter scanner mirrors. The system improves resolution in the light axis (namely z) direction because of the confocal optics. The sampling is managed in a spacing 2.5 μ m along x and y directions. The highest measurement resolution of z direction is 0.05 μ m, which is the more accurate than other methods. For the roughness measurements, core specimens of coarse and fine grained granites were provided. Measurements were performed along three scan lines on each fracture surface. The measured data were represented as 2-D and 3-D digital images showing detailed features of roughness. Spectral analyses by the fast Fourier transform (FFT) were performed to characterize on the roughness data quantitatively and to identify influential frequency of roughness. The FFT results showed that components of low frequencies were dominant in the fracture roughness. This study also verifies that spectral analysis is a good approach to understand complicate characteristics of fracture roughness. For the aperture measurements, digital images of the aperture were acquired under applying five stages of uniaxial normal stresses. This method can characterize the response of aperture directly using the same specimen. Results of measurements show that reduction values of aperture are different at each part due to rough geometry of fracture walls. Laboratory permeability tests were also conducted to evaluate changes of hydraulic conductivities related to aperture variation due to different stress levels. The results showed non-uniform reduction of hydraulic conductivity under increase of the normal stress and different values of
Techniques to derive geometries for image-based Eulerian computations
Dillard, Seth; Buchholz, James; Vigmostad, Sarah; Kim, Hyunggun; Udaykumar, H.S.
2014-01-01
Purpose The performance of three frequently used level set-based segmentation methods is examined for the purpose of defining features and boundary conditions for image-based Eulerian fluid and solid mechanics models. The focus of the evaluation is to identify an approach that produces the best geometric representation from a computational fluid/solid modeling point of view. In particular, extraction of geometries from a wide variety of imaging modalities and noise intensities, to supply to an immersed boundary approach, is targeted. Design/methodology/approach Two- and three-dimensional images, acquired from optical, X-ray CT, and ultrasound imaging modalities, are segmented with active contours, k-means, and adaptive clustering methods. Segmentation contours are converted to level sets and smoothed as necessary for use in fluid/solid simulations. Results produced by the three approaches are compared visually and with contrast ratio, signal-to-noise ratio, and contrast-to-noise ratio measures. Findings While the active contours method possesses built-in smoothing and regularization and produces continuous contours, the clustering methods (k-means and adaptive clustering) produce discrete (pixelated) contours that require smoothing using speckle-reducing anisotropic diffusion (SRAD). Thus, for images with high contrast and low to moderate noise, active contours are generally preferable. However, adaptive clustering is found to be far superior to the other two methods for images possessing high levels of noise and global intensity variations, due to its more sophisticated use of local pixel/voxel intensity statistics. Originality/value It is often difficult to know a priori which segmentation will perform best for a given image type, particularly when geometric modeling is the ultimate goal. This work offers insight to the algorithm selection process, as well as outlining a practical framework for generating useful geometric surfaces in an Eulerian setting. PMID
Computer Aided Design and Descriptive Geometry for School Children.
ERIC Educational Resources Information Center
Edmonds, Geoff
1984-01-01
Discusses the place of descriptive geometry in schools problems of teaching technical graphics to young students. Instructional materials for teaching technical graphics, graphic programs, program development, and the value of school project work are considered. Sample computer-generated drawings are included. (JN)
Using Computer-Assisted Multiple Representations in Learning Geometry Proofs
ERIC Educational Resources Information Center
Wong, Wing-Kwong; Yin, Sheng-Kai; Yang, Hsi-Hsun; Cheng, Ying-Hao
2011-01-01
Geometry theorem proving involves skills that are difficult to learn. Instead of working with abstract and complicated representations, students might start with concrete, graphical representations. A proof tree is a graphical representation of a formal proof, with each node representing a proposition or given conditions. A computer-assisted…
Investigating the geometry of pig airways using computed tomography
NASA Astrophysics Data System (ADS)
Mansy, Hansen A.; Azad, Md Khurshidul; McMurray, Brandon; Henry, Brian; Royston, Thomas J.; Sandler, Richard H.
2015-03-01
Numerical modeling of sound propagation in the airways requires accurate knowledge of the airway geometry. These models are often validated using human and animal experiments. While many studies documented the geometric details of the human airways, information about the geometry of pig airways is scarcer. In addition, the morphology of animal airways can be significantly different from that of humans. The objective of this study is to measure the airway diameter, length and bifurcation angles in domestic pigs using computed tomography. After imaging the lungs of 3 pigs, segmentation software tools were used to extract the geometry of the airway lumen. The airway dimensions were then measured from the resulting 3 D models for the first 10 airway generations. Results showed that the size and morphology of the airways of different animals were similar. The measured airway dimensions were compared with those of the human airways. While the trachea diameter was found to be comparable to the adult human, the diameter, length and branching angles of other airways were noticeably different from that of humans. For example, pigs consistently had an early airway branching from the trachea that feeds the superior (top) right lung lobe proximal to the carina. This branch is absent in the human airways. These results suggested that the human geometry may not be a good approximation of the pig airways and may contribute to increasing the errors when the human airway geometric values are used in computational models of the pig chest.
Computational vaccinology: quantitative approaches.
Flower, Darren R; McSparron, Helen; Blythe, Martin J; Zygouri, Christianna; Taylor, Debra; Guan, Pingping; Wan, Shouzhan; Coveney, Peter V; Walshe, Valerie; Borrow, Persephone; Doytchinova, Irini A
2003-01-01
The immune system is hierarchical and has many levels, exhibiting much emergent behaviour. However, at its heart are molecular recognition events that are indistinguishable from other types of biomacromolecular interaction. These can be addressed well by quantitative experimental and theoretical biophysical techniques, and particularly by methods from drug design. We review here our approach to computational immunovaccinology. In particular, we describe the JenPep database and two new techniques for T cell epitope prediction. One is based on quantitative structure-activity relationships (a 3D-QSAR method based on CoMSIA and another 2D method based on the Free-Wilson approach) and the other on atomistic molecular dynamic simulations using high performance computing. JenPep (http://www.jenner.ar.uk/ JenPep) is a relational database system supporting quantitative data on peptide binding to major histocompatibility complexes, TAP transporters, TCR-pMHC complexes, and an annotated list of B cell and T cell epitopes. Our 2D-QSAR method factors the contribution to peptide binding from individual amino acids as well as 1-2 and 1-3 residue interactions. In the 3D-QSAR approach, the influence of five physicochemical properties (volume, electrostatic potential, hydrophobicity, hydrogen-bond donor and acceptor abilities) on peptide affinity were considered. Both methods are exemplified through their application to the well-studied problem of peptide binding to the human class I MHC molecule HLA-A*0201. PMID:14712934
Deterministic point inclusion methods for computational applications with complex geometry
Khamayseh, Ahmed; Kuprat, Andrew P.
2008-11-21
A fundamental problem in computation is finding practical and efficient algorithms for determining if a query point is contained within a model of a three-dimensional solid. The solid is modeled using a general boundary representation that can contain polygonal elements and/or parametric patches.We have developed two such algorithms: the first is based on a global closest feature query, and the second is based on a local intersection query. Both algorithms work for two- and three-dimensional objects. This paper presents both algorithms, as well as the spatial data structures and queries required for efficient implementation of the algorithms. Applications for these algorithms include computational geometry, mesh generation, particle simulation, multiphysics coupling, and computer graphics. These methods are deterministic in that they do not involve random perturbations of diagnostic rays cast from the query point in order to avoid ‘unclean’ or ‘singular’ intersections of the rays with the geometry. Avoiding the necessity of such random perturbations will become increasingly important as geometries become more convoluted and complex.
DETERMINISTIC POINT INCLUSION METHODS FOR COMPUTATIONAL APPLICATIONS WITH COMPLEX GEOMETRY.
Khamayseh, Ahmed K; Kuprat, Andrew
2008-01-01
A fundamental problem in computation is finding practical and efficient algorithms for determining if a query point is contained within a model of a three-dimensional solid. The solid is modeled using a general boundary representation that can contain polygonal elements and/or parametric patches. We have developed two such algorithms: the first is based on a global closest feature query, and the second is based on a local intersection query. Both algorithms work for two- and three-dimensional objects. This paper presents both algorithms, as well as the spatial data structures and queries required for efficient implementation of the algorithms. Applications for these algorithms include computational geometry, mesh generation, particle simulation, multiphysics coupling, and computer graphics. These methods are deterministic in that they do not involve random perturbations of diagnostic rays cast from the query point in order to avoid "unclean" or "singular" intersections of the rays with the geometry. Avoiding the necessity of such random perturbations will become increasingly important as geometries become more convoluted and complex.
Parallel algorithms for computational geometry utilizing a fixed number of processors
Strader, R.G.
1988-01-01
The design of algorithms for systems where both communication and computation are important is presented. Approaches to parallel computation and the underlying theoretical models are surveyed. two models of computation are developed, both based on a divide-and-conquer strategy. The first utilizes a tree-like merge resulting in several levels of communication and computation, the total number determined by the number of processors. The second model contains a fixed number of levels independent of the number of processors. Using the notation from the survey and the models of computation, algorithms are designed for the computational geometry problems of finding the convex hull and Delaunay triangulation for a set of uniform random points in the Euclidean plane. Communication and computation timing measurements based on these algorithms are presented and analyzed. The results are then generalized to predict the behavior of expanded problems. Architectural support, partitioning issues, and limitations of this approach are discussed.
Computer aided design and analysis of gear tooth geometry
NASA Technical Reports Server (NTRS)
Chang, S. H.; Huston, R. L.
1987-01-01
A simulation method for gear hobbing and shaping of straight and spiral bevel gears is presented. The method is based upon an enveloping theory for gear tooth profile generation. The procedure is applicable in the computer aided design of standard and nonstandard tooth forms. An inverse procedure for finding a conjugate gear tooth profile is presented for arbitrary cutter geometry. The kinematic relations for the tooth surfaces of straight and spiral bevel gears are proposed. The tooth surface equations for these gears are formulated in a manner suitable for their automated numerical development and solution.
Ionization coefficient approach to modeling breakdown in nonuniform geometries.
Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Nicolaysen, Scott D.
2003-11-01
This report summarizes the work on breakdown modeling in nonuniform geometries by the ionization coefficient approach. Included are: (1) fits to primary and secondary ionization coefficients used in the modeling; (2) analytical test cases for sphere-to-sphere, wire-to-wire, corner, coaxial, and rod-to-plane geometries; a compilation of experimental data with source references; comparisons between code results, test case results, and experimental data. A simple criterion is proposed to differentiate between corona and spark. The effect of a dielectric surface on avalanche growth is examined by means of Monte Carlo simulations. The presence of a clean dry surface does not appear to enhance growth.
Computational approaches to vision
NASA Technical Reports Server (NTRS)
Barrow, H. G.; Tenenbaum, J. M.
1986-01-01
Vision is examined in terms of a computational process, and the competence, structure, and control of computer vision systems are analyzed. Theoretical and experimental data on the formation of a computer vision system are discussed. Consideration is given to early vision, the recovery of intrinsic surface characteristics, higher levels of interpretation, and system integration and control. A computational visual processing model is proposed and its architecture and operation are described. Examples of state-of-the-art vision systems, which include some of the levels of representation and processing mechanisms, are presented.
Representing Range Compensators with Computational Geometry in TOPAS
Iandola, Forrest N.; /Illinois U., Urbana /SLAC
2012-09-07
In a proton therapy beamline, the range compensator modulates the beam energy, which subsequently controls the depth at which protons deposit energy. In this paper, we introduce two computational representations of range compensator. One of our compensator representations, which we refer to as a subtraction solid-based range compensator, precisely represents the compensator. Our other representation, the 3D hexagon-based range compensator, closely approximates the compensator geometry. We have implemented both of these compensator models in a proton therapy Monte Carlo simulation called TOPAS (Tool for Particle Simulation). In the future, we will present a detailed study of the accuracy and runtime performance trade-offs between our two range compensator representations.
Computational structure analysis of biomacromolecule complexes by interface geometry.
Mahdavi, Sedigheh; Salehzadeh-Yazdi, Ali; Mohades, Ali; Masoudi-Nejad, Ali
2013-12-01
The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model. PMID:23850846
SU-E-I-12: Flexible Geometry Computed Tomography
Shaw, R
2015-06-15
Purpose: The concept separates the mechanical connection between the radiation source and detector. This design allows the trajectory and orientation of the radiation source/detector to be customized to the object that is being imaged. This is in contrast to the formulaic rotation-translation image acquisition of conventional computed tomography(CT).Background/significance:CT devices that image a full range of: anatomy, patient populations, and imaging procedures are large. The root cause of the expanding size of comprehensive CT is due to the commitment to helical geometry that is hardwired into the image reconstruction. FGCT extends the application of alternative reconstruction techniques, i.e. tomosynthesis, by separating the two main components— radiation source and detector— and allow for 6 degrees of freedom motion for radiation source, detector, or both. The image acquisition geometry is then tailored to how the patient/object is positioned. This provides greater flexibility on the position and location that the patient/object is being imaged. Additionally, removing the need of a rotating gantry reduces the footprint so that CT is more mobile and more available to move to where the patient/object is at, instead of the other way around. Methods: As proof-of-principle, a reconstruction algorithm is designed to produce FGCT images. Using simulated detector data, voxels intersecting a line drawn between the radiation source and an individual detector are traced and modified using the detector signal. The detector signal is modified to compensate for changes in the source to detector distance. Adjacent voxels are modified in proportion to the detector signal, providing a simple image filter. Results: Image-quality from the proposed FGCT reconstruction technique is proving to be a challenge, producing hardily recognizable images from limited projections angles. Conclusion: Preliminary assessment of the reconstruction technique demonstrates the inevitable
SOLVING PDES IN COMPLEX GEOMETRIES: A DIFFUSE DOMAIN APPROACH
LI, X.; LOWENGRUB, J.; RÄTZ, A.; VOIGT, A.
2011-01-01
We extend previous work and present a general approach for solving partial differential equations in complex, stationary, or moving geometries with Dirichlet, Neumann, and Robin boundary conditions. Using an implicit representation of the geometry through an auxilliary phase field function, which replaces the sharp boundary of the domain with a diffuse layer (e.g. diffuse domain), the equation is reformulated on a larger regular domain. The resulting partial differential equation is of the same order as the original equation, with additional lower order terms to approximate the boundary conditions. The reformulated equation can be solved by standard numerical techniques. We use the method of matched asymptotic expansions to show that solutions of the re-formulated equations converge to those of the original equations. We provide numerical simulations which confirm this analysis. We also present applications of the method to growing domains and complex three-dimensional structures and we discuss applications to cell biology and heteroepitaxy. PMID:21603084
NASA Astrophysics Data System (ADS)
Sen, Oishik; Udaykumar, H. S.; Jacobs, Gustaaf
Interaction of a shock wave with dust particles is a complex physical phenomenon. A computational model for studying this two-phase system is the Particle-Source in Cell (PSIC) approach. In this method, the dust particles are tracked as point particles in a Lagrangian frame of reference immersed in a compressible fluid. Two-way interaction between the carrier and the dispersed phases is ensured by coupling the momentum and energy transfer between the two phases as source terms in the respective governing equations. These source terms (e.g. drag force on particles) may be computed from resolved numerical simulations by treating each macroscopic point particle as an ensemble of cylinders immersed in a compressed fluid. However the drag so computed must be independent of the geometry of the mesoscale. In this work, the effect of the stochasticity of the microstructural geometry in construction of drag laws from resolved mesoscale computations is studied. Several different arrangement of cylinders are considered and the mean drag law as a function of Mach Number and Volume Fraction for each arrangement is computed using the Dynamic Kriging Method. The uncertainty in the drag forces arising because of the arrangement of the cylinders for a given volume fraction is quantified as 90% credible sets and the effect of the uncertainty on PSIC computations is studied.
ERIC Educational Resources Information Center
Vaughan, Herbert E.; Szabo, Steven
This is the teacher's edition of a text for the first year of a two-year high school geometry course. The course bases plane and solid geometry and trigonometry on the fact that the translations of a Euclidean space constitute a vector space which has an inner product. Volume 1 deals largely with affine geometry, and the notion of dimension is…
ERIC Educational Resources Information Center
Goodson-Espy, Tracy; Lynch-Davis, Kathleen; Schram, Pamela; Quickenton, Art
2010-01-01
This paper describes the genesis and purpose of our geometry methods course, focusing on a geometry-teaching technology we created using NVIDIA[R] Chameleon demonstration. This article presents examples from a sequence of lessons centered about a 3D computer graphics demonstration of the chameleon and its geometry. In addition, we present data…
A Parametric Geometry Computational Fluid Dynamics (CFD) Study Utilizing Design of Experiments (DOE)
NASA Technical Reports Server (NTRS)
Rhew, Ray D.; Parker, Peter A.
2007-01-01
Design of Experiments (DOE) techniques were applied to the Launch Abort System (LAS) of the NASA Crew Exploration Vehicle (CEV) parametric geometry Computational Fluid Dynamics (CFD) study to efficiently identify and rank the primary contributors to the integrated drag over the vehicles ascent trajectory. Typical approaches to these types of activities involve developing all possible combinations of geometries changing one variable at a time, analyzing them with CFD, and predicting the main effects on an aerodynamic parameter, which in this application is integrated drag. The original plan for the LAS study team was to generate and analyze more than1000 geometry configurations to study 7 geometric parameters. By utilizing DOE techniques the number of geometries was strategically reduced to 84. In addition, critical information on interaction effects among the geometric factors were identified that would not have been possible with the traditional technique. Therefore, the study was performed in less time and provided more information on the geometric main effects and interactions impacting drag generated by the LAS. This paper discusses the methods utilized to develop the experimental design, execution, and data analysis.
Scattering Computations of Snow Aggregates from Simple Geometry Models
NASA Astrophysics Data System (ADS)
Liao, L.; Meneghini, R.; Nowell, H.; Liu, G.
2012-12-01
Accurately characterizing electromagnetic scattering from snow aggregates is one of the essential components in the development of algorithms for the GPM DPR and GMI. Recently several realistic aggregate models have been developed by using randomized procedures. Using pristine ice crystal habits found in nature as the basic elements of which the aggregates are made, more complex randomly aggregated structures can be formed to replicate snowflakes. For these particles, a numerical scheme is needed to compute the scattered fields. These computations, however, are usually time consuming, and are often limited to a certain range of particle sizes and to a few frequencies. The scattering results at other frequencies and sizes are then obtained by either interpolation or extrapolation from nearby computed points (anchor points). Because of the nonlinear nature of the scattering, particularly in the particle resonance region, this sometimes leads to severe errors if the number of anchor points is not sufficiently large to cover the spectral domain and particle size range. As an alternative to these complex models, the simple geometric models, such as sphere and spheroid, are useful for radar and radiometer applications if their scattering results can be shown to closely approximate those from complex aggregate structures. A great advantage of the simple models is their computational efficiency because of existence of analytical solutions, so that the computations can be easily extended to as many frequencies and particle sizes as desired. In this study, two simple models are tested. One approach is to use a snow mass density that is defined as the ratio of the mass of the snow aggregate to the volume, where the volume is taken to be that of a sphere with a diameter equal to the maximum measured dimension of the aggregate; i.e., the diameter of the circumscribing sphere. Because of the way in which the aggregates are generated, where a size-density relation is used, the
Evaluation of a cone beam computed tomography geometry for image guided small animal irradiation
NASA Astrophysics Data System (ADS)
Yang, Yidong; Armour, Michael; Kang-Hsin Wang, Ken; Gandhi, Nishant; Iordachita, Iulian; Siewerdsen, Jeffrey; Wong, John
2015-07-01
The conventional imaging geometry for small animal cone beam computed tomography (CBCT) is that a detector panel rotates around the head-to-tail axis of an imaged animal (‘tubular’ geometry). Another unusual but possible imaging geometry is that the detector panel rotates around the anterior-to-posterior axis of the animal (‘pancake’ geometry). The small animal radiation research platform developed at Johns Hopkins University employs the pancake geometry where a prone-positioned animal is rotated horizontally between an x-ray source and detector panel. This study is to assess the CBCT image quality in the pancake geometry and investigate potential methods for improvement. We compared CBCT images acquired in the pancake geometry with those acquired in the tubular geometry when the phantom/animal was placed upright simulating the conventional CBCT geometry. Results showed signal-to-noise and contrast-to-noise ratios in the pancake geometry were reduced in comparison to the tubular geometry at the same dose level. But the overall spatial resolution within the transverse plane of the imaged cylinder/animal was better in the pancake geometry. A modest exposure increase to two folds in the pancake geometry can improve image quality to a level close to the tubular geometry. Image quality can also be improved by inclining the animal, which reduces streak artifacts caused by bony structures. The major factor resulting in the inferior image quality in the pancake geometry is the elevated beam attenuation along the long axis of the phantom/animal and consequently increased scatter-to-primary ratio in that orientation. Not withstanding, the image quality in the pancake-geometry CBCT is adequate to support image guided animal positioning, while providing unique advantages of non-coplanar and multiple mice irradiation. This study also provides useful knowledge about the image quality in the two very different imaging geometries, i.e. pancake and tubular geometry
Evaluation of a cone beam computed tomography geometry for image guided small animal irradiation.
Yang, Yidong; Armour, Michael; Wang, Ken Kang-Hsin; Gandhi, Nishant; Iordachita, Iulian; Siewerdsen, Jeffrey; Wong, John
2015-07-01
The conventional imaging geometry for small animal cone beam computed tomography (CBCT) is that a detector panel rotates around the head-to-tail axis of an imaged animal ('tubular' geometry). Another unusual but possible imaging geometry is that the detector panel rotates around the anterior-to-posterior axis of the animal ('pancake' geometry). The small animal radiation research platform developed at Johns Hopkins University employs the pancake geometry where a prone-positioned animal is rotated horizontally between an x-ray source and detector panel. This study is to assess the CBCT image quality in the pancake geometry and investigate potential methods for improvement. We compared CBCT images acquired in the pancake geometry with those acquired in the tubular geometry when the phantom/animal was placed upright simulating the conventional CBCT geometry. Results showed signal-to-noise and contrast-to-noise ratios in the pancake geometry were reduced in comparison to the tubular geometry at the same dose level. But the overall spatial resolution within the transverse plane of the imaged cylinder/animal was better in the pancake geometry. A modest exposure increase to two folds in the pancake geometry can improve image quality to a level close to the tubular geometry. Image quality can also be improved by inclining the animal, which reduces streak artifacts caused by bony structures. The major factor resulting in the inferior image quality in the pancake geometry is the elevated beam attenuation along the long axis of the phantom/animal and consequently increased scatter-to-primary ratio in that orientation. Not withstanding, the image quality in the pancake-geometry CBCT is adequate to support image guided animal positioning, while providing unique advantages of non-coplanar and multiple mice irradiation. This study also provides useful knowledge about the image quality in the two very different imaging geometries, i.e. pancake and tubular geometry, respectively
Cadman, Laura K; Bristow, Jessica K; Stubbs, Naomi E; Tiana, Davide; Mahon, Mary F; Walsh, Aron; Burrows, Andrew D
2016-03-14
A new approach is reported for tailoring the pore geometry in five series of multivariate metal–organic frameworks (MOFs) based on the structure [Zn2(bdc)2(dabco)] (bdc = 1,4-benzenedicarboxylate, dabco = 1,8-diazabicyclooctane), DMOF-1. A doping procedure has been adopted to form series of MOFs containing varying linker ratios. The series under investigation are [Zn2(bdc)(2-x)(bdc-Br)x(dabco)]·nDMF 1 (bdc-Br = 2-bromo-1,4-benzenedicarboxylate), [Zn2(bdc)(2-x)(bdc-I)x(dabco)]·nDMF 2 (bdc-I = 2-iodo-1,4-benzenedicarboxylate), [Zn2(bdc)(2-x)(bdc-NO2)x(dabco)]·nDMF 3 (bdc-NO2 = 2-nitro-1,4-benzenedicarboxylate), [Zn2(bdc)(2-x)(bdc-NH2)x(dabco)]·nDMF 4 (bdc-NH2 = 2-amino-1,4-benzenedicarboxylate) and [Zn2(bdc-Br)(2-x)(bdc-I)x(dabco)]·nDMF 5. Series 1-3 demonstrate a functionality-dependent pore geometry transition from the square, open pores of DMOF-1 to rhomboidal, narrow pores with increasing proportion of the 2-substituted bdc linker, with the rhomboidal-pore MOFs also showing a temperature-dependent phase change. In contrast, all members of series 4 and 5 have uniform pore geometries. In series 4 this is a square pore topology, whilst series 5 exhibits the rhomboidal pore form. Computational analyses reveal that the pore size and shape in systems 1 and 2 is altered through non-covalent interactions between the organic linkers within the framework, and that this can be controlled by the ligand functionality and ratio. This approach affords the potential to tailor pore geometry and shape within MOFs through judicious choice of ligand ratios. PMID:26660286
Geometric calculus: a new computational tool for Riemannian geometry
Moussiaux, A.; Tombal, P.
1988-05-01
We compare geometric calculus applied to Riemannian geometry with Cartan's exterior calculus method. The correspondence between the two methods is clearly established. The results obtained by a package written in an algebraic language and doing general manipulations on multivectors are compared. We see that the geometric calculus is as powerful as exterior calculus.
Ideal spiral bevel gears: A new approach to surface geometry
NASA Technical Reports Server (NTRS)
Huston, R. L.; Coy, J. J.
1980-01-01
The fundamental geometrical characteristics of spiral bevel gear tooth surfaces are discussed. The parametric representation of an ideal spiral bevel tooth is developed based on the elements of involute geometry, differential geometry, and fundamental gearing kinematics. A foundation is provided for the study of nonideal gears and the effects of deviations from ideal geometry on the contact stresses, lubrication, wear, fatigue life, and gearing kinematics.
Adjoint Sensitivity Computations for an Embedded-Boundary Cartesian Mesh Method and CAD Geometry
NASA Technical Reports Server (NTRS)
Nemec, Marian; Aftosmis,Michael J.
2006-01-01
Cartesian-mesh methods are perhaps the most promising approach for addressing the issues of flow solution automation for aerodynamic design problems. In these methods, the discretization of the wetted surface is decoupled from that of the volume mesh. This not only enables fast and robust mesh generation for geometry of arbitrary complexity, but also facilitates access to geometry modeling and manipulation using parametric Computer-Aided Design (CAD) tools. Our goal is to combine the automation capabilities of Cartesian methods with an eficient computation of design sensitivities. We address this issue using the adjoint method, where the computational cost of the design sensitivities, or objective function gradients, is esseutially indepeudent of the number of design variables. In previous work, we presented an accurate and efficient algorithm for the solution of the adjoint Euler equations discretized on Cartesian meshes with embedded, cut-cell boundaries. Novel aspects of the algorithm included the computation of surface shape sensitivities for triangulations based on parametric-CAD models and the linearization of the coupling between the surface triangulation and the cut-cells. The objective of the present work is to extend our adjoint formulation to problems involving general shape changes. Central to this development is the computation of volume-mesh sensitivities to obtain a reliable approximation of the objective finction gradient. Motivated by the success of mesh-perturbation schemes commonly used in body-fitted unstructured formulations, we propose an approach based on a local linearization of a mesh-perturbation scheme similar to the spring analogy. This approach circumvents most of the difficulties that arise due to non-smooth changes in the cut-cell layer as the boundary shape evolves and provides a consistent approximation tot he exact gradient of the discretized abjective function. A detailed gradient accurace study is presented to verify our approach
NASA Astrophysics Data System (ADS)
Ganesh, V.; Dongare, Rameshwar K.; Balanarayan, P.; Gadre, Shridhar R.
2006-09-01
A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including α-tocopherol, taxol, γ-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.
A Geometry Based Infra-Structure for Computational Analysis and Design
NASA Technical Reports Server (NTRS)
Haimes, Robert
1998-01-01
). This is particularly onerous for modern CAD systems based on solid modeling. The part was a proper solid and in the translation to IGES has lost this important characteristic. STEP is another standard for CAD data that exists and supports the concept of a solid. The problem with STEP is that a solid modeling geometry kernel is required to query and manipulate the data within this type of file. (2) 'Good' Geometry. A bottleneck in getting results from a solver is the construction of proper geometry to be fed to the grid generator. With 'good' geometry a grid can be constructed in tens of minutes (even with a complex configuration) using unstructured techniques. Adroit multi-block methods are not far behind. This means that a million node steady-state solution can be computed on the order of hours (using current high performance computers) starting from this 'good' geometry. Unfortunately, the geometry usually transmitted from the CAD system is not 'good' in the grid generator sense. The grid generator needs smooth closed solid geometry. It can take a week (or more) of interaction with the CAD output (sometimes by hand) before the process can begin. One way Communication. (3) One-way Communication -- All information travels on from one phase to the next. This makes procedures like node adaptation difficult when attempting to add or move nodes that sit on bounding surfaces (when the actual surface data has been lost after the grid generation phase). Until this process can be automated, more complex problems such as multi-disciplinary analysis or using the above procedure for design becomes prohibitive. There is also no way to easily deal with this system in a modular manner. One can only replace the grid generator, for example, if the software reads and writes the same files. Instead of the serial approach to analysis as described above, CAPRI takes a geometry centric approach. This makes the actual geometry (not a discretized version) accessible to all phases of the
Transport Equation Based Wall Distance Computations Aimed at Flows With Time-Dependent Geometry
NASA Technical Reports Server (NTRS)
Tucker, Paul G.; Rumsey, Christopher L.; Bartels, Robert E.; Biedron, Robert T.
2003-01-01
Eikonal, Hamilton-Jacobi and Poisson equations can be used for economical nearest wall distance computation and modification. Economical computations may be especially useful for aeroelastic and adaptive grid problems for which the grid deforms, and the nearest wall distance needs to be repeatedly computed. Modifications are directed at remedying turbulence model defects. For complex grid structures, implementation of the Eikonal and Hamilton-Jacobi approaches is not straightforward. This prohibits their use in industrial CFD solvers. However, both the Eikonal and Hamilton-Jacobi equations can be written in advection and advection-diffusion forms, respectively. These, like the Poisson s Laplacian, are commonly occurring industrial CFD solver elements. Use of the NASA CFL3D code to solve the Eikonal and Hamilton-Jacobi equations in advective-based forms is explored. The advection-based distance equations are found to have robust convergence. Geometries studied include single and two element airfoils, wing body and double delta configurations along with a complex electronics system. It is shown that for Eikonal accuracy, upwind metric differences are required. The Poisson approach is found effective and, since it does not require offset metric evaluations, easiest to implement. The sensitivity of flow solutions to wall distance assumptions is explored. Generally, results are not greatly affected by wall distance traits.
Transport Equation Based Wall Distance Computations Aimed at Flows With Time-Dependent Geometry
NASA Technical Reports Server (NTRS)
Tucker, Paul G.; Rumsey, Christopher L.; Bartels, Robert E.; Biedron, Robert T.
2003-01-01
Eikonal, Hamilton-Jacobi and Poisson equations can be used for economical nearest wall distance computation and modification. Economical computations may be especially useful for aeroelastic and adaptive grid problems for which the grid deforms, and the nearest wall distance needs to be repeatedly computed. Modifications are directed at remedying turbulence model defects. For complex grid structures, implementation of the Eikonal and Hamilton-Jacobi approaches is not straightforward. This prohibits their use in industrial CFD solvers. However, both the Eikonal and Hamilton-Jacobi equations can be written in advection and advection-diffusion forms, respectively. These, like the Poisson's Laplacian, are commonly occurring industrial CFD solver elements. Use of the NASA CFL3D code to solve the Eikonal and Hamilton-Jacobi equations in advective-based forms is explored. The advection-based distance equations are found to have robust convergence. Geometries studied include single and two element airfoils, wing body and double delta configurations along with a complex electronics system. It is shown that for Eikonal accuracy, upwind metric differences are required. The Poisson approach is found effective and, since it does not require offset metric evaluations, easiest to implement. The sensitivity of flow solutions to wall distance assumptions is explored. Generally, results are not greatly affected by wall distance traits.
Interactive Geometry in the B.C. (Before Computers) Era
ERIC Educational Resources Information Center
Whittaker, Heather; Johnson, Iris DeLoach
2005-01-01
A 3-by-5 card is used to represent two or more sets of parallel lines, four right angles, opposite sides congruent and to investigate the Pythagorean theorem, similar triangles, and the tangent ratio before the introduction of computers. Students were asked to draw two parallel lines, cross them with a transversal and label the angles, which…
DMG-α--a computational geometry library for multimolecular systems.
Szczelina, Robert; Murzyn, Krzysztof
2014-11-24
The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers. PMID:25296168
Computer-Generated Geometry Instruction: A Preliminary Study
ERIC Educational Resources Information Center
Kang, Helen W.; Zentall, Sydney S.
2011-01-01
This study hypothesized that increased intensity of graphic information, presented in computer-generated instruction, could be differentially beneficial for students with hyperactivity and inattention by improving their ability to sustain attention and hold information in-mind. To this purpose, 18 2nd-4th grade students, recruited from general…
Application of Computer Axial Tomography (CAT) to measuring crop canopy geometry. [corn and soybeans
NASA Technical Reports Server (NTRS)
Bauer, M. E.; Vanderbilt, V. C. (Principal Investigator); Kilgore, R. W.
1981-01-01
The feasibility of using the principles of computer axial topography (CAT) to quantify the structure of crop canopies was investigated because six variables are needed to describe the position-orientation with time of a small piece of canopy foliage. Several cross sections were cut through the foliage of healthy, green corn and soybean canopies in the dent and full pod development stages, respectively. A photograph of each cross section representing the intersection of a plane with the foliage was enlarged and the air-foliage boundaries delineated by the plane were digitized. A computer program was written and used to reconstruct the cross section of the canopy. The approach used in applying optical computer axial tomography to measuring crop canopy geometry shows promise of being able to provide needed geometric information for input data to canopy reflectance models. The difficulty of using the CAT scanner to measure large canopies of crops like corn is discussed and a solution is proposed involving the measurement of plants one at a time.
Gauss-Green cubature and moment computation over arbitrary geometries
NASA Astrophysics Data System (ADS)
Sommariva, Alvise; Vianello, Marco
2009-09-01
We have implemented in Matlab a Gauss-like cubature formula over arbitrary bivariate domains with a piecewise regular boundary, which is tracked by splines of maximum degree p (spline curvilinear polygons). The formula is exact for polynomials of degree at most 2n-1 using N~cmn2 nodes, 1<=c<=p, m being the total number of points given on the boundary. It does not need any decomposition of the domain, but relies directly on univariate Gauss-Legendre quadrature via Green's integral formula. Several numerical tests are presented, including computation of standard as well as orthogonal moments over a nonstandard planar region.
Lindemuth, Irvin R.
2009-01-21
For approximately four decades, Z-pinches and related geometries have been computationally modeled using unique Alternating Direction Implicit (ADI) numerical methods. Computational results have provided illuminating and often provocative interpretations of experimental results. A number of past and continuing applications are reviewed and discussed.
Potts models with magnetic field: Arithmetic, geometry, and computation
NASA Astrophysics Data System (ADS)
Dasu, Shival; Marcolli, Matilde
2015-11-01
We give a sheaf theoretic interpretation of Potts models with external magnetic field, in terms of constructible sheaves and their Euler characteristics. We show that the polynomial countability question for the hypersurfaces defined by the vanishing of the partition function is affected by changes in the magnetic field: elementary examples suffice to see non-polynomially countable cases that become polynomially countable after a perturbation of the magnetic field. The same recursive formula for the Grothendieck classes, under edge-doubling operations, holds as in the case without magnetic field, but the closed formulae for specific examples like banana graphs differ in the presence of magnetic field. We give examples of computation of the Euler characteristic with compact support, for the set of real zeros, and find a similar exponential growth with the size of the graph. This can be viewed as a measure of topological and algorithmic complexity. We also consider the computational complexity question for evaluations of the polynomial, and show both tractable and NP-hard examples, using dynamic programming.
Computational Approaches to Vestibular Research
NASA Technical Reports Server (NTRS)
Ross, Muriel D.; Wade, Charles E. (Technical Monitor)
1994-01-01
The Biocomputation Center at NASA Ames Research Center is dedicated to a union between computational, experimental and theoretical approaches to the study of neuroscience and of life sciences in general. The current emphasis is on computer reconstruction and visualization of vestibular macular architecture in three-dimensions (3-D), and on mathematical modeling and computer simulation of neural activity in the functioning system. Our methods are being used to interpret the influence of spaceflight on mammalian vestibular maculas in a model system, that of the adult Sprague-Dawley rat. More than twenty 3-D reconstructions of type I and type II hair cells and their afferents have been completed by digitization of contours traced from serial sections photographed in a transmission electron microscope. This labor-intensive method has now been replace d by a semiautomated method developed in the Biocomputation Center in which conventional photography is eliminated. All viewing, storage and manipulation of original data is done using Silicon Graphics workstations. Recent improvements to the software include a new mesh generation method for connecting contours. This method will permit the investigator to describe any surface, regardless of complexity, including highly branched structures such as are routinely found in neurons. This same mesh can be used for 3-D, finite volume simulation of synapse activation and voltage spread on neuronal surfaces visualized via the reconstruction process. These simulations help the investigator interpret the relationship between neuroarchitecture and physiology, and are of assistance in determining which experiments will best test theoretical interpretations. Data are also used to develop abstract, 3-D models that dynamically display neuronal activity ongoing in the system. Finally, the same data can be used to visualize the neural tissue in a virtual environment. Our exhibit will depict capabilities of our computational approaches and
Computational aeroelastic analysis of aircraft wings including geometry nonlinearity
NASA Astrophysics Data System (ADS)
Tian, Binyu
The objective of the present study is to show the ability of solving fluid structural interaction problems more realistically by including the geometric nonlinearity of the structure so that the aeroelastic analysis can be extended into the onset of flutter, or in the post flutter regime. A nonlinear Finite Element Analysis software is developed based on second Piola-Kirchhoff stress and Green-Lagrange strain. The second Piola-Kirchhoff stress and Green-Lagrange strain is a pair of energetically conjugated tensors that can accommodate arbitrary large structural deformations and deflection, to study the flutter phenomenon. Since both of these tensors are objective tensors, i.e., the rigid-body motion has no contribution to their components, the movement of the body, including maneuvers and deformation, can be included. The nonlinear Finite Element Analysis software developed in this study is verified with ANSYS, NASTRAN, ABAQUS, and IDEAS for the linear static, nonlinear static, linear dynamic and nonlinear dynamic structural solutions. To solve the flow problems by Euler/Navier equations, the current nonlinear structural software is then embedded into ENSAERO, which is an aeroelastic analysis software package developed at NASA Ames Research Center. The coupling of the two software, both nonlinear in their own field, is achieved by domain decomposition method first proposed by Guruswamy. A procedure has been set for the aeroelastic analysis process. The aeroelastic analysis results have been obtained for fight wing in the transonic regime for various cases. The influence dynamic pressure on flutter has been checked for a range of Mach number. Even though the current analysis matches the general aeroelastic characteristic, the numerical value not match very well with previous studies and needs farther investigations. The flutter aeroelastic analysis results have also been plotted at several time points. The influences of the deforming wing geometry can be well seen
A Self-Paced Instructional Approach for Engineering Descriptive Geometry.
ERIC Educational Resources Information Center
Beck, Eugene J.
These materials, used in a self-paced course in engineering descriptive geometry for freshman and sophomore college-level students, cover three modules: basic spatial relationships; intersections, parallelism, and perpendicularity; and graphic analysis and development. Each module contains five instructional units. Each unit includes a rationale,…
Geometry of Covariance Matrices and Computation of Median
NASA Astrophysics Data System (ADS)
Yang, Le; Arnaudon, Marc; Barbaresco, Frédéric
2011-03-01
In this paper, we consider the manifold of covariance matrices of order n parametrized by reflection coefficients which are derived from Levinson's recursion of autoregressive model. The explicit expression of the reparametrization and its inverse are obtained. With the Riemannian metric given by the Hessian of a Kähler potential, we show that the manifold is in fact a Cartan-Hadamard manifold with lower sectional curvature bound -4. The explicit expressions of geodesics are also obtained. After that we introduce the notion of Riemannian median of points lying on a Riemannian manifold and give a simple algorithm to compute it. Finally, some simulation examples are given to illustrate the applications of the median method to radar signal processing.
Software-based geometry operations for 3D computer graphics
NASA Astrophysics Data System (ADS)
Sima, Mihai; Iancu, Daniel; Glossner, John; Schulte, Michael; Mamidi, Suman
2006-02-01
In order to support a broad dynamic range and a high degree of precision, many of 3D renderings fundamental algorithms have been traditionally performed in floating-point. However, fixed-point data representation is preferable over floating-point representation in graphics applications on embedded devices where performance is of paramount importance, while the dynamic range and precision requirements are limited due to the small display sizes (current PDA's are 640 × 480 (VGA), while cell-phones are even smaller). In this paper we analyze the efficiency of a CORDIC-augmented Sandbridge processor when implementing a vertex processor in software using fixed-point arithmetic. A CORDIC-based solution for vertex processing exhibits a number of advantages over classical Multiply-and-Acumulate solutions. First, since a single primitive is used to describe the computation, the code can easily be vectorized and multithreaded, and thus fits the major Sandbridge architectural features. Second, since a CORDIC iteration consists of only a shift operation followed by an addition, the computation may be deeply pipelined. Initially, we outline the Sandbridge architecture extension which encompasses a CORDIC functional unit and the associated instructions. Then, we consider rigid-body rotation, lighting, exponentiation, vector normalization, and perspective division (which are some of the most important data-intensive 3D graphics kernels) and propose a scheme to implement them on the CORDIC-augmented Sandbridge processor. Preliminary results indicate that the performance improvement within the extended instruction set ranges from 3× to 10× (with the exception of rigid body rotation).
Fuzzy multiple linear regression: A computational approach
NASA Technical Reports Server (NTRS)
Juang, C. H.; Huang, X. H.; Fleming, J. W.
1992-01-01
This paper presents a new computational approach for performing fuzzy regression. In contrast to Bardossy's approach, the new approach, while dealing with fuzzy variables, closely follows the conventional regression technique. In this approach, treatment of fuzzy input is more 'computational' than 'symbolic.' The following sections first outline the formulation of the new approach, then deal with the implementation and computational scheme, and this is followed by examples to illustrate the new procedure.
Redundancy approaches in spacecraft computers
NASA Astrophysics Data System (ADS)
Schonfeld, Chaim
Twelve redundancy techniques for spacecraft computers are analyzed. The redundancy schemes include: a single unit; two active units; triple modular redundancy; NMR; a single unit with one and two spares; two units with one, two, and three spares; triple units with one and two spares; and a single unit with a spare per module; the basic properties of these schemes are described. The reliability of each scheme is evaluated as a function of the reliability of a single unit. The redundancy schemes are compared in terms of reliability, the number of failures the system can tolerate, coverage, recovery time, and mean time between failure improvement. The error detection and recovery systems and the random access memory redundancy of the schemes are examined. The data reveal that the single unit with a spare per module is the most effective redundancy approach; a description of the scheme is provided.
The flux-coordinate independent approach applied to X-point geometries
Hariri, F. Hill, P.; Ottaviani, M.; Sarazin, Y.
2014-08-15
A Flux-Coordinate Independent (FCI) approach for anisotropic systems, not based on magnetic flux coordinates, has been introduced in Hariri and Ottaviani [Comput. Phys. Commun. 184, 2419 (2013)]. In this paper, we show that the approach can tackle magnetic configurations including X-points. Using the code FENICIA, an equilibrium with a magnetic island has been used to show the robustness of the FCI approach to cases in which a magnetic separatrix is present in the system, either by design or as a consequence of instabilities. Numerical results are in good agreement with the analytic solutions of the sound-wave propagation problem. Conservation properties are verified. Finally, the critical gain of the FCI approach in situations including the magnetic separatrix with an X-point is demonstrated by a fast convergence of the code with the numerical resolution in the direction of symmetry. The results highlighted in this paper show that the FCI approach can efficiently deal with X-point geometries.
Han, Min Cheol; Yeom, Yeon Soo; Kim, Chan Hyeong; Kim, Seonghoon; Sohn, Jason W
2015-02-21
In the present study, to achieve accurate 4D Monte Carlo dose calculation in radiation therapy, we devised a new approach that combines (1) modeling of the patient body using tetrahedral-mesh geometry based on the patient's 4D CT data, (2) continuous movement/deformation of the tetrahedral patient model by interpolation of deformation vector fields acquired through deformable image registration, and (3) direct transportation of radiation particles during the movement and deformation of the tetrahedral patient model. The results of our feasibility study show that it is certainly possible to construct 4D patient models (= phantoms) with sufficient accuracy using the tetrahedral-mesh geometry and to directly transport radiation particles during continuous movement and deformation of the tetrahedral patient model. This new approach not only produces more accurate dose distribution in the patient but also replaces the current practice of using multiple 3D voxel phantoms and combining multiple dose distributions after Monte Carlo simulations. For routine clinical application of our new approach, the use of fast automatic segmentation algorithms is a must. In order to achieve, simultaneously, both dose accuracy and computation speed, the number of tetrahedrons for the lungs should be optimized. Although the current computation speed of our new 4D Monte Carlo simulation approach is slow (i.e. ~40 times slower than that of the conventional dose accumulation approach), this problem is resolvable by developing, in Geant4, a dedicated navigation class optimized for particle transportation in tetrahedral-mesh geometry. PMID:25615567
Antiga, Luca; Ene-Iordache, Bogdan; Remuzzi, Andrea
2003-05-01
Investigation of three-dimensional (3-D) geometry and fluid-dynamics in human arteries is an important issue in vascular disease characterization and assessment. Thanks to recent advances in magnetic resonance (MR) and computed tomography (CT), it is now possible to address the problem of patient-specific modeling of blood vessels, in order to take into account interindividual anatomic variability of vasculature. Generation of models suitable for computational fluid dynamics is still commonly performed by semiautomatic procedures, in general based on operator-dependent tasks, which cannot be easily extended to a significant number of clinical cases. In this paper, we overcome these limitations making use of computational geometry techniques. In particular, 3-D modeling was carried out by means of 3-D level sets approach. Model editing was also implemented ensuring harmonic mean curvature vectors distribution on the surface, and model geometric analysis was performed with a novel approach, based on solving Eikonal equation on Voronoi diagram. This approach provides calculation of central paths, maximum inscribed sphere estimation and geometric characterization of the surface. Generation of adaptive-thickness boundary layer finite elements is finally presented. The use of the techniques presented here makes it possible to introduce patient-specific modeling of blood vessels at clinical level. PMID:12846436
ERIC Educational Resources Information Center
Gambari, Isiaka Amosa; Ezenwa, Victoria Ifeoma; Anyanwu, Romanus Chogozie
2014-01-01
The study examined the effects of two modes of computer-assisted instructional package on solid geometry achievement amongst senior secondary school students in Minna, Niger State, Nigeria. Also, the influence of gender on the performance of students exposed to CAI(AT) and CAI(AN) packages were examined. This study adopted a pretest-posttest…
Multivariate geometry as an approach to algal community analysis
Allen, T.F.H.; Skagen, S.
1973-01-01
Multivariate analyses are put in the context of more usual approaches to phycological investigations. The intuitive common-sense involved in methods of ordination, classification and discrimination are emphasised by simple geometric accounts which avoid jargon and matrix algebra. Warnings are given that artifacts result from technique abuses by the naive or over-enthusiastic. An analysis of a simple periphyton data set is presented as an example of the approach. Suggestions are made as to situations in phycological investigations, where the techniques could be appropriate. The discipline is reprimanded for its neglect of the multivariate approach.
Machine Computation; An Algorithmic Approach.
ERIC Educational Resources Information Center
Gonzalez, Richard F.; McMillan, Claude, Jr.
Designed for undergraduate social science students, this textbook concentrates on using the computer in a straightforward way to manipulate numbers and variables in order to solve problems. The text is problem oriented and assumes that the student has had little prior experience with either a computer or programing languages. An introduction to…
NASA Astrophysics Data System (ADS)
Assadi, Amir H.; Eghbalnia, Hamid
2000-06-01
In standard differential geometry, the Fundamental Theorem of Space Curves states that two differential invariants of a curve, namely curvature and torsion, determine its geometry, or equivalently, the isometry class of the curve up to rigid motions in the Euclidean three-dimensional space. Consider a physical model of a space curve made from a sufficiently thin, yet visible rigid wire, and the problem of perceptual identification (by a human observer or a robot) of two given physical model curves. In a previous paper (perceptual geometry) we have emphasized a learning theoretic approach to construct a perceptual geometry of the surfaces in the environment. In particular, we have described a computational method for mathematical representation of objects in the perceptual geometry inspired by the ecological theory of Gibson, and adhering to the principles of Gestalt in perceptual organization of vision. In this paper, we continue our learning theoretic treatment of perceptual geometry of objects, focusing on the case of physical models of space curves. In particular, we address the question of perceptually distinguishing two possibly novel space curves based on observer's prior visual experience of physical models of curves in the environment. The Fundamental Theorem of Space Curves inspires an analogous result in perceptual geometry as follows. We apply learning theory to the statistics of a sufficiently rich collection of physical models of curves, to derive two statistically independent local functions, that we call by analogy, the curvature and torsion. This pair of invariants distinguish physical models of curves in the sense of perceptual geometry. That is, in an appropriate resolution, an observer can distinguish two perceptually identical physical models in different locations. If these pairs of functions are approximately the same for two given space curves, then after possibly some changes of viewing planes, the observer confirms the two are the same.
Rodriguez, Alejandro; Ibanescu, Mihai; Joannopoulos, J. D.; Johnson, Steven G.; Iannuzzi, Davide; Capasso, Federico
2007-08-24
We present a method of computing Casimir forces for arbitrary geometries, with any desired accuracy, that can directly exploit the efficiency of standard numerical-electromagnetism techniques. Using the simplest possible finite-difference implementation of this approach, we obtain both agreement with past results for cylinder-plate geometries, and also present results for new geometries. In particular, we examine a pistonlike problem involving two dielectric and metallic squares sliding between two metallic walls, in two and three dimensions, respectively, and demonstrate nonadditive and nonmonotonic changes in the force due to these lateral walls.
Rodriguez, Alejandro; Ibanescu, Mihai; Iannuzzi, Davide; Capasso, Federico; Joannopoulos, J D; Johnson, Steven G
2007-08-24
We present a method of computing Casimir forces for arbitrary geometries, with any desired accuracy, that can directly exploit the efficiency of standard numerical-electromagnetism techniques. Using the simplest possible finite-difference implementation of this approach, we obtain both agreement with past results for cylinder-plate geometries, and also present results for new geometries. In particular, we examine a pistonlike problem involving two dielectric and metallic squares sliding between two metallic walls, in two and three dimensions, respectively, and demonstrate nonadditive and nonmonotonic changes in the force due to these lateral walls. PMID:17930932
Computer Algebra, Instrumentation and the Anthropological Approach
ERIC Educational Resources Information Center
Monaghan, John
2007-01-01
This article considers research and scholarship on the use of computer algebra in mathematics education following the instrumentation and the anthropological approaches. It outlines what these approaches are, positions them with regard to other approaches, examines tensions between the two approaches and makes suggestions for how work in this…
Computational approaches to motor control
Flash, Tamar; Sejnowski, Terrence J
2010-01-01
New concepts and computational models that integrate behavioral and neurophysiological observations have addressed several of the most fundamental long-standing problems in motor control. These problems include the selection of particular trajectories among the large number of possibilities, the solution of inverse kinematics and dynamics problems, motor adaptation and the learning of sequential behaviors. PMID:11741014
Comparative study of auxetic geometries by means of computer-aided design and engineering
NASA Astrophysics Data System (ADS)
Álvarez Elipe, Juan Carlos; Díaz Lantada, Andrés
2012-10-01
Auxetic materials (or metamaterials) are those with a negative Poisson ratio (NPR) and display the unexpected property of lateral expansion when stretched, as well as an equal and opposing densification when compressed. Such geometries are being progressively employed in the development of novel products, especially in the fields of intelligent expandable actuators, shape morphing structures and minimally invasive implantable devices. Although several auxetic and potentially auxetic geometries have been summarized in previous reviews and research, precise information regarding relevant properties for design tasks is not always provided. In this study we present a comparative study of two-dimensional and three-dimensional auxetic geometries carried out by means of computer-aided design and engineering tools (from now on CAD-CAE). The first part of the study is focused on the development of a CAD library of auxetics. Once the library is developed we simulate the behavior of the different auxetic geometries and elaborate a systematic comparison, considering relevant properties of these geometries, such as Poisson ratio(s), maximum volume or area reductions attainable and equivalent Young’s modulus, hoping it may provide useful information for future designs of devices based on these interesting structures.
NASA Technical Reports Server (NTRS)
Foster, Lancert; Engblom, William A.
2003-01-01
Computational results are presented for the performance and flow behavior of various injector geometries employed in transverse injection into a non-reacting Mach 1.2 flow. 3-D Reynolds-Averaged Navier Stokes (RANS) results are obtained for the various injector geometries using the Wind code with the Mentor s Shear Stress Transport turbulence model in both single and multi-species modes. Computed results for the injector mixing, penetration, and induced wall forces are presented. In the case of rectangular injectors, those longer in the direction of the freestream flow are predicted to generate the most mixing and penetration of the injector flow into the primary stream. These injectors are also predicted to provide the largest discharge coefficients and induced wall forces. Minor performance differences are indicated among diamond, circle, and square orifices. Grid sensitivity study results are presented which indicate consistent qualitative trends in the injector performance comparisons with increasing grid fineness.
Mitchell, Scott A.; Ebeida, Mohamed Salah; Romero, Vicente J.; Swiler, Laura Painton; Rushdi, Ahmad A.; Abdelkader, Ahmad
2015-09-01
This SAND report summarizes our work on the Sandia National Laboratory LDRD project titled "Efficient Probability of Failure Calculations for QMU using Computational Geometry" which was project #165617 and proposal #13-0144. This report merely summarizes our work. Those interested in the technical details are encouraged to read the full published results, and contact the report authors for the status of the software and follow-on projects.
Design geometry and design/off-design performance computer codes for compressors and turbines
NASA Technical Reports Server (NTRS)
Glassman, Arthur J.
1995-01-01
This report summarizes some NASA Lewis (i.e., government owned) computer codes capable of being used for airbreathing propulsion system studies to determine the design geometry and to predict the design/off-design performance of compressors and turbines. These are not CFD codes; velocity-diagram energy and continuity computations are performed fore and aft of the blade rows using meanline, spanline, or streamline analyses. Losses are provided by empirical methods. Both axial-flow and radial-flow configurations are included.
A Parallel Cartesian Approach for External Aerodynamics of Vehicles with Complex Geometry
NASA Technical Reports Server (NTRS)
Aftosmis, M. J.; Berger, M. J.; Adomavicius, G.
2001-01-01
This workshop paper presents the current status in the development of a new approach for the solution of the Euler equations on Cartesian meshes with embedded boundaries in three dimensions on distributed and shared memory architectures. The approach uses adaptively refined Cartesian hexahedra to fill the computational domain. Where these cells intersect the geometry, they are cut by the boundary into arbitrarily shaped polyhedra which receive special treatment by the solver. The presentation documents a newly developed multilevel upwind solver based on a flexible domain-decomposition strategy. One novel aspect of the work is its use of space-filling curves (SFC) for memory efficient on-the-fly parallelization, dynamic re-partitioning and automatic coarse mesh generation. Within each subdomain the approach employs a variety reordering techniques so that relevant data are on the same page in memory permitting high-performance on cache-based processors. Details of the on-the-fly SFC based partitioning are presented as are construction rules for the automatic coarse mesh generation. After describing the approach, the paper uses model problems and 3- D configurations to both verify and validate the solver. The model problems demonstrate that second-order accuracy is maintained despite the presence of the irregular cut-cells in the mesh. In addition, it examines both parallel efficiency and convergence behavior. These investigations demonstrate a parallel speed-up in excess of 28 on 32 processors of an SGI Origin 2000 system and confirm that mesh partitioning has no effect on convergence behavior.
Computational approaches for systems metabolomics.
Krumsiek, Jan; Bartel, Jörg; Theis, Fabian J
2016-06-01
Systems genetics is defined as the simultaneous assessment and analysis of multi-omics datasets. In the past few years, metabolomics has been established as a robust tool describing an important functional layer in this approach. The metabolome of a biological system represents an integrated state of genetic and environmental factors and has been referred to as a 'link between genotype and phenotype'. In this review, we summarize recent progresses in statistical analysis methods for metabolomics data in combination with other omics layers. We put a special focus on complex, multivariate statistical approaches as well as pathway-based and network-based analysis methods. Moreover, we outline current challenges and pitfalls of metabolomics-focused multi-omics analyses and discuss future steps for the field. PMID:27135552
ERIC Educational Resources Information Center
Zhou, Mingming; Chan, Kan Kan; Teo, Timothy
2016-01-01
Dynamic geometry environments (DGEs) provide computer-based environments to construct and manipulate geometric figures with great ease. Research has shown that DGEs has positive impact on student motivation, engagement, and achievement in mathematics learning. However, the adoption of DGEs by mathematics teachers varies substantially worldwide.…
Quantitative approaches to computational vaccinology.
Doytchinova, Irini A; Flower, Darren R
2002-06-01
This article reviews the newly released JenPep database and two new powerful techniques for T-cell epitope prediction: (i) the additive method; and (ii) a 3D-Quantitative Structure Activity Relationships (3D-QSAR) method, based on Comparative Molecular Similarity Indices Analysis (CoMSIA). The JenPep database is a family of relational databases supporting the growing need of immunoinformaticians for quantitative data on peptide binding to major histocompatibility complexes and to the Transporters associated with Antigen Processing (TAP). It also contains an annotated list of T-cell epitopes. The database is available free via the Internet (http://www.jenner.ac.uk/JenPep). The additive prediction method is based on the assumption that the binding affinity of a peptide depends on the contributions from each amino acid as well as on the interactions between the adjacent and every second side-chain. In the 3D-QSAR approach, the influence of five physicochemical properties (steric bulk, electrostatic potential, local hydrophobicity, hydrogen-bond donor and hydrogen-bond acceptor abilities) on the affinity of peptides binding to MHC molecules were considered. Both methods were exemplified through their application to the well-studied problem of peptides binding to the human class I MHC molecule HLA-A*0201. PMID:12067414
NASA Technical Reports Server (NTRS)
Choo, Yung K.; Slater, John W.; Vickerman, Mary B.; VanZante, Judith F.; Wadel, Mary F. (Technical Monitor)
2002-01-01
Issues associated with analysis of 'icing effects' on airfoil and wing performances are discussed, along with accomplishments and efforts to overcome difficulties with ice. Because of infinite variations of ice shapes and their high degree of complexity, computational 'icing effects' studies using available software tools must address many difficulties in geometry acquisition and modeling, grid generation, and flow simulation. The value of each technology component needs to be weighed from the perspective of the entire analysis process, from geometry to flow simulation. Even though CFD codes are yet to be validated for flows over iced airfoils and wings, numerical simulation, when considered together with wind tunnel tests, can provide valuable insights into 'icing effects' and advance our understanding of the relationship between ice characteristics and their effects on performance degradation.
Computational studies of flow through cross flow fans - effect of blade geometry
NASA Astrophysics Data System (ADS)
Govardhan, M.; Sampat, D. Lakshmana
2005-09-01
This present paper describes three dimensional computational analysis of complex internal flow in a cross flow fan. A commercial computational fluid dynamics (CFD) software code CFX was used for the computation. RNG k-ɛ two equation turbulence model was used to simulate the model with unstructured mesh. Sliding mesh interface was used at the interface between the rotating and stationary domains to capture the unsteady interactions. An accurate assessment of the present investigation is made by comparing various parameters with the available experimental data. Three impeller geometries with different blade angles and radius ratio are used in the present study. Maximum energy transfer through the impeller takes place in the region where the flow follows the blade curvature. Radial velocity is not uniform through blade channels. Some blades work in turbine mode at very low flow coefficients. Static pressure is always negative in and around the impeller region.
NASA Astrophysics Data System (ADS)
Alonso-Marroquín, Fernando; Galindo-Torres, Sergio-Andres; Tordesillas, Antoinette; Wang, Yucang
2009-06-01
One of the most challenging problems in the realistic modeling of granular materials is how to capture the real shape of the particles. Here we present a method to simulate systems with complex-shaped particles. This method integrates developments in two traditionally separate research areas: computational geometry and molecular dynamics. The computational geometry involves the implementation of techniques of computer graphics to represent particle shape and collision detection. Traditional techniques from molecular dynamics are used to integrate the equations of motion and to perform an efficient calculation of contact forces. The algorithm to solve the dynamics of the system is much more efficient, accurate and easier to implement than other models. The algorithm is used to simulate quasistatic deformation of granular materials using two different models. The first model consists of non-circular particles interacting via frictional forces. The second model consists of circular particles interacting via rolling and sliding resistance. The comparison of both models help us to understand and quantify the extend to which the effects of particle shape can be captured by the introduction of artificial rolling resistance on circular particles. Biaxial test simulation show that the overall response of the system and the collapse of force chains at the critical state is qualitatively similar in both 2D and 3D simulations.
NASA Technical Reports Server (NTRS)
McCloud, Peter L.
2010-01-01
Thermal Protection System (TPS) Cavity Heating is predicted using Computational Fluid Dynamics (CFD) on unstructured grids for both simplified cavities and actual cavity geometries. Validation was performed using comparisons to wind tunnel experimental results and CFD predictions using structured grids. Full-scale predictions were made for simplified and actual geometry configurations on the Space Shuttle Orbiter in a mission support timeframe.
A Comparison of Two Approaches to Teaching Selected Elements of College Level Descriptive Geometry.
ERIC Educational Resources Information Center
Beck, Eugene Jerome
This study was designed to ascertain the relative effectiveness of two approaches for teaching descriptive geometry by a comparison of the following behavioral variables--(1) performance in the solution of graphical problems, (2) spatial perception, (3) abstract reasoning ability, (4) technical information achievement, and (5) attitude toward…
Answering Typical Student Questions in Hyperbolic Geometry: A Transformation Group Approach
ERIC Educational Resources Information Center
Reyes, Edgar N.; Gray, Elizabeth D.
2002-01-01
It is shown that the bisector of a segment of a geodesic and the bisector of an angle in hyperbolic geometry can be expressed in terms of points which are equidistant from the end points of the segment, and points that are equidistant from the rays of the angle, respectively. An important tool in the approach is that the shortest distance between…
Toward exascale computing through neuromorphic approaches.
James, Conrad D.
2010-09-01
While individual neurons function at relatively low firing rates, naturally-occurring nervous systems not only surpass manmade systems in computing power, but accomplish this feat using relatively little energy. It is asserted that the next major breakthrough in computing power will be achieved through application of neuromorphic approaches that mimic the mechanisms by which neural systems integrate and store massive quantities of data for real-time decision making. The proposed LDRD provides a conceptual foundation for SNL to make unique advances toward exascale computing. First, a team consisting of experts from the HPC, MESA, cognitive and biological sciences and nanotechnology domains will be coordinated to conduct an exercise with the outcome being a concept for applying neuromorphic computing to achieve exascale computing. It is anticipated that this concept will involve innovative extension and integration of SNL capabilities in MicroFab, material sciences, high-performance computing, and modeling and simulation of neural processes/systems.
NASA Astrophysics Data System (ADS)
McBride, D.; Cross, M.; Croft, N.; Bennett, C.; Gebhardt, J.
2006-03-01
A computational procedure is presented for solving complex variably saturated flows in porous media, that may easily be implemented into existing conventional finite-volume-based computational fluid dynamics codes, so that their functionality might be geared upon to readily enable the modelling of a complex suite of interacting fluid, thermal and chemical reaction process physics. This procedure has been integrated within a multi-physics finite volume unstructured mesh framework, allowing arbitrarily complex three-dimensional geometries to be modelled. The model is particularly targeted at ore heap-leaching processes, which encounter complex flow problems, such as infiltration into dry soil, drainage, perched water tables and flow through heterogeneous materials, but is equally applicable to any process involving flow through porous media, such as in environmental recovery processes. The computational procedure is based on the mixed form of the classical Richards equation, employing an adaptive transformed mixed algorithm that is numerically robust and significantly reduces compute (or CPU) time. The computational procedure is accurate (compares well with other methods and analytical data), comprehensive (representing any kind of porous flow model), and is computationally efficient. As such, this procedure provides a suitable basis for the implementation of large-scale industrial heap-leach models.
An interactive user-friendly approach to surface-fitting three-dimensional geometries
NASA Technical Reports Server (NTRS)
Cheatwood, F. Mcneil; Dejarnette, Fred R.
1988-01-01
A surface-fitting technique has been developed which addresses two problems with existing geometry packages: computer storage requirements and the time required of the user for the initial setup of the geometry model. Coordinates of cross sections are fit using segments of general conic sections. The next step is to blend the cross-sectional curve-fits in the longitudinal direction using general conics to fit specific meridional half-planes. Provisions are made to allow the fitting of fuselages and wings so that entire wing-body combinations may be modeled. This report includes the development of the technique along with a User's Guide for the various menus within the program. Results for the modeling of the Space Shuttle and a proposed Aeroassist Flight Experiment geometry are presented.
ERIC Educational Resources Information Center
Vaughan, Herbert E.; Szabo, Steven
This is the teacher's edition of a text for the second year of a two-year high school geometry course. The course bases plane and solid geometry and trigonometry on the fact that the translations of a Euclidean space constitute a vector space which has an inner product. Congruence is a geometric topic reserved for Volume 2. Volume 2 opens with an…
NASA Astrophysics Data System (ADS)
Wang, Tianyang; Wüchner, Roland; Sicklinger, Stefan; Bletzinger, Kai-Uwe
2016-05-01
This paper investigates data mapping between non-matching meshes and geometries in fluid-structure interaction. Mapping algorithms for surface meshes including nearest element interpolation, the standard mortar method and the dual mortar method are studied and comparatively assessed. The inconsistency problem of mortar methods at curved edges of fluid-structure-interfaces is solved by a newly developed enforcing consistency approach, which is robust enough to handle even the case that fluid boundary facets are totally not in contact with structure boundary elements due to high fluid refinement. Besides, tests with representative geometries show that the mortar methods are suitable for conservative mapping but it is better to use the nearest element interpolation in a direct way, and moreover, the dual mortar method can give slight oscillations. This work also develops a co-rotating mapping algorithm for 1D beam elements. Its novelty lies in the ability of handling large displacements and rotations.
NASA Technical Reports Server (NTRS)
Boyalakuntla, Kishore; Soni, Bharat K.; Thornburg, Hugh J.; Yu, Robert
1996-01-01
During the past decade, computational simulation of fluid flow around complex configurations has progressed significantly and many notable successes have been reported, however, unsteady time-dependent solutions are not easily obtainable. The present effort involves unsteady time dependent simulation of temporally deforming geometries. Grid generation for a complex configuration can be a time consuming process and temporally varying geometries necessitate the regeneration of such grids for every time step. Traditional grid generation techniques have been tried and demonstrated to be inadequate to such simulations. Non-Uniform Rational B-splines (NURBS) based techniques provide a compact and accurate representation of the geometry. This definition can be coupled with a distribution mesh for a user defined spacing. The present method greatly reduces cpu requirements for time dependent remeshing, facilitating the simulation of more complex unsteady problems. A thrust vectoring nozzle has been chosen to demonstrate the capability as it is of current interest in the aerospace industry for better maneuverability of fighter aircraft in close combat and in post stall regimes. This current effort is the first step towards multidisciplinary design optimization which involves coupling the aerodynamic heat transfer and structural analysis techniques. Applications include simulation of temporally deforming bodies and aeroelastic problems.
A Geometry Based Infra-structure for Computational Analysis and Design
NASA Technical Reports Server (NTRS)
Haimes, Robert
1997-01-01
The computational steps traditionally taken for most engineering analysis (CFD, structural analysis, and etc.) are: Surface Generation - usually by employing a CAD system; Grid Generation - preparing the volume for the simulation; Flow Solver - producing the results at the specified operational point; and Post-processing Visualization - interactively attempting to understand the results For structural analysis, integrated systems can be obtained from a number of commercial vendors. For CFD, these steps have worked well in the past for simple steady-state simulations at the expense of much user interaction. The data was transmitted between phases via files. Specifically the problems with this procedure are: (1) File based. Information flows from one step to the next via data files with formats specified for that procedure. (2) 'Good' Geometry. A bottleneck in getting results from a solver is the construction of proper geometry to be fed to the grid generator. With 'good' geometry a grid can be constructed in tens of minutes (even with a complex configuration) using unstructured techniques. (3) One-Way communication. All information travels on from one phase to the next. Until this process can be automated, more complex problems such as multi-disciplinary analysis or using the above procedure for design becomes prohibitive.
NASA Technical Reports Server (NTRS)
Craidon, C. B.
1975-01-01
A computer program that uses a three-dimensional geometric technique for fitting a smooth surface to the component parts of an aircraft configuration is presented. The resulting surface equations are useful in performing various kinds of calculations in which a three-dimensional mathematical description is necessary. Programs options may be used to compute information for three-view and orthographic projections of the configuration as well as cross-section plots at any orientation through the configuration. The aircraft geometry input section of the program may be easily replaced with a surface point description in a different form so that the program could be of use for any three-dimensional surface equations.
Computational Approaches to Study Microbes and Microbiomes
Greene, Casey S.; Foster, James A.; Stanton, Bruce A.; Hogan, Deborah A.; Bromberg, Yana
2016-01-01
Technological advances are making large-scale measurements of microbial communities commonplace. These newly acquired datasets are allowing researchers to ask and answer questions about the composition of microbial communities, the roles of members in these communities, and how genes and molecular pathways are regulated in individual community members and communities as a whole to effectively respond to diverse and changing environments. In addition to providing a more comprehensive survey of the microbial world, this new information allows for the development of computational approaches to model the processes underlying microbial systems. We anticipate that the field of computational microbiology will continue to grow rapidly in the coming years. In this manuscript we highlight both areas of particular interest in microbiology as well as computational approaches that begin to address these challenges. PMID:26776218
Computational Approach for Developing Blood Pump
NASA Technical Reports Server (NTRS)
Kwak, Dochan
2002-01-01
This viewgraph presentation provides an overview of the computational approach to developing a ventricular assist device (VAD) which utilizes NASA aerospace technology. The VAD is used as a temporary support to sick ventricles for those who suffer from late stage congestive heart failure (CHF). The need for donor hearts is much greater than their availability, and the VAD is seen as a bridge-to-transplant. The computational issues confronting the design of a more advanced, reliable VAD include the modelling of viscous incompressible flow. A computational approach provides the possibility of quantifying the flow characteristics, which is especially valuable for analyzing compact design with highly sensitive operating conditions. Computational fluid dynamics (CFD) and rocket engine technology has been applied to modify the design of a VAD which enabled human transplantation. The computing requirement for this project is still large, however, and the unsteady analysis of the entire system from natural heart to aorta involves several hundred revolutions of the impeller. Further study is needed to assess the impact of mechanical VADs on the human body
Römgens, Anne M; Bader, Dan L; Bouwstra, Joke A; Oomens, Cees W J
2016-11-01
Microneedle arrays have been developed to deliver a range of biomolecules including vaccines into the skin. These microneedles have been designed with a wide range of geometries and arrangements within an array. However, little is known about the effect of the geometry on the potency of the induced immune response. The aim of this study was to develop a computational model to predict the optimal design of the microneedles and their arrangement within an array. The three-dimensional finite element model described the diffusion and kinetics in the skin following antigen delivery with a microneedle array. The results revealed an optimum distance between microneedles based on the number of activated antigen presenting cells, which was assumed to be related to the induced immune response. This optimum depends on the delivered dose. In addition, the microneedle length affects the number of cells that will be involved in either the epidermis or dermis. By contrast, the radius at the base of the microneedle and release rate only minimally influenced the number of cells that were activated. The model revealed the importance of various geometric parameters to enhance the induced immune response. The model can be developed further to determine the optimal design of an array by adjusting its various parameters to a specific situation. PMID:27557398
Three-dimensional analysis of root canal geometry by high-resolution computed tomography.
Peters, O A; Laib, A; Rüegsegger, P; Barbakow, F
2000-06-01
A detailed understanding of the complexity of root canal systems is imperative to ensure successful root canal preparation. The aim of this study was to evaluate the potential and accuracy of a three-dimensional, non-destructive technique for detailing root canal geometry by means of high-resolution tomography. The anatomy of root canals in 12 extracted human maxillary molars was analyzed by means of a micro-computed tomography scanner (microCT, cubic resolution 34 microm). A special mounting device facilitated repeated precise repositioning of the teeth in the microCT. Surface areas and volumes of each canal were calculated by triangulation, and means were determined. Model-independent methods were used to evaluate the canals' diameters and configuration. The calculated and measured volumes and the areas of artificial root canals, produced by the drilling of precision holes into dentin disks, were well-correlated. Semi-automated repositioning of specimens resulted in near-perfect matching (< 1 voxel) when outer canal contours were assessed. Root canal geometry was accurately assessed by this innovative technique; therefore, variables and indices presented may serve as a basis for further analyses of root canal anatomy in experimental endodontology. PMID:10890720
On the noncommutative spin geometry of the standard Podleś sphere and index computations
NASA Astrophysics Data System (ADS)
Wagner, Elmar
2009-07-01
The purpose of the paper is twofold: First, known results of the noncommutative spin geometry of the standard Podleś sphere are extended by discussing Poincaré duality and orientability. In the discussion of orientability, Hochschild homology is replaced by a twisted version which avoids the dimension drop. The twisted Hochschild cycle representing an orientation is related to the volume form of the distinguished covariant differential calculus. Integration over the volume form defines a twisted cyclic 2-cocycle which computes the q-winding numbers of quantum line bundles. Second, a "twisted" Chern character from equivariant K0-theory to even twisted cyclic homology is introduced which gives rise to a Chern-Connes pairing between equivariant K0-theory and twisted cyclic cohomology. The Chern-Connes pairing between the equivariant K0-group of the standard Podleś sphere and the generators of twisted cyclic cohomology relative to the modular automorphism and its inverse are computed. This includes the pairings with the twisted cyclic 2-cocycle associated to the volume form, and the one corresponding to the "no-dimension drop" case. From explicit index computations, it follows that the pairings with these cocycles give the q-indices of the known equivariant 0-summable Dirac operator on the standard Podleś sphere.
Approach to constructing reconfigurable computer vision system
NASA Astrophysics Data System (ADS)
Xue, Jianru; Zheng, Nanning; Wang, Xiaoling; Zhang, Yongping
2000-10-01
In this paper, we propose an approach to constructing reconfigurable vision system. We found that timely and efficient execution of early tasks can significantly enhance the performance of whole computer vision tasks, and abstract out a set of basic, computationally intensive stream operations that may be performed in parallel and embodies them in a series of specific front-end processors. These processors which based on FPGAs (Field programmable gate arrays) can be re-programmable to permit a range of different types of feature maps, such as edge detection & linking, image filtering. Front-end processors and a powerful DSP constitute a computing platform which can perform many CV tasks. Additionally we adopt the focus-of-attention technologies to reduce the I/O and computational demands by performing early vision processing only within a particular region of interest. Then we implement a multi-page, dual-ported image memory interface between the image input and computing platform (including front-end processors, DSP). Early vision features were loaded into banks of dual-ported image memory arrays, which are continually raster scan updated at high speed from the input image or video data stream. Moreover, the computing platform can be complete asynchronous, random access to the image data or any other early vision feature maps through the dual-ported memory banks. In this way, the computing platform resources can be properly allocated to a region of interest and decoupled from the task of dealing with a high speed serial raster scan input. Finally, we choose PCI Bus as the main channel between the PC and computing platform. Consequently, front-end processors' control registers and DSP's program memory were mapped into the PC's memory space, which provides user access to reconfigure the system at any time. We also present test result of a computer vision application based on the system.
NASA Astrophysics Data System (ADS)
Ramírez-López, A.; Muñoz-Negrón, D.; Palomar-Pardavé, M.; Escarela-Perez, R.; Cruz-Morales, V.
In materials science the properties representation in anisotropic materials is a very important topic. Porous media are heterogeneous in nature. Their representation is frequently assumed as a complex problem and difficult to be treated using normal numerical methods. Chaos theory is used to treat problems without established rules in different topics. The present work is focused to show the development of some computational algorithms to simulate the porous media properties such as porosity, permeability and saturation. The procedures involve the employ of a random number generator to assign properties. The result is amorphous media formed using a cellular automaton. This work also includes the development of some amorphous geometry to represent solid walls in empty samples in order to represent tortuosity of a porous media specimen. Finally advantages and disadvantages of the models developed are commented.
A computational geometry framework for the optimisation of atom probe reconstructions.
Felfer, Peter; Cairney, Julie
2016-10-01
In this paper, we present pathways for improving the reconstruction of atom probe data on a coarse (>10nm) scale, based on computational geometry. We introduce a way to iteratively improve an atom probe reconstruction by adjusting it, so that certain known shape criteria are fulfilled. This is achieved by creating an implicit approximation of the reconstruction through a barycentric coordinate transform. We demonstrate the application of these techniques to the compensation of trajectory aberrations and the iterative improvement of the reconstruction of a dataset containing a grain boundary. We also present a method for obtaining a hull of the dataset in both detector and reconstruction space. This maximises data utilisation, and can be used to compensate for ion trajectory aberrations caused by residual fields in the ion flight path through a 'master curve' and correct for overall shape deviations in the data. PMID:27449275
Effects of frequency, irradiation geometry and polarisation on computation of SAR in human brain.
Zhou, Hongmei; Su, Zhentao; Ning, Jing; Wang, Changzhen; Xie, Xiangdong; Qu, Decheng; Wu, Ke; Zhang, Xiaomin; Pan, Jie; Yang, Guoshan
2014-12-01
The power absorbed by the human brain has possible implications in the study of the central nervous system-related biological effects of electromagnetic fields. In order to determine the specific absorption rate (SAR) of radio frequency (RF) waves in the human brain, and to investigate the effects of geometry and polarisation on SAR value, the finite-difference time-domain method was applied for the SAR computation. An anatomically realistic model scaled to a height of 1.70 m and a mass of 63 kg was selected, which included 14 million voxels segmented into 39 tissue types. The results suggested that high SAR values were found in the brain, i.e. ∼250 MHz for vertical polarisation and 900-1200 MHz both for vertical and horizontal polarisation, which may be the result of head resonance at these frequencies. PMID:24399107
NASA geometry data exchange specification for computational fluid dynamics (NASA IGES)
NASA Technical Reports Server (NTRS)
Blake, Matthew W.; Kerr, Patricia A.; Thorp, Scott A.; Jou, Jin J.
1994-01-01
This document specifies a subset of an existing product data exchange specification that is widely used in industry and government. The existing document is called the Initial Graphics Exchange Specification. This document, a subset of IGES, is intended for engineers analyzing product performance using tools such as computational fluid dynamics (CFD) software. This document specifies how to define mathematically and exchange the geometric model of an object. The geometry is represented utilizing nonuniform rational B-splines (NURBS) curves and surfaces. Only surface models are represented; no solid model representation is included. This specification does not include most of the other types of product information available in IGES (e.g., no material properties or surface finish properties) and does not provide all the specific file format details of IGES. The data exchange protocol specified in this document is fully conforming to the American National Standard (ANSI) IGES 5.2.
Description of the F-16XL Geometry and Computational Grids Used in CAWAPI
NASA Technical Reports Server (NTRS)
Boelens, O. J.; Badcock, K. J.; Gortz, S.; Morton, S.; Fritz, W.; Karman, S. L., Jr.; Michal, T.; Lamar, J. E.
2009-01-01
The objective of the Cranked-Arrow Wing Aerodynamics Project International (CAWAPI) was to allow a comprehensive validation of Computational Fluid Dynamics methods against the CAWAP flight database. A major part of this work involved the generation of high-quality computational grids. Prior to the grid generation an IGES file containing the air-tight geometry of the F-16XL aircraft was generated by a cooperation of the CAWAPI partners. Based on this geometry description both structured and unstructured grids have been generated. The baseline structured (multi-block) grid (and a family of derived grids) has been generated by the National Aerospace Laboratory NLR. Although the algorithms used by NLR had become available just before CAWAPI and thus only a limited experience with their application to such a complex configuration had been gained, a grid of good quality was generated well within four weeks. This time compared favourably with that required to produce the unstructured grids in CAWAPI. The baseline all-tetrahedral and hybrid unstructured grids has been generated at NASA Langley Research Center and the USAFA, respectively. To provide more geometrical resolution, trimmed unstructured grids have been generated at EADS-MAS, the UTSimCenter, Boeing Phantom Works and KTH/FOI. All grids generated within the framework of CAWAPI will be discussed in the article. Both results obtained on the structured grids and the unstructured grids showed a significant improvement in agreement with flight test data in comparison with those obtained on the structured multi-block grid used during CAWAP.
NASA Astrophysics Data System (ADS)
Galanis, George; Famelis, Ioannis; Kalogeri, Christina
2014-10-01
The last years a new highly demanding framework has been set for environmental sciences and applied mathematics as a result of the needs posed by issues that are of interest not only of the scientific community but of today's society in general: global warming, renewable resources of energy, natural hazards can be listed among them. Two are the main directions that the research community follows today in order to address the above problems: The utilization of environmental observations obtained from in situ or remote sensing sources and the meteorological-oceanographic simulations based on physical-mathematical models. In particular, trying to reach credible local forecasts the two previous data sources are combined by algorithms that are essentially based on optimization processes. The conventional approaches in this framework usually neglect the topological-geometrical properties of the space of the data under study by adopting least square methods based on classical Euclidean geometry tools. In the present work new optimization techniques are discussed making use of methodologies from a rapidly advancing branch of applied Mathematics, the Information Geometry. The latter prove that the distributions of data sets are elements of non-Euclidean structures in which the underlying geometry may differ significantly from the classical one. Geometrical entities like Riemannian metrics, distances, curvature and affine connections are utilized in order to define the optimum distributions fitting to the environmental data at specific areas and to form differential systems that describes the optimization procedures. The methodology proposed is clarified by an application for wind speed forecasts in the Kefaloniaisland, Greece.
NASA Technical Reports Server (NTRS)
Benyo, Theresa L.
2002-01-01
Integration of a supersonic inlet simulation with a computer aided design (CAD) system is demonstrated. The integration is performed using the Project Integration Architecture (PIA). PIA provides a common environment for wrapping many types of applications. Accessing geometry data from CAD files is accomplished by incorporating appropriate function calls from the Computational Analysis Programming Interface (CAPRI). CAPRI is a CAD vendor neutral programming interface that aids in acquiring geometry data directly from CAD files. The benefits of wrapping a supersonic inlet simulation into PIA using CAPRI are; direct access of geometry data, accurate capture of geometry data, automatic conversion of data units, CAD vendor neutral operation, and on-line interactive history capture. This paper describes the PIA and the CAPRI wrapper and details the supersonic inlet simulation demonstration.
Fractal geometry-based classification approach for the recognition of lung cancer cells
NASA Astrophysics Data System (ADS)
Xia, Deshen; Gao, Wenqing; Li, Hua
1994-05-01
This paper describes a new fractal geometry based classification approach for the recognition of lung cancer cells, which is used in the health inspection for lung cancers, because cancer cells grow much faster and more irregularly than normal cells do, the shape of the segmented cancer cells is very irregular and considered as a graph without characteristic length. We use Texture Energy Intensity Rn to do fractal preprocessing to segment the cells from the image and to calculate the fractal dimention value for extracting the fractal features, so that we can get the figure characteristics of different cancer cells and normal cells respectively. Fractal geometry gives us a correct description of cancer-cell shapes. Through this method, a good recognition of Adenoma, Squamous, and small cancer cells can be obtained.
Computational Approaches to Nucleic Acid Origami.
Jabbari, Hosna; Aminpour, Maral; Montemagno, Carlo
2015-10-12
Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms. PMID:26348196
An immersed boundary computational model for acoustic scattering problems with complex geometries.
Sun, Xiaofeng; Jiang, Yongsong; Liang, An; Jing, Xiaodong
2012-11-01
An immersed boundary computational model is presented in order to deal with the acoustic scattering problem by complex geometries, in which the wall boundary condition is treated as a direct body force determined by satisfying the non-penetrating boundary condition. Two distinct discretized grids are used to discrete the fluid domain and immersed boundary, respectively. The immersed boundaries are represented by Lagrangian points and the direct body force determined on these points is applied on the neighboring Eulerian points. The coupling between the Lagrangian points and Euler points is linked by a discrete delta function. The linearized Euler equations are spatially discretized with a fourth-order dispersion-relation-preserving scheme and temporal integrated with a low-dissipation and low-dispersion Runge-Kutta scheme. A perfectly matched layer technique is applied to absorb out-going waves and in-going waves in the immersed bodies. Several benchmark problems for computational aeroacoustic solvers are performed to validate the present method. PMID:23145603
Hankemeier, S; Gosling, T; Richter, M; Hufner, T; Hochhausen, C; Krettek, C
2006-03-01
Exact radiographic evaluation of lower limb alignment, joint orientation and leg length is crucial for preoperative planning and successful treatment of deformities, fractures and osteoarthritis. Improvement of the accuracy of radiographic measurements is highly desirable. To determine the intraobserver reliability of conventional analysis of lower extremity geometry, 59 long leg radiographs were randomly analyzed 5 times by a single surgeon. The measurements revealed a standard deviation between 0.36 degrees and 1.17 degrees for the angles mLPFA, mLDFA, MPTA, LDTA, JLCA and AMA (nomenclature according to Paley), and 0.94 mm and 0.90 mm for the MAD and leg length, respectively. Computer-assisted analysis with a special software significantly reduced the standard deviation of the mLDFA, MPTA, LDTA, JLCA (each p < 0.001), AMA (p = 0.032) and MAD (p = 0.023) by 0.05-0.36 degrees and 0.14 mm, respectively. Measuring time was reduced by 44% to 6:34 +/- 0:45 min (p < 0.001). Digital calibration by the software revealed an average magnification of conventional long leg radiographs of 4.6 +/- 1.8% (range: 2.7-11.9%). Computer-assisted analysis increases the intraobserver reliability and reduces the time needed for the analysis. Another major benefit is the ease of storage and transfer of digitized images. Due to the varying magnification factors on long leg radiographs, the use of magnification markers for calibration is recommended. PMID:16782643
A Combined Geometric Approach for Computational Fluid Dynamics on Dynamic Grids
NASA Technical Reports Server (NTRS)
Slater, John W.
1995-01-01
A combined geometric approach for computational fluid dynamics is presented for the analysis of unsteady flow about mechanisms in which its components are in moderate relative motion. For a CFD analysis, the total dynamics problem involves the dynamics of the aspects of geometry modeling, grid generation, and flow modeling. The interrelationships between these three aspects allow for a more natural formulation of the problem and the sharing of information which can be advantageous to the computation of the dynamics. The approach is applied to planar geometries with the use of an efficient multi-block, structured grid generation method to compute unsteady, two-dimensional and axisymmetric flow. The applications presented include the computation of the unsteady, inviscid flow about a hinged-flap with flap deflections and a high-speed inlet with centerbody motion as part of the unstart / restart operation.
ERIC Educational Resources Information Center
Lin, John Jr-Hung; Lin, Sunny S. J.
2014-01-01
The present study investigated (a) whether the perceived cognitive load was different when geometry problems with various levels of configuration comprehension were solved and (b) whether eye movements in comprehending geometry problems showed sources of cognitive loads. In the first investigation, three characteristics of geometry configurations…
Boccaccio, Antonio; Uva, Antonio Emmanuele; Fiorentino, Michele; Mori, Giorgio; Monno, Giuseppe
2016-01-01
Functionally Graded Scaffolds (FGSs) are porous biomaterials where porosity changes in space with a specific gradient. In spite of their wide use in bone tissue engineering, possible models that relate the scaffold gradient to the mechanical and biological requirements for the regeneration of the bony tissue are currently missing. In this study we attempt to bridge the gap by developing a mechanobiology-based optimization algorithm aimed to determine the optimal graded porosity distribution in FGSs. The algorithm combines the parametric finite element model of a FGS, a computational mechano-regulation model and a numerical optimization routine. For assigned boundary and loading conditions, the algorithm builds iteratively different scaffold geometry configurations with different porosity distributions until the best microstructure geometry is reached, i.e. the geometry that allows the amount of bone formation to be maximized. We tested different porosity distribution laws, loading conditions and scaffold Young’s modulus values. For each combination of these variables, the explicit equation of the porosity distribution law–i.e the law that describes the pore dimensions in function of the spatial coordinates–was determined that allows the highest amounts of bone to be generated. The results show that the loading conditions affect significantly the optimal porosity distribution. For a pure compression loading, it was found that the pore dimensions are almost constant throughout the entire scaffold and using a FGS allows the formation of amounts of bone slightly larger than those obtainable with a homogeneous porosity scaffold. For a pure shear loading, instead, FGSs allow to significantly increase the bone formation compared to a homogeneous porosity scaffolds. Although experimental data is still necessary to properly relate the mechanical/biological environment to the scaffold microstructure, this model represents an important step towards optimizing geometry
Influence of aquifer geometry on karst hydraulics using different distributive modeling approaches
NASA Astrophysics Data System (ADS)
Oehlmann, Sandra; Geyer, Tobias; Licha, Tobias; Birk, Steffen
2013-04-01
The simulation of flow and transport processes in karst systems is a challenge due to the unknown location of highly conductive karst conduit networks. In this work, the influence of aquifer geometry, particularly the geometry of highly conductive discrete elements, on three-dimensional groundwater flow in a large-scale aquifer system is examined. The area of investigation comprises several springs on the Western Swabian Alb / Germany and has an area of approximately 150 km2. The largest spring therein is the Gallusquelle with an annual average discharge of 0.5 m3/s. Long-term spring hydrographs and hydraulic head measurements, as well as several tracer tests, are available from previous work and are used for model calibration. Four distributive continuum and discrete flow models with different degrees of complexity were set-up employing the finite element simulation software Comsol Multiphysics®. Stationary groundwater flow equations were implemented for single continuum and hybrid modeling. The aquifer geometry was modeled previously with the software Geological Objects Computer Aided Design® (GoCAD®) and transferred to Comsol® software. Simulation results show that not only the location of karst conduits but also their geometry has significant impact on the simulated spring discharge and hydraulic head distribution. A constant conduit radius leads to distorted hydraulic head contour lines and a conduit restrained flow regime close to the spring, while a linearly increasing radius towards the spring leads to evenly distributed contour lines. Models with such an increase in conduit diameters allow the simulation of annual discharge for several springs. This result is in agreement with synthetic karst genesis models, which suggest an increase of conduit diameters towards karst springs because of a positive correlation between flow rates and carbonate solution. The software Comsol Multiphysics®, while rarely used for groundwater flow modeling, was found to meet
High performance parallel computing of flows in complex geometries: II. Applications
NASA Astrophysics Data System (ADS)
Gourdain, N.; Gicquel, L.; Staffelbach, G.; Vermorel, O.; Duchaine, F.; Boussuge, J.-F.; Poinsot, T.
2009-01-01
Present regulations in terms of pollutant emissions, noise and economical constraints, require new approaches and designs in the fields of energy supply and transportation. It is now well established that the next breakthrough will come from a better understanding of unsteady flow effects and by considering the entire system and not only isolated components. However, these aspects are still not well taken into account by the numerical approaches or understood whatever the design stage considered. The main challenge is essentially due to the computational requirements inferred by such complex systems if it is to be simulated by use of supercomputers. This paper shows how new challenges can be addressed by using parallel computing platforms for distinct elements of a more complex systems as encountered in aeronautical applications. Based on numerical simulations performed with modern aerodynamic and reactive flow solvers, this work underlines the interest of high-performance computing for solving flow in complex industrial configurations such as aircrafts, combustion chambers and turbomachines. Performance indicators related to parallel computing efficiency are presented, showing that establishing fair criterions is a difficult task for complex industrial applications. Examples of numerical simulations performed in industrial systems are also described with a particular interest for the computational time and the potential design improvements obtained with high-fidelity and multi-physics computing methods. These simulations use either unsteady Reynolds-averaged Navier-Stokes methods or large eddy simulation and deal with turbulent unsteady flows, such as coupled flow phenomena (thermo-acoustic instabilities, buffet, etc). Some examples of the difficulties with grid generation and data analysis are also presented when dealing with these complex industrial applications.
Introducing Computational Approaches in Intermediate Mechanics
NASA Astrophysics Data System (ADS)
Cook, David M.
2006-12-01
In the winter of 2003, we at Lawrence University moved Lagrangian mechanics and rigid body dynamics from a required sophomore course to an elective junior/senior course, freeing 40% of the time for computational approaches to ordinary differential equations (trajectory problems, the large amplitude pendulum, non-linear dynamics); evaluation of integrals (finding centers of mass and moment of inertia tensors, calculating gravitational potentials for various sources); and finding eigenvalues and eigenvectors of matrices (diagonalizing the moment of inertia tensor, finding principal axes), and to generating graphical displays of computed results. Further, students begin to use LaTeX to prepare some of their submitted problem solutions. Placed in the middle of the sophomore year, this course provides the background that permits faculty members as appropriate to assign computer-based exercises in subsequent courses. Further, students are encouraged to use our Computational Physics Laboratory on their own initiative whenever that use seems appropriate. (Curricular development supported in part by the W. M. Keck Foundation, the National Science Foundation, and Lawrence University.)
Computer Forensics Education - the Open Source Approach
NASA Astrophysics Data System (ADS)
Huebner, Ewa; Bem, Derek; Cheung, Hon
In this chapter we discuss the application of the open source software tools in computer forensics education at tertiary level. We argue that open source tools are more suitable than commercial tools, as they provide the opportunity for students to gain in-depth understanding and appreciation of the computer forensic process as opposed to familiarity with one software product, however complex and multi-functional. With the access to all source programs the students become more than just the consumers of the tools as future forensic investigators. They can also examine the code, understand the relationship between the binary images and relevant data structures, and in the process gain necessary background to become the future creators of new and improved forensic software tools. As a case study we present an advanced subject, Computer Forensics Workshop, which we designed for the Bachelor's degree in computer science at the University of Western Sydney. We based all laboratory work and the main take-home project in this subject on open source software tools. We found that without exception more than one suitable tool can be found to cover each topic in the curriculum adequately. We argue that this approach prepares students better for forensic field work, as they gain confidence to use a variety of tools, not just a single product they are familiar with.
Computational Approaches for Predicting Biomedical Research Collaborations
Zhang, Qing; Yu, Hong
2014-01-01
Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at https://github.com/qingzhanggithub/medline-collaboration-datasets. PMID:25375164
Predicting microbial interactions through computational approaches.
Li, Chenhao; Lim, Kun Ming Kenneth; Chng, Kern Rei; Nagarajan, Niranjan
2016-06-01
Microorganisms play a vital role in various ecosystems and characterizing interactions between them is an essential step towards understanding the organization and function of microbial communities. Computational prediction has recently become a widely used approach to investigate microbial interactions. We provide a thorough review of emerging computational methods organized by the type of data they employ. We highlight three major challenges in inferring interactions using metagenomic survey data and discuss the underlying assumptions and mathematics of interaction inference algorithms. In addition, we review interaction prediction methods relying on metabolic pathways, which are increasingly used to reveal mechanisms of interactions. Furthermore, we also emphasize the importance of mining the scientific literature for microbial interactions - a largely overlooked data source for experimentally validated interactions. PMID:27025964
Sculpting the band gap: a computational approach.
Prasai, Kiran; Biswas, Parthapratim; Drabold, D A
2015-01-01
Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations. PMID:26490203
Sculpting the band gap: a computational approach
Prasai, Kiran; Biswas, Parthapratim; Drabold, D. A.
2015-01-01
Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations. PMID:26490203
Computational modeling approaches in gonadotropin signaling.
Ayoub, Mohammed Akli; Yvinec, Romain; Crépieux, Pascale; Poupon, Anne
2016-07-01
Follicle-stimulating hormone and LH play essential roles in animal reproduction. They exert their function through binding to their cognate receptors, which belong to the large family of G protein-coupled receptors. This recognition at the plasma membrane triggers a plethora of cellular events, whose processing and integration ultimately lead to an adapted biological response. Understanding the nature and the kinetics of these events is essential for innovative approaches in drug discovery. The study and manipulation of such complex systems requires the use of computational modeling approaches combined with robust in vitro functional assays for calibration and validation. Modeling brings a detailed understanding of the system and can also be used to understand why existing drugs do not work as well as expected, and how to design more efficient ones. PMID:27165991
Computational approaches for predicting mutant protein stability.
Kulshreshtha, Shweta; Chaudhary, Vigi; Goswami, Girish K; Mathur, Nidhi
2016-05-01
Mutations in the protein affect not only the structure of protein, but also its function and stability. Prediction of mutant protein stability with accuracy is desired for uncovering the molecular aspects of diseases and design of novel proteins. Many advanced computational approaches have been developed over the years, to predict the stability and function of a mutated protein. These approaches based on structure, sequence features and combined features (both structure and sequence features) provide reasonably accurate estimation of the impact of amino acid substitution on stability and function of protein. Recently, consensus tools have been developed by incorporating many tools together, which provide single window results for comparison purpose. In this review, a useful guide for the selection of tools that can be employed in predicting mutated proteins' stability and disease causing capability is provided. PMID:27160393
NASA Astrophysics Data System (ADS)
Zhang, L.; Eskin, D. G.; Miroux, A.; Subroto, T.; Katgerman, L.
2012-07-01
Controlling macrosegregation is one of the major challenges in direct-chill (DC) casting of aluminium alloys. In this paper, the effect of the inlet geometry (which influences the melt distribution) on macrosegregation during the DC casting of 7050 alloy billets was studied experimentally and by using 2D computer modelling. The ALSIM model was used to determine the temperature and flow patterns during DC casting. The results from the computer simulations show that the sump profiles and flow patterns in the billet are strongly influenced by the melt flow distribution determined by the inlet geometry. These observations were correlated to the actual macrosegregation patterns found in the as-cast billets produced by having two different inlet geometries. The macrosegregation analysis presented here may assist in determining the critical parameters to consider for improving the casting of 7XXX aluminium alloys.
Geometry, analysis, and computation in mathematics and applied sciences. Final report
Kusner, R.B.; Hoffman, D.A.; Norman, P.; Pedit, F.; Whitaker, N.; Oliver, D.
1995-12-31
Since 1993, the GANG laboratory has been co-directed by David Hoffman, Rob Kusner and Peter Norman. A great deal of mathematical research has been carried out here by them and by GANG faculty members Franz Pedit and Nate Whitaker. Also new communication tools, such as the GANG Webserver have been developed. GANG has trained and supported nearly a dozen graduate students, and at least half as many undergrads in REU projects.The GANG Seminar continues to thrive, making Amherst a site for short and long term visitors to come to work with the GANG. Some of the highlights of recent or ongoing research at GANG include: CMC surfaces, minimal surfaces, fluid dynamics, harmonic maps, isometric immersions, knot energies, foam structures, high dimensional soap film singularities, elastic curves and surfaces, self-similar curvature evolution, integrable systems and theta functions, fully nonlinear geometric PDE, geometric chemistry and biology. This report is divided into the following sections: (1) geometric variational problems; (2) soliton geometry; (3) embedded minimal surfaces; (4) numerical fluid dynamics and mathematical modeling; (5) GANG graphics and mathematical software; (6) description of the computational and visual analysis facility; and (7) research by undergraduates and GANG graduate seminar.
ERIC Educational Resources Information Center
Sinclair, Margaret P.
2005-01-01
A case study, originally set up to identify and describe some benefits and limitations of using dynamic web-based geometry sketches, provided an opportunity to examine peer interactions in a lab. Since classes were held in a computer lab, teachers and pairs faced the challenges of working and communicating in a lab environment. Research has shown…
ERIC Educational Resources Information Center
Papadopoulos, Ioannis; Dagdilelis, Vassilios
2006-01-01
In this paper, difficulties of students in the case of computer-mediated teaching of geometry in a traditional classroom are considered within the framework of "transactional distance", a concept well known in distance education. The main interest of this paper is to record and describe in detail the different forms of "distance" during students'…
ERIC Educational Resources Information Center
Cihak, David F.; Bowlin, Tammy
2009-01-01
The researchers examined the use of video modeling by means of a handheld computer as an alternative instructional delivery system for learning basic geometry skills. Three high school students with learning disabilities participated in this study. Through video modeling, teacher-developed video clips showing step-by-step problem solving processes…
Computational approaches to motor learning by imitation.
Schaal, Stefan; Ijspeert, Auke; Billard, Aude
2003-01-01
Movement imitation requires a complex set of mechanisms that map an observed movement of a teacher onto one's own movement apparatus. Relevant problems include movement recognition, pose estimation, pose tracking, body correspondence, coordinate transformation from external to egocentric space, matching of observed against previously learned movement, resolution of redundant degrees-of-freedom that are unconstrained by the observation, suitable movement representations for imitation, modularization of motor control, etc. All of these topics by themselves are active research problems in computational and neurobiological sciences, such that their combination into a complete imitation system remains a daunting undertaking-indeed, one could argue that we need to understand the complete perception-action loop. As a strategy to untangle the complexity of imitation, this paper will examine imitation purely from a computational point of view, i.e. we will review statistical and mathematical approaches that have been suggested for tackling parts of the imitation problem, and discuss their merits, disadvantages and underlying principles. Given the focus on action recognition of other contributions in this special issue, this paper will primarily emphasize the motor side of imitation, assuming that a perceptual system has already identified important features of a demonstrated movement and created their corresponding spatial information. Based on the formalization of motor control in terms of control policies and their associated performance criteria, useful taxonomies of imitation learning can be generated that clarify different approaches and future research directions. PMID:12689379
Computational Flow Modeling of a Simplified Integrated Tractor-Trailer Geometry
Salari, K; McWherter-Payne, M
2003-09-15
For several years, Sandia National Laboratories and Lawrence Livermore National Laboratory have been part of a consortium funded by the Department of Energy to improve fuel efficiency of heavy vehicles such as Class 8 trucks through aerodynamic drag reduction. The objective of this work is to demonstrate the feasibility of using the steady Reynolds-Averaged Navier-Stokes (RANS) approach to predict the flow field around heavy vehicles, with special emphasis on the base region of the trailer, and to compute the aerodynamic forces. In particular, Sandia's computational fluid dynamics code, SACCARA, was used to simulate the flow on a simplified model of a tractor-trailer vehicle. The results are presented and compared with NASA Ames experimental data to assess the predictive capability of RANS to model the flow field and predict the aerodynamic forces.
Computational flow modeling of a simplified integrated tractor-trailer geometry.
McWherter-Payne, Mary Anna; Salari, Kambiz
2003-09-01
For several years, Sandia National Laboratories and Lawrence Livermore National Laboratory have been part of a consortium funded by the Department of Energy to improve fuel efficiency of heavy vehicles such as Class 8 trucks through aerodynamic drag reduction. The objective of this work is to demonstrate the feasibility of using the steady Reynolds-Averaged Navier-Stokes (RANS) approach to predict the flow field around heavy vehicles, with special emphasis on the base region of the trailer, and to compute the aerodynamic forces. In particular, Sandia's computational fluid dynamics code, SACCARA, was used to simulate the flow on a simplified model of a tractor-trailer vehicle. The results are presented and compared with NASA Ames experimental data to assess the predictive capability of RANS to model the flow field and predict the aerodynamic forces.
A Parametric Geometry Computational Fluid Dynamics (CFD) Study Utilizing Design of Experiments (DOE)
NASA Technical Reports Server (NTRS)
Rhew, Ray D.; Parker, Peter A.
2007-01-01
Design of Experiments (DOE) was applied to the LAS geometric parameter study to efficiently identify and rank primary contributors to integrated drag over the vehicles ascent trajectory in an order of magnitude fewer CFD configurations thereby reducing computational resources and solution time. SME s were able to gain a better understanding on the underlying flowphysics of different geometric parameter configurations through the identification of interaction effects. An interaction effect, which describes how the effect of one factor changes with respect to the levels of other factors, is often the key to product optimization. A DOE approach emphasizes a sequential approach to learning through successive experimentation to continuously build on previous knowledge. These studies represent a starting point for expanded experimental activities that will eventually cover the entire design space of the vehicle and flight trajectory.
Effect of ocular shape and vascular geometry on retinal hemodynamics: a computational model.
Dziubek, Andrea; Guidoboni, Giovanna; Harris, Alon; Hirani, Anil N; Rusjan, Edmond; Thistleton, William
2016-08-01
A computational model for retinal hemodynamics accounting for ocular curvature is presented. The model combines (i) a hierarchical Darcy model for the flow through small arterioles, capillaries and small venules in the retinal tissue, where blood vessels of different size are comprised in different hierarchical levels of a porous medium; and (ii) a one-dimensional network model for the blood flow through retinal arterioles and venules of larger size. The non-planar ocular shape is included by (i) defining the hierarchical Darcy flow model on a two-dimensional curved surface embedded in the three-dimensional space; and (ii) mapping the simplified one-dimensional network model onto the curved surface. The model is solved numerically using a finite element method in which spatial domain and hierarchical levels are discretized separately. For the finite element method, we use an exterior calculus-based implementation which permits an easier treatment of non-planar domains. Numerical solutions are verified against suitably constructed analytical solutions. Numerical experiments are performed to investigate how retinal hemodynamics is influenced by the ocular shape (sphere, oblate spheroid, prolate spheroid and barrel are compared) and vascular architecture (four vascular arcs and a branching vascular tree are compared). The model predictions show that changes in ocular shape induce non-uniform alterations of blood pressure and velocity in the retina. In particular, we found that (i) the temporal region is affected the least by changes in ocular shape, and (ii) the barrel shape departs the most from the hemispherical reference geometry in terms of associated pressure and velocity distributions in the retinal microvasculature. These results support the clinical hypothesis that alterations in ocular shape, such as those occurring in myopic eyes, might be associated with pathological alterations in retinal hemodynamics. PMID:26445874
A computational approach to negative priming
NASA Astrophysics Data System (ADS)
Schrobsdorff, H.; Ihrke, M.; Kabisch, B.; Behrendt, J.; Hasselhorn, M.; Herrmann, J. Michael
2007-09-01
Priming is characterized by a sensitivity of reaction times to the sequence of stimuli in psychophysical experiments. The reduction of the reaction time observed in positive priming is well-known and experimentally understood (Scarborough et al., J. Exp. Psycholol: Hum. Percept. Perform., 3, pp. 1-17, 1977). Negative priming—the opposite effect—is experimentally less tangible (Fox, Psychonom. Bull. Rev., 2, pp. 145-173, 1995). The dependence on subtle parameter changes (such as response-stimulus interval) usually varies. The sensitivity of the negative priming effect bears great potential for applications in research in fields such as memory, selective attention, and ageing effects. We develop and analyse a computational realization, CISAM, of a recent psychological model for action decision making, the ISAM (Kabisch, PhD thesis, Friedrich-Schiller-Universitat, 2003), which is sensitive to priming conditions. With the dynamical systems approach of the CISAM, we show that a single adaptive threshold mechanism is sufficient to explain both positive and negative priming effects. This is achieved by comparing results obtained by the computational modelling with experimental data from our laboratory. The implementation provides a rich base from which testable predictions can be derived, e.g. with respect to hitherto untested stimulus combinations (e.g. single-object trials).
Duanmu, Kaining; Truhlar, Donald G.
2015-04-30
We report a systematic study of small silver clusters, Agn, Agn+, and Agn–, n = 1–7. We studied all possible isomers of clusters with n = 5–7. We tested 42 exchange–correlation functionals, and we assess these functionals for their accuracy in three respects: geometries (quantitative prediction of internuclear distances), structures (the nature of the lowest-energy structure, for example, whether it is planar or nonplanar), and energies. We find that the ingredients of exchange–correlation functionals are indicators of their success in predicting geometries and structures: local exchange–correlation functionals are generally better than hybrid functionals for geometries; functionals depending on kinetic energy density are the best for predicting the lowest-energy isomer correctly, especially for predicting two-dimensional to three-dimenstional transitions correctly. The accuracy for energies is less sensitive to the ingredient list. Our findings could be useful for guiding the selection of methods for computational catalyst design.
Rutkowski, Tomasz M
2016-07-01
A novel multimodal and bio-inspired approach to biomedical signal processing and classification is presented in the paper. This approach allows for an automatic semantic labeling (interpretation) of sleep apnea events based the proposed data-driven biomedical signal processing and classification. The presented signal processing and classification methods have been already successfully applied to real-time unimodal brainwaves (EEG only) decoding in brain-computer interfaces developed by the author. In the current project the very encouraging results are obtained using multimodal biomedical (brainwaves and peripheral physiological) signals in a unified processing approach allowing for the automatic semantic data description. The results thus support a hypothesis of the data-driven and bio-inspired signal processing approach validity for medical data semantic interpretation based on the sleep apnea events machine-learning-related classification. PMID:27194241
Computations of Viscous Flows in Complex Geometries Using Multiblock Grid Systems
NASA Technical Reports Server (NTRS)
Steinthorsson, Erlendur; Ameri, Ali A.
1995-01-01
Generating high quality, structured, continuous, body-fitted grid systems (multiblock grid systems) for complicated geometries has long been a most labor-intensive and frustrating part of simulating flows in complicated geometries. Recently, new methodologies and software have emerged that greatly reduce the human effort required to generate high quality multiblock grid systems for complicated geometries. These methods and software require minimal input form the user-typically, only information about the topology of the block structure and number of grid points. This paper demonstrates the use of the new breed of multiblock grid systems in simulations of internal flows in complicated geometries. The geometry used in this study is a duct with a sudden expansion, a partition, and an array of cylindrical pins. This geometry has many of the features typical of internal coolant passages in turbine blades. The grid system used in this study was generated using a commercially available grid generator. The simulations were done using a recently developed flow solver, TRAF3D.MB, that was specially designed to use multiblock grid systems.
Shapiro, A.B.
1983-08-01
The computer code FACET calculates the radiation geometric view factor (alternatively called shape factor, angle factor, or configuration factor) between surfaces for axisymmetric, two-dimensional planar and three-dimensional geometries with interposed third surface obstructions. FACET was developed to calculate view factors for input to finite-element heat-transfer analysis codes. The first section of this report is a brief review of previous radiation-view-factor computer codes. The second section presents the defining integral equation for the geometric view factor between two surfaces and the assumptions made in its derivation. Also in this section are the numerical algorithms used to integrate this equation for the various geometries. The third section presents the algorithms used to detect self-shadowing and third-surface shadowing between the two surfaces for which a view factor is being calculated. The fourth section provides a user's input guide followed by several example problems.
Parallel methods for the computation of unsteady separated flows around complex geometries
NASA Astrophysics Data System (ADS)
Souliez, Frederic Jean
A numerical investigation of separated flows is made using unstructured meshes around complex geometries. The flow data in the wake of a 60-degree vertex angle cone are analyzed for various versions of our finite volume solver, including a generic version without turbulence model, and a Large Eddy Simulation model with different sub-grid scale constant values. While the primary emphasis is on the comparison of the results against experimental data, the solution is also used as a benchmark tool for an aeroacoustic post-processing utility combined with the Ffowcs Williams-Hawkings (FW-H) equation. A concurrent study is performed of the flow around two 4-wheel landing gear models, with the difference residing in the addition of two additional support struts. These unsteady calculations are used to provide aerodynamic and aeroacoustic data. The impact of the two configurations on the forces as well as on the acoustic near- and far-field is evaluated with the help of the above-mentioned aeroacoustic program. For both the cone and landing gear runs, parallel versions of the flow solver and of the FW-H utility are used via the implementation of the Message Passing Interface (MPI) library, resulting in very good scaling performance. The speed-up results for these cases are described for different platforms including inexpensive Beowulf-class clusters, which are the computing workhorse for the present numerical investigation. Furthermore, the analysis of the flow around a Bell 214 Super Transport (ST) fuselage is presented. A mesh sensitivity analysis is compared against experimental and numerical results collected by the helicopter manufacturer. Parameters such as surface pressure coefficient, lift and drag are evaluated resulting from both steady-state and time-accurate simulations. Various flight conditions are tested, with a slightly negative angle of attack, a large positive angle of attack and a positive yaw angle, all of which resulting in massive flow separation
Geometry acquisition and grid generation: Recent experiences with complex aircraft configurations
NASA Technical Reports Server (NTRS)
Gatzke, Timothy D.; Labozzetta, Walter F.; Cooley, John W.; Finfrock, Gregory P.
1992-01-01
Important issues involved in working with complex geometries are discussed. Approaches taken to address complex geometry issues in the McDonnell Aircraft Computational Grid System and related geometry processing tools are discussed. The efficiency of acquiring a suitable geometry definition, the need to manipulate the geometry, and the time and skill level required to generate the grid while preserving geometric fidelity are discussed.
Barone, Vincenzo; Bloino, Julien; Biczysko, Malgorzata; Santoro, Fabrizio
2009-03-10
A general and effective time-independent approach to compute vibrationally resolved electronic spectra from first principles has been integrated into the Gaussian computational chemistry package. This computational tool offers a simple and easy-to-use way to compute theoretical spectra starting from geometry optimization and frequency calculations for each electronic state. It is shown that in such a way it is straightforward to combine calculation of Franck-Condon integrals with any electronic computational model. The given examples illustrate the calculation of absorption and emission spectra, all in the UV-vis region, of various systems from small molecules to large ones, in gas as well as in condensed phases. The computational models applied range from fully quantum mechanical descriptions to discrete/continuum quantum mechanical/molecular mechanical/polarizable continuum models. PMID:26610221
A geometric calibration method for inverse geometry computed tomography using P-matrices
NASA Astrophysics Data System (ADS)
Slagowski, Jordan M.; Dunkerley, David A. P.; Hatt, Charles R.; Speidel, Michael A.
2016-03-01
Accurate and artifact free reconstruction of tomographic images requires precise knowledge of the imaging system geometry. This work proposes a novel projection matrix (P-matrix) based calibration method to enable C-arm inverse geometry CT (IGCT). The method is evaluated for scanning-beam digital x-ray (SBDX), a C-arm mounted inverse geometry fluoroscopic technology. A helical configuration of fiducials is imaged at each gantry angle in a rotational acquisition. For each gantry angle, digital tomosynthesis is performed at multiple planes and a composite image analogous to a cone-beam projection is generated from the plane stack. The geometry of the C-arm, source array, and detector array is determined at each angle by constructing a parameterized 3D-to-2D projection matrix that minimizes the sum-of-squared deviations between measured and projected fiducial coordinates. Simulations were used to evaluate calibration performance with translations and rotations of the source and detector. In a geometry with 1 mm translation of the central ray relative to the axis-of-rotation and 1 degree yaw of the detector and source arrays, the maximum error in the recovered translational parameters was 0.4 mm and maximum error in the rotation parameter was 0.02 degrees. The relative rootmean- square error in a reconstruction of a numerical thorax phantom was 0.4% using the calibration method, versus 7.7% without calibration. Changes in source-detector-distance were the most challenging to estimate. Reconstruction of experimental SBDX data using the proposed method eliminated double contour artifacts present in a non-calibrated reconstruction. The proposed IGCT geometric calibration method reduces image artifacts when uncertainties exist in system geometry.
Along-strike complex geometry of subduction zones - an experimental approach
NASA Astrophysics Data System (ADS)
Midtkandal, I.; Gabrielsen, R. H.; Brun, J.-P.; Huismans, R.
2012-04-01
Recent knowledge of the great geometric and dynamic complexity insubduction zones, combined with new capacity for analogue mechanical and numerical modeling has sparked a number of studies on subduction processes. Not unexpectedly, such models reveal a complex relation between physical conditions during subduction initiation, strength profile of the subducting plate, the thermo-dynamic conditions and the subduction zones geometries. One rare geometrical complexity of subduction that remains particularly controversial, is the potential for polarity shift in subduction systems. The present experiments were therefore performed to explore the influence of the architecture, strength and strain velocity on complexities in subduction zones, focusing on along-strike variation of the collision zone. Of particular concern were the consequences for the geometry and kinematics of the transition zones between segments of contrasting subduction direction. Although the model design to some extent was inspired by the configuration along the Iberian - Eurasian suture zone, the results are also of significance for other orogens with complex along-strike geometries. The experiments were set up to explore the initial state of subduction only, and were accordingly terminated before slab subduction occurred. The model wasbuilt from layers of silicone putty and sand, tailored to simulate the assumed lithospheric geometries and strength-viscosity profiles along the plate boundary zone prior to contraction, and comprises two 'continental' plates separated by a thinner 'oceanic' plate that represents the narrow seaway. The experiment floats on a substrate of sodiumpolytungstate, representing mantle. 24 experimental runs were performed, varying the thickness (and thus strength) of the upper mantle lithosphere, as well as the strain rate. Keeping all other parameters identical for each experiment, the models were shortened by a computer-controlled jackscrew while time-lapse images were
Computer-aided three-dimensional analysis of the small-geometry effects of a MOSFET
Hsueh, K.L.K.
1987-01-01
The 3-D effects of a small-geometry MOSFET can only be analyzed accurately by using a 3-D simulator. A 3-D MOSFET simulator, called MICROMOS, therefore, was developed for this purpose. The history of numerical analysis used to simulate semiconductor devices was reviewed. Numerical methods, their mathematical background, and the iteration techniques commonly used in the semiconductor simulation are also discussed. The three-dimensional graphic results of the numerical analysis give valuable information for the understanding the physics of the small-geometry effects in a VLSI MOSFET. A mutual modulation of the depletion depth underneath the gate is described. This leads to an accurate 3-D analytical model for the prediction of the threshold voltage of a small-geometry MOSFET with a fully-recessed isolation oxide structure. Also, there is a mutual modulation between the transverse electric field and its two perpendicular components. This modulation was proven to be the source of the small-geometry effects of a small-size MOSFET. The enhanced drain-induced barrier lowering (DIBL) due to the scaling of the device is also presented.
Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection.
Ding, Hong; Dwaraknath, Shyam S; Garten, Lauren; Ndione, Paul; Ginley, David; Persson, Kristin A
2016-05-25
With the ultimate goal of finding new polymorphs through targeted synthesis conditions and techniques, we outline a computational framework to select optimal substrates for epitaxial growth using first principle calculations of formation energies, elastic strain energy, and topological information. To demonstrate the approach, we study the stabilization of metastable VO2 compounds which provides a rich chemical and structural polymorph space. We find that common polymorph statistics, lattice matching, and energy above hull considerations recommends homostructural growth on TiO2 substrates, where the VO2 brookite phase would be preferentially grown on the a-c TiO2 brookite plane while the columbite and anatase structures favor the a-b plane on the respective TiO2 phases. Overall, we find that a model which incorporates a geometric unit cell area matching between the substrate and the target film as well as the resulting strain energy density of the film provide qualitative agreement with experimental observations for the heterostructural growth of known VO2 polymorphs: rutile, A and B phases. The minimal interfacial geometry matching and estimated strain energy criteria provide several suggestions for substrates and substrate-film orientations for the heterostructural growth of the hitherto hypothetical anatase, brookite, and columbite polymorphs. These criteria serve as a preliminary guidance for the experimental efforts stabilizing new materials and/or polymorphs through epitaxy. The current screening algorithm is being integrated within the Materials Project online framework and data and hence publicly available. PMID:27145398
Summers, M.F.; South, T.L.; Kim, B. ); Hare, D.R. )
1990-01-16
A new method is described for determining molecular structures from NMR data. The approach utilizes 2D NOESY back-calculations to generate simulated spectra for structures obtained from distance geometry (DG) computations. Comparison of experimental and back-calculated spectra, including analysis of cross-peak buildup and auto-peak decay with increasing mixing time, provides a quantitative measure of the consistence between the experimental data and generated structures and allows for use of tighter interproton distance constraints. For the first time, the goodness of the generated structures is evaluated on the basis of their consistence with the actual experimental data rather than on the basis of consistence with other generated structures. This method is applied to the structure determination of an 18-residue peptide with an amino acid sequence comprising the first zinc fingerlike domain from the gag protein p55 of HIV. This is the first structure determination to atomic resolution for a retroviral zinc fingerlike complex. The peptide (Zn(p55F1)) exhibits a novel folding pattern that includes type I and type II NH-S tight turns and is stabilized both by coordination of the three Cys and one His residues to zinc and by extensive internal hydrogen bonding. The backbone folding is significant different from that of a classical DNA-binding zinc finger. The side chains of conservatively substituted Phe and Ile residues implicated in genomic RNA recognition form a hydrophobic patch on the peptide surface.
CasimirSim - A Tool to Compute Casimir Polder Forces for Nontrivial 3D Geometries
Sedmik, Rene; Tajmar, Martin
2007-01-30
The so-called Casimir effect is one of the most interesting macro-quantum effects. Being negligible on the macro-scale it becomes a governing factor below structure sizes of 1 {mu}m where it accounts for typically 100 kN m-2. The force does not depend on gravity, or electric charge but solely on the materials properties, and geometrical shape. This makes the effect a strong candidate for micro(nano)-mechanical devices M(N)EMS. Despite a long history of research the theory lacks a uniform description valid for arbitrary geometries which retards technical application. We present an advanced state-of-the-art numerical tool overcoming all the usual geometrical restrictions, capable of calculating arbitrary 3D geometries by utilizing the Casimir Polder approximation for the Casimir force.
Dehbi, A.; Badreddine, H.
2012-07-01
In CFD simulations of flow mixing in a steam generator (SG) during natural circulation, one is faced with the problem of representing the thousands of SG U-tubes. Typically simplifications are made to render the problem computationally tractable. In particular, one or a number of tubes are lumped in one volume which is treated as a single porous medium. This approach dramatically reduces the computational size of the problem and hence simulation time. In this work, we endeavor to investigate the adequacy of this approach by performing two separate simulations of flow in a mock-up with 262 U-tubes, i.e. one in which the porous media model is used for the tube bundle, and another in which the full geometry is represented. In both simulations, the Reynolds Stress (RMS) model of turbulence is used. We show that in steady state conditions, the porous media treatment yields results which are comparable to those of the full geometry representation (temperature distribution, recirculation ratio, hot plume spread, etc). Hence, the porous media approach can be extended with a good degree of confidence to the full scale SG. (authors)
Computer-aided evaluation of the railway track geometry on the basis of satellite measurements
NASA Astrophysics Data System (ADS)
Specht, Cezary; Koc, Władysław; Chrostowski, Piotr
2016-05-01
In recent years, all over the world there has been a period of intensive development of GNSS (Global Navigation Satellite Systems) measurement techniques and their extension for the purpose of their applications in the field of surveying and navigation. Moreover, in many countries a rising trend in the development of rail transportation systems has been noticed. In this paper, a method of railway track geometry assessment based on mobile satellite measurements is presented. The paper shows the implementation effects of satellite surveying railway geometry. The investigation process described in the paper is divided on two phases. The first phase is the GNSS mobile surveying and the analysis obtained data. The second phase is the analysis of the track geometry using the flat coordinates from the surveying. The visualization of the measured route, separation and quality assessment of the uniform geometric elements (straight sections, arcs), identification of the track polygon (main directions and intersection angles) are discussed and illustrated by the calculation example within the article.
NASA Technical Reports Server (NTRS)
Hawke, Veronica; Gage, Peter; Manning, Ted
2007-01-01
ComGeom2, a tool developed to generate Common Geometry representation for multidisciplinary analysis, has been used to create a large set of geometries for use in a design study requiring analysis by two computational codes. This paper describes the process used to generate the large number of configurations and suggests ways to further automate the process and make it more efficient for future studies. The design geometry for this study is the launch abort system of the NASA Crew Launch Vehicle.
Alternative Computational Approaches for Probalistic Fatigue Analysis
NASA Technical Reports Server (NTRS)
Ebbeler, D. H.; Newlin, L. E.; Sutharshana, S.; Moore, N. R.; Grigoriu, M.
1995-01-01
The feasibility is discussed for alternative methods of direct Monte Carlo simulation for failure probability computations. First and second order reliability methods are used for fatigue crack growth and low cycle fatigue structural failure modes to illustrate typical problems.
ERIC Educational Resources Information Center
Schloff, Charles E.
The purpose of this study was to design a series of inservice seminars with teaching guides in geometry for fifth and sixth grade teachers in order to improve student competence in geometry. The guides stressed the use of a discovery approach. Twelve teachers and 293 children participated. Students took a pretest in geometry, the teachers attended…
ERIC Educational Resources Information Center
Gurevich, Irina; Gurev, Dvora
2012-01-01
In the current study we follow the development of the pedagogical procedure for the course "Constructions in Geometry" that resulted from using dynamic geometry software (DGS), where the computer became an integral part of the educational process. Furthermore, we examine the influence of integrating DGS into the course on students' achievement and…
GENIE - Generation of computational geometry-grids for internal-external flow configurations
NASA Technical Reports Server (NTRS)
Soni, B. K.
1988-01-01
Progress realized in the development of a master geometry-grid generation code GENIE is presented. The grid refinement process is enhanced by developing strategies to utilize bezier curves/surfaces and splines along with weighted transfinite interpolation technique and by formulating new forcing function for the elliptic solver based on the minimization of a non-orthogonality functional. A two step grid adaptation procedure is developed by optimally blending adaptive weightings with weighted transfinite interpolation technique. Examples of 2D-3D grids are provided to illustrate the success of these methods.
Computational dynamics for robotics systems using a non-strict computational approach
NASA Technical Reports Server (NTRS)
Orin, David E.; Wong, Ho-Cheung; Sadayappan, P.
1989-01-01
A Non-Strict computational approach for real-time robotics control computations is proposed. In contrast to the traditional approach to scheduling such computations, based strictly on task dependence relations, the proposed approach relaxes precedence constraints and scheduling is guided instead by the relative sensitivity of the outputs with respect to the various paths in the task graph. An example of the computation of the Inverse Dynamics of a simple inverted pendulum is used to demonstrate the reduction in effective computational latency through use of the Non-Strict approach. A speedup of 5 has been obtained when the processes of the task graph are scheduled to reduce the latency along the crucial path of the computation. While error is introduced by the relaxation of precedence constraints, the Non-Strict approach has a smaller error than the conventional Strict approach for a wide range of input conditions.
NASA Astrophysics Data System (ADS)
Chigullapalli, Sruti
Micro-electro-mechanical systems (MEMS) are widely used in automotive, communications and consumer electronics applications with microactuators, micro gyroscopes and microaccelerometers being just a few examples. However, in areas where high reliability is critical, such as in aerospace and defense applications, very few MEMS technologies have been adopted so far. Further development of high frequency microsystems such as resonators, RF MEMS, microturbines and pulsed-detonation microengines require improved understanding of unsteady gas dynamics at the micro scale. Accurate computational simulation of such flows demands new approaches beyond the conventional formulations based on the macroscopic constitutive laws. This is due to the breakdown of the continuum hypothesis in the presence of significant non-equilibrium and rarefaction because of large gradients and small scales, respectively. More generally, the motion of molecules in a gas is described by the kinetic Boltzmann equation which is valid for arbitrary Knudsen numbers. However, due to the multidimensionality of the phase space and the complex non-linearity of the collision term, numerical solution of the Boltzmann equation is challenging for practical problems. In this thesis a fully deterministic, as opposed to a statistical, finite volume based three-dimensional solution of Boltzmann ES-BGK model kinetic equation is formulated to enable simulations of unsteady rarefied flows. The main goal of this research is to develop an unsteady rarefied solver integrated with finite volume method (FVM) solver in MEMOSA (MEMS Overall Simulation Administrator) developed by PRISM: NNSA center for Prediction of Reliability, Integrity and Survivability of Microsystems (PRISM) at Purdue and apply it to study micro-scale gas damping. Formulation and verification of finite volume method for unsteady rarefied flow solver based on Boltzmann-ESBGK equations in arbitrary three-dimensional geometries are presented. The solver is
Human brain mapping: Experimental and computational approaches
Wood, C.C.; George, J.S.; Schmidt, D.M.; Aine, C.J.; Sanders, J.; Belliveau, J.
1998-11-01
This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). This program developed project combined Los Alamos' and collaborators' strengths in noninvasive brain imaging and high performance computing to develop potential contributions to the multi-agency Human Brain Project led by the National Institute of Mental Health. The experimental component of the project emphasized the optimization of spatial and temporal resolution of functional brain imaging by combining: (a) structural MRI measurements of brain anatomy; (b) functional MRI measurements of blood flow and oxygenation; and (c) MEG measurements of time-resolved neuronal population currents. The computational component of the project emphasized development of a high-resolution 3-D volumetric model of the brain based on anatomical MRI, in which structural and functional information from multiple imaging modalities can be integrated into a single computational framework for modeling, visualization, and database representation.
NASA Technical Reports Server (NTRS)
Lilley, D. G.; Rhode, D. L.
1982-01-01
A primitive pressure-velocity variable finite difference computer code was developed to predict swirling recirculating inert turbulent flows in axisymmetric combustors in general, and for application to a specific idealized combustion chamber with sudden or gradual expansion. The technique involves a staggered grid system for axial and radial velocities, a line relaxation procedure for efficient solution of the equations, a two-equation k-epsilon turbulence model, a stairstep boundary representation of the expansion flow, and realistic accommodation of swirl effects. A user's manual, dealing with the computational problem, showing how the mathematical basis and computational scheme may be translated into a computer program is presented. A flow chart, FORTRAN IV listing, notes about various subroutines and a user's guide are supplied as an aid to prospective users of the code.
Computed tomography in trauma: An atlas approach
Toombs, B.D.; Sandler, C.
1986-01-01
This book discussed computed tomography in trauma. The text is organized according to mechanism of injury and site of injury. In addition to CT, some correlation with other imaging modalities is included. Blunt trauma, penetrating trauma, complications and sequelae of trauma, and use of other modalities are covered.
An Approach to Developing Computer Catalogs
ERIC Educational Resources Information Center
MacDonald, Robin W.; Elrod, J. McRee
1973-01-01
A method of developing computer catalogs is proposed which does not require unit card conversion but rather the accumulation of data from operating programs. It is proposed that the bibliographic and finding functions of the catalog be separated, with the latter being the first automated. (8 references) (Author)
Designing Your Computer Curriculum: A Process Approach.
ERIC Educational Resources Information Center
Wepner, Shelley; Kramer, Steven
Four essential steps for integrating computer technology into a school districts' reading curriculum--needs assessment, planning, implementation, and evaluation--are described in terms of what educators can do at the district and building level to facilitate optimal instructional conditions for students. With regard to needs assessment,…
Reduced-Order Modeling: New Approaches for Computational Physics
NASA Technical Reports Server (NTRS)
Beran, Philip S.; Silva, Walter A.
2001-01-01
In this paper, we review the development of new reduced-order modeling techniques and discuss their applicability to various problems in computational physics. Emphasis is given to methods ba'sed on Volterra series representations and the proper orthogonal decomposition. Results are reported for different nonlinear systems to provide clear examples of the construction and use of reduced-order models, particularly in the multi-disciplinary field of computational aeroelasticity. Unsteady aerodynamic and aeroelastic behaviors of two- dimensional and three-dimensional geometries are described. Large increases in computational efficiency are obtained through the use of reduced-order models, thereby justifying the initial computational expense of constructing these models and inotivatim,- their use for multi-disciplinary design analysis.
Computational Analysis of an effect of aerodynamic pressure on the side view mirror geometry
NASA Astrophysics Data System (ADS)
Murukesavan, P.; Mu'tasim, M. A. N.; Sahat, I. M.
2013-12-01
This paper describes the evaluation of aerodynamic flow effects on side mirror geometry for a passenger car using ANSYS Fluent CFD simulation software. Results from analysis of pressure coefficient on side view mirror designs is evaluated to analyse the unsteady forces that cause fluctuations to mirror surface and image blurring. The fluctuation also causes drag forces that increase the overall drag coefficient, with an assumption resulting in higher fuel consumption and emission. Three features of side view mirror design were investigated with two input velocity parameters of 17 m/s and 33 m/s. Results indicate that the half-sphere design shows the most effective design with less pressure coefficient fluctuation and drag coefficient.
Elasticity and geometry: a computational model of the Heineke-Mikulicz strictureplasty.
Tsamis, Alkiviadis; Pocivavsek, Luka; Vorp, David A
2014-11-01
Crohn's disease is a challenging inflammatory process with a propensity for focal gastro-intestinal tract inflammation and stricture. Surgically, Crohn's is often treated with resection. However, a subtype of diffuse disease with multiple strictures is treated by strictureplasty procedures in hope of avoiding short-gut syndrome. Prior work by Pocivavsek et al. defined the geometry of a Heineke-Mikulicz strictureplasty. Here, we bring this analysis one step closer to clinical and biological relevance by calculating the mechanical stresses and strains that the strictureplasty deformation generates on a model intestinal wall. The small bowel is simulated as a linearly elastic isotropic deformable cylindrical shell using finite element modeling. Data show a divergence in elastic response between the anti-mesenteric and mesenteric halves. The anti-mesenteric surface shows a bending dominated elastic response that correlates with the prior purely geometric analysis. However, the mesenteric half is not a neutral bystander during strictureplasty formation, as geometric arguments predict. Strong in-plane stretching strains develop in a rim around the image of the transverse closure, which may impact local perfusion and serve as sites of disease recurrence. Lastly, nearly all the deformation energy is stored in the central vertex stitch, placing this part at highest risk of dehiscence. This study enhances our understanding of mechanical response in complex nonlinear cylindrical geometries like the surgically manipulated intestinal tract. The developed framework serves as a platform for future addition of more complex clinically relevant parameters to our model, including real tissue properties, anisotropy, blood supply modeling, and patient deriver anatomic factors. PMID:24671519
Changes in root canal geometry after preparation assessed by high-resolution computed tomography.
Peters, O A; Laib, A; Göhring, T N; Barbakow, F
2001-01-01
Root canal morphology changes during canal preparation, and these changes may vary depending on the technique used. Such changes have been studied in vitro by measuring cross-sections of canals before and after preparation. This current study used nondestructive high-resolution scanning tomography to assess changes in the canals' paths after preparation. A microcomputed tomography scanner (cubic resolution 34 microm) was used to analyze 18 canals in 6 extracted maxillary molars. Canals were scanned before and after preparation using either K-Files, Lightspeed, or ProFile .04 rotary instruments. A special mounting device enabled precise repositioning and scanning of the specimens after preparation. Differences in surface area (deltaA in mm2) and volume (deltaV in mm3) of each canal before and after preparation were calculated using custom-made software. deltaV ranged from 0.64 to 2.86, with a mean of 1.61 +/- 0.7, whereas deltaA varied from 0.72 to 9.66, with a mean of 4.16 +/- 2.63. Mean deltaV and deltaA for the K-File, ProFile, and Lightspeed groups were 1.28 +/- 0.57 and 2.58 +/- 1.83; 1.79 +/- 0.66 and 4.86 +/- 2.53; and 1.81 +/- 0.57 and 5.31 +/- 2.98, respectively. Canal anatomy and the effects of preparation were further analyzed using the Structure Model Index and the Transportation of Centers of Mass. Under the conditions of this study variations in canal geometry before preparation had more influence on the changes during preparation than the techniques themselves. Consequently studies comparing the effects of root canal instruments on canal anatomy should also consider details of the preoperative canal geometry. PMID:11487156
A declarative approach to visualizing concurrent computations
Roman, G.C.; Cox, K.C. )
1989-10-01
That visualization can play a key role in the exploration of concurrent computations is central to the ideas presented. Equally important, although given less emphasis, is concern that the full potential of visualization may not be reached unless the art of generating beautiful pictures is rooted in a solid, formally technical foundation. The authors show that program verification provides a formal framework around which such a foundation can be built. Making these ideas a practical reality will require both research and experimentation.
Information theoretic approaches to multidimensional neural computations
NASA Astrophysics Data System (ADS)
Fitzgerald, Jeffrey D.
Many systems in nature process information by transforming inputs from their environments into observable output states. These systems are often difficult to study because they are performing computations on multidimensional inputs with many degrees of freedom using highly nonlinear functions. The work presented in this dissertation deals with some of the issues involved with characterizing real-world input/output systems and understanding the properties of idealized systems using information theoretic methods. Using the principle of maximum entropy, a family of models are created that are consistent with certain measurable correlations from an input/output dataset but are maximally unbiased in all other respects, thereby eliminating all unjustified assumptions about the computation. In certain cases, including spiking neurons, we show that these models also minimize the mutual information. This property gives one the advantage of being able to identify the relevant input/output statistics by calculating their information content. We argue that these maximum entropy models provide a much needed quantitative framework for characterizing and understanding sensory processing neurons that are selective for multiple stimulus features. To demonstrate their usefulness, these ideas are applied to neural recordings from macaque retina and thalamus. These neurons, which primarily respond to two stimulus features, are shown to be well described using only first and second order statistics, indicating that their firing rates encode information about stimulus correlations. In addition to modeling multi-feature computations in the relevant feature space, we also show that maximum entropy models are capable of discovering the relevant feature space themselves. This technique overcomes the disadvantages of two commonly used dimensionality reduction methods and is explored using several simulated neurons, as well as retinal and thalamic recordings. Finally, we ask how neurons in a
Acoustic gravity waves: A computational approach
NASA Technical Reports Server (NTRS)
Hariharan, S. I.; Dutt, P. K.
1987-01-01
This paper discusses numerical solutions of a hyperbolic initial boundary value problem that arises from acoustic wave propagation in the atmosphere. Field equations are derived from the atmospheric fluid flow governed by the Euler equations. The resulting original problem is nonlinear. A first order linearized version of the problem is used for computational purposes. The main difficulty in the problem as with any open boundary problem is in obtaining stable boundary conditions. Approximate boundary conditions are derived and shown to be stable. Numerical results are presented to verify the effectiveness of these boundary conditions.
High performance parallel computing of flows in complex geometries: I. Methods
NASA Astrophysics Data System (ADS)
Gourdain, N.; Gicquel, L.; Montagnac, M.; Vermorel, O.; Gazaix, M.; Staffelbach, G.; Garcia, M.; Boussuge, J.-F.; Poinsot, T.
2009-01-01
Efficient numerical tools coupled with high-performance computers, have become a key element of the design process in the fields of energy supply and transportation. However flow phenomena that occur in complex systems such as gas turbines and aircrafts are still not understood mainly because of the models that are needed. In fact, most computational fluid dynamics (CFD) predictions as found today in industry focus on a reduced or simplified version of the real system (such as a periodic sector) and are usually solved with a steady-state assumption. This paper shows how to overcome such barriers and how such a new challenge can be addressed by developing flow solvers running on high-end computing platforms, using thousands of computing cores. Parallel strategies used by modern flow solvers are discussed with particular emphases on mesh-partitioning, load balancing and communication. Two examples are used to illustrate these concepts: a multi-block structured code and an unstructured code. Parallel computing strategies used with both flow solvers are detailed and compared. This comparison indicates that mesh-partitioning and load balancing are more straightforward with unstructured grids than with multi-block structured meshes. However, the mesh-partitioning stage can be challenging for unstructured grids, mainly due to memory limitations of the newly developed massively parallel architectures. Finally, detailed investigations show that the impact of mesh-partitioning on the numerical CFD solutions, due to rounding errors and block splitting, may be of importance and should be accurately addressed before qualifying massively parallel CFD tools for a routine industrial use.
A Computational Approach to Competitive Range Expansions
NASA Astrophysics Data System (ADS)
Weber, Markus F.; Poxleitner, Gabriele; Hebisch, Elke; Frey, Erwin; Opitz, Madeleine
2014-03-01
Bacterial communities represent complex and dynamic ecological systems. Environmental conditions and microbial interactions determine whether a bacterial strain survives an expansion to new territory. In our work, we studied competitive range expansions in a model system of three Escherichia coli strains. In this system, a colicin producing strain competed with a colicin resistant, and with a colicin sensitive strain for new territory. Genetic engineering allowed us to tune the strains' growth rates and to study their expansion in distinct ecological scenarios (with either cyclic or hierarchical dominance). The control over growth rates also enabled us to construct and to validate a predictive computational model of the bacterial dynamics. The model rested on an agent-based, coarse-grained description of the expansion process and we conducted independent experiments on the growth of single-strain colonies for its parametrization. Furthermore, the model considered the long-range nature of the toxin interaction between strains. The integration of experimental analysis with computational modeling made it possible to quantify how the level of biodiversity depends on the interplay between bacterial growth rates, the initial composition of the inoculum, and the toxin range.
A unified approach to computational drug discovery.
Tseng, Chih-Yuan; Tuszynski, Jack
2015-11-01
It has been reported that a slowdown in the development of new medical therapies is affecting clinical outcomes. The FDA has thus initiated the Critical Path Initiative project investigating better approaches. We review the current strategies in drug discovery and focus on the advantages of the maximum entropy method being introduced in this area. The maximum entropy principle is derived from statistical thermodynamics and has been demonstrated to be an inductive inference tool. We propose a unified method to drug discovery that hinges on robust information processing using entropic inductive inference. Increasingly, applications of maximum entropy in drug discovery employ this unified approach and demonstrate the usefulness of the concept in the area of pharmaceutical sciences. PMID:26189935
A 3D Computational fluid dynamics model validation for candidate molybdenum-99 target geometry
NASA Astrophysics Data System (ADS)
Zheng, Lin; Dale, Greg; Vorobieff, Peter
2014-11-01
Molybdenum-99 (99Mo) is the parent product of technetium-99m (99mTc), a radioisotope used in approximately 50,000 medical diagnostic tests per day in the U.S. The primary uses of this product include detection of heart disease, cancer, study of organ structure and function, and other applications. The US Department of Energy seeks new methods for generating 99Mo without the use of highly enriched uranium, to eliminate proliferation issues and provide a domestic supply of 99mTc for medical imaging. For this project, electron accelerating technology is used by sending an electron beam through a series of 100Mo targets. During this process a large amount of heat is created, which directly affects the operating temperature dictated by the tensile stress limit of the wall material. To maintain the required temperature range, helium gas is used as a cooling agent that flows through narrow channels between the target disks. In our numerical study, we investigate the cooling performance on a series of new geometry designs of the cooling channel. This research is supported by Los Alamos National Laboratory.
NASA Astrophysics Data System (ADS)
Gillespie, Robert J., Sr.
1986-12-01
This thesis, sponsored by the Marine Corps Development and Education Command, Quantico, Va., examines the far field patterns of five high frequency long wire antenna configurations through the use of the Numerical Electromagnetics Code (NEC). Lossy ground and the effects of variations made to these structures are considered. The resulting far field patterns are contained in the appendix. The antenna configurations vary in length from 1.87 to 17.19 wavelengths and in their height above ground from 0.103 to 0.610 wavelengths. Variations in the antennas end-regions include: the use of a ground rod or radial screen attached to the transmitter, terminating the far end of the antenna, and varying the shape of the transmitter from a small box (radio-sized) to a large (vehicle-sized) configuration. It is concluded that both the antenna height and length determine the far field geometry, and that end-region variations also impact, though to a lesser degree, on the pattern. Tables of comparative results are provided.
Astakhov, Vadim
2009-01-01
Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment. PMID:19623488
ERIC Educational Resources Information Center
Kwon, Oh Hoon
2012-01-01
This dissertation documents a new way of conceptualizing vectors in college mathematics, especially in geometry. First, I will introduce three problems to show the complexity and subtlety of the construct of vectors with the classical vector representations. These highlight the need for a new framework that: (1) differentiates abstraction from a…
A Pilot Study of a Cultural-Historical Approach to Teaching Geometry
ERIC Educational Resources Information Center
Rowlands, Stuart
2010-01-01
There appears to be a widespread assumption that deductive geometry is inappropriate for most learners and that they are incapable of engaging with the abstract and rule-governed intellectual processes that became the world's first fully developed and comprehensive formalised system of thought. This article discusses a curriculum initiative that…
Glakpe, E.K.
1987-01-23
The goal of the research program at Howard University is to develop ad document a general purpose computer code that can be used to obtain flow and heat transfer data for the transport or storage of spent fuel configurations. We believe that this work is relevant to DOE/OCRWM storage and transportation programs for the protection of public health and quality of the environment. The computer code is expected to be used to support primarily the following activities: (a) to obtain heat transfer and flow data for the design of sealed storage casks for transport to, and storage at the proposed MRS facility; (b) to obtain heat transfer and flow data for storage of spent fuel assemblies in pools or transportable metal casks at reactor sites. It is therefore proposed that the research work be continued to modify and add to the BODYFIT-1FE code physical models and applicable equations that will simulate realistic configurations of shipping/storage casks.
Computational approaches to natural product discovery
Medema, Marnix H.; Fischbach, Michael A.
2016-01-01
From the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data, and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering long-standing questions in microbial ecology regarding the roles of metabolites in interspecies interactions. PMID:26284671
Metabolomics and Diabetes: Analytical and Computational Approaches
Sas, Kelli M.; Karnovsky, Alla; Michailidis, George
2015-01-01
Diabetes is characterized by altered metabolism of key molecules and regulatory pathways. The phenotypic expression of diabetes and associated complications encompasses complex interactions between genetic, environmental, and tissue-specific factors that require an integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate small molecule metabolites from biological systems. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled identification of complex metabolic phenotypes. Continued development of bioinformatics and analytical strategies has facilitated the discovery of causal links in understanding the pathophysiology of diabetes and its complications. Here, we summarize the metabolomics workflow, including analytical, statistical, and computational tools, highlight recent applications of metabolomics in diabetes research, and discuss the challenges in the field. PMID:25713200
Computational Approaches for Understanding Energy Metabolism
Shestov, Alexander A; Barker, Brandon; Gu, Zhenglong; Locasale, Jason W
2013-01-01
There has been a surge of interest in understanding the regulation of metabolic networks involved in disease in recent years. Quantitative models are increasingly being used to i nterrogate the metabolic pathways that are contained within this complex disease biology. At the core of this effort is the mathematical modeling of central carbon metabolism involving glycolysis and the citric acid cycle (referred to as energy metabolism). Here we discuss several approaches used to quantitatively model metabolic pathways relating to energy metabolism and discuss their formalisms, successes, and limitations. PMID:23897661
One-eyed stereo: a general approach to modeling 3-d scene geometry.
Strat, T M; Fischler, M A
1986-06-01
A single two-dimensional image is an ambiguous representation of the three-dimensional world¿many different scenes could have produced the same image¿yet the human visual system is ex-tremely successful at recovering a qualitatively correct depth model from this type of representation. Workers in the field of computational vision have devised a number of distinct schemes that attempt to emulate this human capability; these schemes are collectively known as ``shape from...'' methods (e.g., shape from shading, shape from texture, or shape from contour). In this paper we contend that the distinct assumptions made in each of these schemes is tantamount to providing a second (virtual) image of the original scene, and that each of these approaches can be translated into a conventional stereo formalism. In particular, we show that it is frequently possible to structure the problem as one of recovering depth from a stereo pair consisting of the supplied perspective image (the original image) and an hypothesized orthographic image (the virtual image). We present a new algorithm of the form required to accomplish this type of stereo reconstruction task. PMID:21869368
Hyperdimensional computing approach to word sense disambiguation.
Berster, Bjoern-Toby; Goodwin, J Caleb; Cohen, Trevor
2012-01-01
Coping with the ambiguous meanings of words has long been a hurdle for information retrieval and natural language processing systems. This paper presents a new word sense disambiguation approach using high-dimensional binary vectors, which encode meanings of words based on the different contexts in which they occur. In our approach, a randomly constructed vector is assigned to each ambiguous term, and another to each sense of this term. In the context of a sense-annotated training set, a reversible vector transformation is used to combine these vectors, such that both the term and the sense assigned to a context in which the term occurs are encoded into vectors representing the surrounding terms in this context. When a new context is encountered, the information required to disambiguate this term is extracted from the trained semantic vectors for the terms in this context by reversing the vector transformation to recover the correct sense of the term. On repeated experiments using ten-fold cross-validation and a standard test set, we obtained results comparable to the best obtained in previous studies. These results demonstrate the potential of our methodology, and suggest directions for future research. PMID:23304389
Computational study of pulsatile blood flow in prototype vessel geometries of coronary segments.
Chaniotis, A K; Kaiktsis, L; Katritsis, D; Efstathopoulos, E; Pantos, I; Marmarellis, V
2010-01-01
The spatial and temporal distributions of wall shear stress (WSS) in prototype vessel geometries of coronary segments are investigated via numerical simulation, and the potential association with vascular disease and specifically atherosclerosis and plaque rupture is discussed. In particular, simulation results of WSS spatio-temporal distributions are presented for pulsatile, non-Newtonian blood flow conditions for: (a) curved pipes with different curvatures, and (b) bifurcating pipes with different branching angles and flow division. The effects of non-Newtonian flow on WSS (compared to Newtonian flow) are found to be small at Reynolds numbers representative of blood flow in coronary arteries. Specific preferential sites of average low WSS (and likely atherogenesis) were found at the outer regions of the bifurcating branches just after the bifurcation, and at the outer-entry and inner-exit flow regions of the curved vessel segment. The drop in WSS was more dramatic at the bifurcating vessel sites (less than 5% of the pre-bifurcation value). These sites were also near rapid gradients of WSS changes in space and time - a fact that increases the risk of rupture of plaque likely to develop at these sites. The time variation of the WSS spatial distributions was very rapid around the start and end of the systolic phase of the cardiac cycle, when strong fluctuations of intravascular pressure were also observed. These rapid and strong changes of WSS and pressure coincide temporally with the greatest flexion and mechanical stresses induced in the vessel wall by myocardial motion (ventricular contraction). The combination of these factors may increase the risk of plaque rupture and thrombus formation at these sites. PMID:20400349
Numerical Computation of Sensitivities and the Adjoint Approach
NASA Technical Reports Server (NTRS)
Lewis, Robert Michael
1997-01-01
We discuss the numerical computation of sensitivities via the adjoint approach in optimization problems governed by differential equations. We focus on the adjoint problem in its weak form. We show how one can avoid some of the problems with the adjoint approach, such as deriving suitable boundary conditions for the adjoint equation. We discuss the convergence of numerical approximations of the costate computed via the weak form of the adjoint problem and show the significance for the discrete adjoint problem.
Starting Computer Science Using C++ with Objects: A Workable Approach.
ERIC Educational Resources Information Center
Connolly, Mary V.
Saint Mary's College (Indiana) offers a minor program in computer science. The program's introductory computer science class traditionally taught Pascal. The decision to change the introductory programming language to C++ with an object oriented approach was made when it became clear that there were good texts available for beginning students.…
A Social Constructivist Approach to Computer-Mediated Instruction.
ERIC Educational Resources Information Center
Pear, Joseph J.; Crone-Todd, Darlene E.
2002-01-01
Describes a computer-mediated teaching system called computer-aided personalized system of instruction (CAPSI) that incorporates a social constructivist approach, maintaining that learning occurs primarily through a socially interactive process. Discusses use of CAPSI in an undergraduate course at the University of Manitoba that showed students…
Computational fluid dynamics in ventilation: Practical approach
NASA Astrophysics Data System (ADS)
Fontaine, J. R.
The potential of computation fluid dynamics (CFD) for conceiving ventilation systems is shown through the simulation of five practical cases. The following examples are considered: capture of pollutants on a surface treating tank equipped with a unilateral suction slot in the presence of a disturbing air draft opposed to suction; dispersion of solid aerosols inside fume cupboards; performances comparison of two general ventilation systems in a silkscreen printing workshop; ventilation of a large open painting area; and oil fog removal inside a mechanical engineering workshop. Whereas the two first problems are analyzed through two dimensional numerical simulations, the three other cases require three dimensional modeling. For the surface treating tank case, numerical results are compared to laboratory experiment data. All simulations are carried out using EOL, a CFD software specially devised to deal with air quality problems in industrial ventilated premises. It contains many analysis tools to interpret the results in terms familiar to the industrial hygienist. Much experimental work has been engaged to validate the predictions of EOL for ventilation flows.
Multivariate analysis: A statistical approach for computations
NASA Astrophysics Data System (ADS)
Michu, Sachin; Kaushik, Vandana
2014-10-01
Multivariate analysis is a type of multivariate statistical approach commonly used in, automotive diagnosis, education evaluating clusters in finance etc and more recently in the health-related professions. The objective of the paper is to provide a detailed exploratory discussion about factor analysis (FA) in image retrieval method and correlation analysis (CA) of network traffic. Image retrieval methods aim to retrieve relevant images from a collected database, based on their content. The problem is made more difficult due to the high dimension of the variable space in which the images are represented. Multivariate correlation analysis proposes an anomaly detection and analysis method based on the correlation coefficient matrix. Anomaly behaviors in the network include the various attacks on the network like DDOs attacks and network scanning.
Kroos, Julia M.; Diez, Ibai; Cortes, Jesus M.; Stramaglia, Sebastiano; Gerardo-Giorda, Luca
2016-01-01
Cortical spreading depression (CSD), a depolarization wave which originates in the visual cortex and travels toward the frontal lobe, has been suggested to be one neural correlate of aura migraine. To the date, little is known about the mechanisms which can trigger or stop aura migraine. Here, to shed some light on this problem and, under the hypothesis that CSD might mediate aura migraine, we aim to study different aspects favoring or disfavoring the propagation of CSD. In particular, by using a computational neuronal model distributed throughout a realistic cortical mesh, we study the role that the geometry has in shaping CSD. Our results are two-fold: first, we found significant differences in the propagation traveling patterns of CSD, both intra and inter-hemispherically, revealing important asymmetries in the propagation profile. Second, we developed methods able to identify brain regions featuring a peculiar behavior during CSD propagation. Our study reveals dynamical aspects of CSD, which, if applied to subject-specific cortical geometry, might shed some light on how to differentiate between healthy subjects and those suffering migraine. PMID:26869913
Kroos, Julia M; Diez, Ibai; Cortes, Jesus M; Stramaglia, Sebastiano; Gerardo-Giorda, Luca
2016-01-01
Cortical spreading depression (CSD), a depolarization wave which originates in the visual cortex and travels toward the frontal lobe, has been suggested to be one neural correlate of aura migraine. To the date, little is known about the mechanisms which can trigger or stop aura migraine. Here, to shed some light on this problem and, under the hypothesis that CSD might mediate aura migraine, we aim to study different aspects favoring or disfavoring the propagation of CSD. In particular, by using a computational neuronal model distributed throughout a realistic cortical mesh, we study the role that the geometry has in shaping CSD. Our results are two-fold: first, we found significant differences in the propagation traveling patterns of CSD, both intra and inter-hemispherically, revealing important asymmetries in the propagation profile. Second, we developed methods able to identify brain regions featuring a peculiar behavior during CSD propagation. Our study reveals dynamical aspects of CSD, which, if applied to subject-specific cortical geometry, might shed some light on how to differentiate between healthy subjects and those suffering migraine. PMID:26869913
Aluminium in Biological Environments: A Computational Approach
Mujika, Jon I; Rezabal, Elixabete; Mercero, Jose M; Ruipérez, Fernando; Costa, Dominique; Ugalde, Jesus M; Lopez, Xabier
2014-01-01
The increased availability of aluminium in biological environments, due to human intervention in the last century, raises concerns on the effects that this so far “excluded from biology” metal might have on living organisms. Consequently, the bioinorganic chemistry of aluminium has emerged as a very active field of research. This review will focus on our contributions to this field, based on computational studies that can yield an understanding of the aluminum biochemistry at a molecular level. Aluminium can interact and be stabilized in biological environments by complexing with both low molecular mass chelants and high molecular mass peptides. The speciation of the metal is, nonetheless, dictated by the hydrolytic species dominant in each case and which vary according to the pH condition of the medium. In blood, citrate and serum transferrin are identified as the main low molecular mass and high molecular mass molecules interacting with aluminium. The complexation of aluminium to citrate and the subsequent changes exerted on the deprotonation pathways of its tritable groups will be discussed along with the mechanisms for the intake and release of aluminium in serum transferrin at two pH conditions, physiological neutral and endosomatic acidic. Aluminium can substitute other metals, in particular magnesium, in protein buried sites and trigger conformational disorder and alteration of the protonation states of the protein's sidechains. A detailed account of the interaction of aluminium with proteic sidechains will be given. Finally, it will be described how alumnium can exert oxidative stress by stabilizing superoxide radicals either as mononuclear aluminium or clustered in boehmite. The possibility of promotion of Fenton reaction, and production of hydroxyl radicals will also be discussed. PMID:24757505
NASA Astrophysics Data System (ADS)
Feng, C. M.; Liu, T. S.
2014-10-01
Inspired from biology, this study presents a method for designing the fold geometry of deployable reflectors. Since the space available inside rockets for transporting satellites with reflector antennas is typically cylindrical in shape, and its cross-sectional area is considerably smaller than the reflector antenna after deployment, the cross-sectional area of the folded reflector must be smaller than the available rocket interior space. Membrane reflectors in aerospace are a type of lightweight structure that can be packaged compactly. To design membrane reflectors from the perspective of deployment processes, bionic applications from morphological changes of plants are investigated. Creating biologically inspired reflectors, this paper deals with fold geometry of reflectors, which imitate flower buds. This study uses mathematical formulation to describe geometric profiles of flower buds. Based on the formulation, new designs for deployable membrane reflectors derived from bionics are proposed. Adjusting parameters in the formulation of these designs leads to decreases in reflector area before deployment.
A Pilot Study of a Cultural-Historical Approach to Teaching Geometry
NASA Astrophysics Data System (ADS)
Rowlands, Stuart
2010-01-01
There appears to be a widespread assumption that deductive geometry is inappropriate for most learners and that they are incapable of engaging with the abstract and rule-governed intellectual processes that became the world’s first fully developed and comprehensive formalised system of thought. This article discusses a curriculum initiative that aims to ‘bring to life’ the major transformative (primary) events in the history of Greek geometry, aims to encourage a meta-discourse that can develop a reflective consciousness and aims to provide an opportunity for the induction into the formalities of proof and to engage with the abstract. The results of a pilot study to see whether 14-15 year old ‘mixed ability’ and 15-16 year old ‘gifted and talented’ students can be meaningfully engaged with two such transformative events are discussed.
Computing 3-D steady supersonic flow via a new Lagrangian approach
NASA Technical Reports Server (NTRS)
Loh, C. Y.; Liou, M.-S.
1993-01-01
The new Lagrangian method introduced by Loh and Hui (1990) is extended for 3-D steady supersonic flow computation. Details of the conservation form, the implementation of the local Riemann solver, and the Godunov and the high resolution TVD schemes are presented. The new approach is robust yet accurate, capable of handling complicated geometry and reactions between discontinuous waves. It keeps all the advantages claimed in the 2-D method of Loh and Hui, e.g., crisp resolution for a slip surface (contact discontinuity) and automatic grid generation along the stream.
Computation of leading edge film cooling from a CONSOLE geometry (CONverging Slot hOLE)
NASA Astrophysics Data System (ADS)
Guelailia, A.; Khorsi, A.; Hamidou, M. K.
2016-01-01
The aim of this study is to investigate the effect of mass flow rate on film cooling effectiveness and heat transfer over a gas turbine rotor blade with three staggered rows of shower-head holes which are inclined at 30° to the spanwise direction, and are normal to the streamwise direction on the blade. To improve film cooling effectiveness, the standard cylindrical holes, located on the leading edge region, are replaced with the converging slot holes (console). The ANSYS CFX has been used for this computational simulation. The turbulence is approximated by a k-ɛ model. Detailed film effectiveness distributions are presented for different mass flow rate. The numerical results are compared with experimental data.
Computational approach to the study of thermal spin crossover phenomena
Rudavskyi, Andrii; Broer, Ria; Sousa, Carmen
2014-05-14
The key parameters associated to the thermally induced spin crossover process have been calculated for a series of Fe(II) complexes with mono-, bi-, and tridentate ligands. Combination of density functional theory calculations for the geometries and for normal vibrational modes, and highly correlated wave function methods for the energies, allows us to accurately compute the entropy variation associated to the spin transition and the zero-point corrected energy difference between the low- and high-spin states. From these values, the transition temperature, T{sub 1/2}, is estimated for different compounds.
Burian, Agata; Uyttewaal, Magalie
2013-01-01
Cortical microtubules (CMTs) are often aligned in a particular direction in individual cells or even in groups of cells and play a central role in the definition of growth anisotropy. How the CMTs themselves are aligned is not well known, but two hypotheses have been proposed. According to the first hypothesis, CMTs align perpendicular to the maximal growth direction, and, according to the second, CMTs align parallel to the maximal stress direction. Since both hypotheses were formulated on the basis of mainly qualitative assessments, the link between CMT organization, organ geometry, and cell growth is revisited using a quantitative approach. For this purpose, CMT orientation, local curvature, and growth parameters for each cell were measured in the growing shoot apical meristem (SAM) of Arabidopsis thaliana. Using this approach, it has been shown that stable CMTs tend to be perpendicular to the direction of maximal growth in cells at the SAM periphery, but parallel in the cells at the boundary domain. When examining the local curvature of the SAM surface, no strict correlation between curvature and CMT arrangement was found, which implies that SAM geometry, and presumed geometry-derived stress distribution, is not sufficient to prescribe the CMT orientation. However, a better match between stress and CMTs was found when mechanical stress derived from differential growth was also considered. PMID:24153420
What is Intrinsic Motivation? A Typology of Computational Approaches
Oudeyer, Pierre-Yves; Kaplan, Frederic
2007-01-01
Intrinsic motivation, centrally involved in spontaneous exploration and curiosity, is a crucial concept in developmental psychology. It has been argued to be a crucial mechanism for open-ended cognitive development in humans, and as such has gathered a growing interest from developmental roboticists in the recent years. The goal of this paper is threefold. First, it provides a synthesis of the different approaches of intrinsic motivation in psychology. Second, by interpreting these approaches in a computational reinforcement learning framework, we argue that they are not operational and even sometimes inconsistent. Third, we set the ground for a systematic operational study of intrinsic motivation by presenting a formal typology of possible computational approaches. This typology is partly based on existing computational models, but also presents new ways of conceptualizing intrinsic motivation. We argue that this kind of computational typology might be useful for opening new avenues for research both in psychology and developmental robotics. PMID:18958277
A new approach for fault identification in computer networks
NASA Astrophysics Data System (ADS)
Zhao, Dong; Wang, Tao
2004-04-01
Effective management of computer networks has become a more and more difficult job because of the rapid development of the network systems. Fault identification is to find where is the problem of the network and what is it. Data mining generally refers to the process of extracting models from large stores of data. We can use data mining techniques to help us in the fault identification task. Existing approaches of fault identification are introduced and a new approach of fault identification is proposed. This approach improves MSDD algorithm but it need more computation. So some new techniques are used to increase the efficiency.
Computational analysis of a rarefied hypersonic flow over combined gap/step geometries
NASA Astrophysics Data System (ADS)
Leite, P. H. M.; Santos, W. F. N.
2015-06-01
This work describes a computational analysis of a hypersonic flow over a combined gap/step configuration at zero degree angle of attack, in chemical equilibrium and thermal nonequilibrium. Effects on the flowfield structure due to changes on the step frontal-face height have been investigated by employing the Direct Simulation Monte Carlo (DSMC) method. The work focuses the attention of designers of hypersonic configurations on the fundamental parameter of surface discontinuity, which can have an important impact on even initial designs. The results highlight the sensitivity of the primary flowfield properties, velocity, density, pressure, and temperature due to changes on the step frontal-face height. The analysis showed that the upstream disturbance in the gap/step configuration increased with increasing the frontal-face height. In addition, it was observed that the separation region for the gap/step configuration increased with increasing the step frontal-face height. It was found that density and pressure for the gap/step configuration dramatically increased inside the gap as compared to those observed for the gap configuration, i. e., a gap without a step.
NASA Technical Reports Server (NTRS)
Litvin, Faydor L.; Tsay, Chung-Biau
1987-01-01
The authors have proposed a method for the generation of circular arc helical gears which is based on the application of standard equipment, worked out all aspects of the geometry of the gears, proposed methods for the computer aided simulation of conditions of meshing and bearing contact, investigated the influence of manufacturing and assembly errors, and proposed methods for the adjustment of gears to these errors. The results of computer aided solutions are illustrated with computer graphics.
NASA Astrophysics Data System (ADS)
Gan, Chenquan; Yang, Xiaofan; Liu, Wanping; Zhu, Qingyi; Jin, Jian; He, Li
2014-08-01
Based on the assumption that external computers (particularly, infected external computers) are connected to the Internet, and by considering the influence of the Internet topology on computer virus spreading, this paper establishes a novel computer virus propagation model with a complex-network approach. This model possesses a unique (viral) equilibrium which is globally attractive. Some numerical simulations are also given to illustrate this result. Further study shows that the computers with higher node degrees are more susceptible to infection than those with lower node degrees. In this regard, some appropriate protective measures are suggested.
Ultrasonic approach for formation of erbium oxide nanoparticles with variable geometries.
Radziuk, Darya; Skirtach, André; Gessner, Andre; Kumke, Michael U; Zhang, Wei; Möhwald, Helmuth; Shchukin, Dmitry
2011-12-01
Ultrasound (20 kHz, 29 W·cm(-2)) is employed to form three types of erbium oxide nanoparticles in the presence of multiwalled carbon nanotubes as a template material in water. The nanoparticles are (i) erbium carboxioxide nanoparticles deposited on the external walls of multiwalled carbon nanotubes and Er(2)O(3) in the bulk with (ii) hexagonal and (iii) spherical geometries. Each type of ultrasonically formed nanoparticle reveals Er(3+) photoluminescence from crystal lattice. The main advantage of the erbium carboxioxide nanoparticles on the carbon nanotubes is the electromagnetic emission in the visible region, which is new and not examined up to the present date. On the other hand, the photoluminescence of hexagonal erbium oxide nanoparticles is long-lived (μs) and enables the higher energy transition ((4)S(3/2)-(4)I(15/2)), which is not observed for spherical nanoparticles. Our work is unique because it combines for the first time spectroscopy of Er(3+) electronic transitions in the host crystal lattices of nanoparticles with the geometry established by ultrasound in aqueous solution of carbon nanotubes employed as a template material. The work can be of great interest for "green" chemistry synthesis of photoluminescent nanoparticles in water. PMID:22022886
An approach to computing direction relations between separated object groups
NASA Astrophysics Data System (ADS)
Yan, H.; Wang, Z.; Li, J.
2013-06-01
Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on Gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups; and then it constructs the Voronoi Diagram between the two groups using the triangular network; after this, the normal of each Vornoi edge is calculated, and the quantitative expression of the direction relations is constructed; finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.
An approach to computing direction relations between separated object groups
NASA Astrophysics Data System (ADS)
Yan, H.; Wang, Z.; Li, J.
2013-09-01
Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups, and then it constructs the Voronoi diagram between the two groups using the triangular network. After this, the normal of each Voronoi edge is calculated, and the quantitative expression of the direction relations is constructed. Finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.
A tale of three bio-inspired computational approaches
NASA Astrophysics Data System (ADS)
Schaffer, J. David
2014-05-01
I will provide a high level walk-through for three computational approaches derived from Nature. First, evolutionary computation implements what we may call the "mother of all adaptive processes." Some variants on the basic algorithms will be sketched and some lessons I have gleaned from three decades of working with EC will be covered. Then neural networks, computational approaches that have long been studied as possible ways to make "thinking machines", an old dream of man's, and based upon the only known existing example of intelligence. Then, a little overview of attempts to combine these two approaches that some hope will allow us to evolve machines we could never hand-craft. Finally, I will touch on artificial immune systems, Nature's highly sophisticated defense mechanism, that has emerged in two major stages, the innate and the adaptive immune systems. This technology is finding applications in the cyber security world.
NASA Astrophysics Data System (ADS)
Mekuria, Rufael N.; Cesar, Pablo; Bulterman, Dick C. A.
2014-09-01
Live 3D reconstruction of a human as a 3D mesh with commodity electronics is becoming a reality. Immersive applications (i.e. cloud gaming, tele-presence) benefit from effective transmission of such content over a bandwidth limited link. In this paper we outline different approaches for compressing live reconstructed mesh geometry based on distributing mesh reconstruction functions between sender and receiver. We evaluate rate-performance-complexity of different configurations. First, we investigate 3D mesh compression methods (i.e. dynamic/static) from MPEG-4. Second, we evaluate the option of using octree based point cloud compression and receiver side surface reconstruction.
The process group approach to reliable distributed computing
NASA Technical Reports Server (NTRS)
Birman, Kenneth P.
1992-01-01
The difficulty of developing reliable distribution software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems that are substantially easier to develop, exploit sophisticated forms of cooperative computation, and achieve high reliability. Six years of research on ISIS, describing the model, its implementation challenges, and the types of applications to which ISIS has been applied are reviewed.
Sensing and perception: Connectionist approaches to subcognitive computing
NASA Technical Reports Server (NTRS)
Skrrypek, J.
1987-01-01
New approaches to machine sensing and perception are presented. The motivation for crossdisciplinary studies of perception in terms of AI and neurosciences is suggested. The question of computing architecture granularity as related to global/local computation underlying perceptual function is considered and examples of two environments are given. Finally, the examples of using one of the environments, UCLA PUNNS, to study neural architectures for visual function are presented.
A geometry-based particle filtering approach to white matter tractography.
Savadjiev, Peter; Rathi, Yogesh; Malcolm, James G; Shenton, Martha E; Westin, Carl-Fredrik
2010-01-01
We introduce a fibre tractography framework based on a particle filter which estimates a local geometrical model of the underlying white matter tract, formulated as a 'streamline flow' using generalized helicoids. The method is not dependent on the diffusion model, and is applicable to diffusion tensor (DT) data as well as to high angular resolution reconstructions. The geometrical model allows for a robust inference of local tract geometry, which, in the context of the causal filter estimation, guides tractography through regions with partial volume effects. We validate the method on synthetic data and present results on two types in vivo data: diffusion tensors and a spherical harmonic reconstruction of the fibre orientation distribution function (fODF). PMID:20879320
Computational molecular biology approaches to ligand-target interactions
Lupieri, Paola; Nguyen, Chuong Ha Hung; Bafghi, Zhaleh Ghaemi; Giorgetti, Alejandro; Carloni, Paolo
2009-01-01
Binding of small molecules to their targets triggers complex pathways. Computational approaches are keys for predictions of the molecular events involved in such cascades. Here we review current efforts at characterizing the molecular determinants in the largest membrane-bound receptor family, the G-protein-coupled receptors (GPCRs). We focus on odorant receptors, which constitute more than half GPCRs. The work presented in this review uncovers structural and energetic aspects of components of the cellular cascade. Finally, a computational approach in the context of radioactive boron-based antitumoral therapies is briefly described. PMID:20119480
An Eulerian approach for computing the finite time Lyapunov exponent
NASA Astrophysics Data System (ADS)
Leung, Shingyu
2011-05-01
We propose efficient Eulerian methods for approximating the finite-time Lyapunov exponent (FTLE). The idea is to compute the related flow map using the Level Set Method and the Liouville equation. There are several advantages of the proposed approach. Unlike the usual Lagrangian-type computations, the resulting method requires the velocity field defined only at discrete locations. No interpolation of the velocity field is needed. Also, the method automatically stops a particle trajectory in the case when the ray hits the boundary of the computational domain. The computational complexity of the algorithm is O(Δ x-( d+1) ) with d the dimension of the physical space. Since there are the same number of mesh points in the x- t space, the computational complexity of the proposed Eulerian approach is optimal in the sense that each grid point is visited for only O(1) time. We also extend the algorithm to compute the FTLE on a co-dimension one manifold. The resulting algorithm does not require computation on any local coordinate system and is simple to implement even for an evolving manifold.
Ding, Lei; He, Bin
2006-09-01
The subspace source localization approach, i.e., first principle vectors (FINE), is able to enhance the spatial resolvability and localization accuracy for closely-spaced neural sources from EEG and MEG measurements. Computer simulations were conducted to evaluate the performance of the FINE algorithm in an inhomogeneous realistic geometry head model under a variety of conditions. The source localization abilities of FINE were examined at different cortical regions and at different depths. The present computer simulation results indicate that FINE has enhanced source localization capability, as compared with MUSIC and RAP-MUSIC, when sources are closely spaced, highly noise-contaminated, or inter-correlated. The source localization accuracy of FINE is better, for closely-spaced sources, than MUSIC at various noise levels, i.e., signal-to-noise ratio (SNR) from 6 dB to 16 dB, and RAP-MUSIC at relatively low noise levels, i.e., 6 dB to 12 dB. The FINE approach has been further applied to localize brain sources of motor potentials, obtained during the finger tapping tasks in a human subject. The experimental results suggest that the detailed neural activity distribution could be revealed by FINE. The present study suggests that FINE provides enhanced performance in localizing multiple closely spaced, and inter-correlated sources under low SNR, and may become an important alternative to brain source localization from EEG or MEG. PMID:16941829
Aircraft Engine Noise Scattering by Fuselage and Wings: A Computational Approach
NASA Technical Reports Server (NTRS)
Farassat, F.; Stanescu, D.; Hussaini, M. Y.
2003-01-01
The paper presents a time-domain method for computation of sound radiation from aircraft engine sources to the far field. The effects of non-uniform flow around the aircraft and scattering of sound by fuselage and wings are accounted for in the formulation. The approach is based on the discretization of the inviscid flow equations through a collocation form of the discontinuous Galerkin spectral element method. An isoparametric representation of the underlying geometry is used in order to take full advantage of the spectral accuracy of the method. Large-scale computations are made possible by a parallel implementation based on message passing. Results obtained for radiation from an axisymmetric nacelle alone are compared with those obtained when the same nacelle is installed in a generic configuration, with and without a wing. 0 2002 Elsevier Science Ltd. All rights reserved.
Aircraft Engine Noise Scattering by Fuselage and Wings: A Computational Approach
NASA Technical Reports Server (NTRS)
Stanescu, D.; Hussaini, M. Y.; Farassat, F.
2003-01-01
The paper presents a time-domain method for computation of sound radiation from aircraft engine sources to the far-field. The effects of nonuniform flow around the aircraft and scattering of sound by fuselage and wings are accounted for in the formulation. The approach is based on the discretization of the inviscid flow equations through a collocation form of the Discontinuous Galerkin spectral element method. An isoparametric representation of the underlying geometry is used in order to take full advantage of the spectral accuracy of the method. Large-scale computations are made possible by a parallel implementation based on message passing. Results obtained for radiation from an axisymmetric nacelle alone are compared with those obtained when the same nacelle is installed in a generic configuration, with and without a wing.
Aircraft Engine Noise Scattering By Fuselage and Wings: A Computational Approach
NASA Technical Reports Server (NTRS)
Stanescu, D.; Hussaini, M. Y.; Farassat, F.
2003-01-01
The paper presents a time-domain method for computation of sound radiation from aircraft engine sources to the far-field. The effects of nonuniform flow around the aircraft and scattering of sound by fuselage and wings are accounted for in the formulation. The approach is based on the discretization of the inviscid flow equations through a collocation form of the Discontinuous Galerkin spectral element method. An isoparametric representation of the underlying geometry is used in order to take full advantage of the spectral accuracy of the method. Large-scale computations are made possible by a parallel implementation based on message passing. Results obtained for radiation from an axisymmetric nacelle alone are compared with those obtained when the same nacelle is installed in a generic configuration, with and without a wing.
Estrada, T; Zhang, B; Cicotti, P; Armen, R S; Taufer, M
2012-07-01
We present a scalable and accurate method for classifying protein-ligand binding geometries in molecular docking. Our method is a three-step process: the first step encodes the geometry of a three-dimensional (3D) ligand conformation into a single 3D point in the space; the second step builds an octree by assigning an octant identifier to every single point in the space under consideration; and the third step performs an octree-based clustering on the reduced conformation space and identifies the most dense octant. We adapt our method for MapReduce and implement it in Hadoop. The load-balancing, fault-tolerance, and scalability in MapReduce allow screening of very large conformation spaces not approachable with traditional clustering methods. We analyze results for docking trials for 23 protein-ligand complexes for HIV protease, 21 protein-ligand complexes for Trypsin, and 12 protein-ligand complexes for P38alpha kinase. We also analyze cross docking trials for 24 ligands, each docking into 24 protein conformations of the HIV protease, and receptor ensemble docking trials for 24 ligands, each docking in a pool of HIV protease receptors. Our method demonstrates significant improvement over energy-only scoring for the accurate identification of native ligand geometries in all these docking assessments. The advantages of our clustering approach make it attractive for complex applications in real-world drug design efforts. We demonstrate that our method is particularly useful for clustering docking results using a minimal ensemble of representative protein conformational states (receptor ensemble docking), which is now a common strategy to address protein flexibility in molecular docking. PMID:22658682
Higher spin approaches to quantum field theory and (psuedo)-Riemannian geometries
NASA Astrophysics Data System (ADS)
Hallowell, Karl Evan
In this thesis, we study a number of higher spin quantum field theories and some of their algebraic and geometric consequences. These theories apply mostly either over constant curvature or more generally symmetric pseudo-Riemannian manifolds. The first part of this dissertation covers a superalgebra coming from a family of particle models over symmetric spaces. These theories are novel in that the symmetries of the (super)algebra osp( Q|2p) are larger and more elaborate than traditional symmetries. We construct useful (super)algebras related to and generalizing old work by Lichnerowicz and describe their role in developing the geometry of massless models with osp(Q|2 p) symmetry. The result is two practical applications of these (super)algebras: (1) a lunch more concise description of a family of higher spin quantum field theories; and (2) an interesting algebraic probe of underlying background geometries. We also consider massive models over constant curvature spaces. We use a radial dimensional reduction process which converts massless models into massive ones over a lower dimensional space. In our case, we take from the family of theories above the particular free, massless model over flat space associated with sp(2, R ) and derive a massive model. In the process, we develop a novel associative algebra, which is a deformation of the original differential operator algebra associated with the sp(2, R ) model. This algebra is interesting in its own right since its operators realize the representation structure of the sp(2, R ) group. The massive model also has implications for a sequence of unusual, "partially massless" theories. The derivation illuminates how reduced degrees of freedom become manifest in these particular models. Finally, we study a Yang-Mills model using an on-shell Poincare Yang-Mills twist of the Maxwell complex along with a non-minimal coupling. This is a special, higher spin case of a quantum field theory called a Yang-Mills detour complex
Antisolvent crystallization approach to construction of CuI superstructures with defined geometries.
Kozhummal, Rajeevan; Yang, Yang; Güder, Firat; Küçükbayrak, Umut M; Zacharias, Margit
2013-03-26
A facile high-yield production of cuprous iodide (CuI) superstructures is reported by antisolvent crystallization using acetonitrile/water as a solvent/antisolvent couple under ambient conditions. In the presence of trace water, the metastable water droplets act as templates to induce the precipitation of hollow spherical CuI superstructures consisting of orderly aligned building blocks after drop coating. With water in excess in the mixed solution, an instant precipitation of CuI random aggregates takes place due to rapid crystal growth via ion-by-ion attachment induced by a strong antisolvent effect. However, this uncontrolled process can be modified by adding polymer polyvinyl pyrrolidone (PVP) in water to restrict the size of initially formed CuI crystal nuclei through the effective coordination effect of PVP. As a result, CuI superstructures with a cuboid geometry are constructed by gradual self-assembly of the small CuI crystals via oriented attachment. The precipitated CuI superstructures have been used as competent adsorbents to remove organic dyes from the water due to their mesocrystal feature. Besides, the CuI superstructures have been applied either as a self-sacrificial template or only as a structuring template for the flexible design of other porous materials such as CuO and TiO2. This system provides an ideal platform to simultaneously investigate the superstructure formation enforced by antisolvent crystallization with and without organic additives. PMID:23441989
Shi, Yunfei; Yao, Jiang; Young, Jonathan M.; Fee, Judy A.; Perucchio, Renato; Taber, Larry A.
2014-01-01
The morphogenetic process of cardiac looping transforms the straight heart tube into a curved tube that resembles the shape of the future four-chambered heart. Although great progress has been made in identifying the molecular and genetic factors involved in looping, the physical mechanisms that drive this process have remained poorly understood. Recent work, however, has shed new light on this complicated problem. After briefly reviewing the current state of knowledge, we propose a relatively comprehensive hypothesis for the mechanics of the first phase of looping, termed c-looping, as the straight heart tube deforms into a c-shaped tube. According to this hypothesis, differential hypertrophic growth in the myocardium supplies the main forces that cause the heart tube to bend ventrally, while regional growth and cytoskeletal contraction in the omphalomesenteric veins (primitive atria) and compressive loads exerted by the splanchnopleuric membrane drive rightward torsion. A computational model based on realistic embryonic heart geometry is used to test the physical plausibility of this hypothesis. The behavior of the model is in reasonable agreement with available experimental data from control and perturbed embryos, offering support for our hypothesis. The results also suggest, however, that several other mechanisms contribute secondarily to normal looping, and we speculate that these mechanisms play backup roles when looping is perturbed. Finally, some outstanding questions are discussed for future study. PMID:25161623
A Process Approach to Writing with a Computer.
ERIC Educational Resources Information Center
Miller-Jacobs, Sandy
The word processor helps teachers to use the process approach to writing. In using the word processor, the teacher can create tasks on the computer to assist students during each step of the writing process, i.e., prewriting or idea processing, drafting or writing, revising/rewriting or editing, and the publishing process or communicating. Ideas…
Computer-Assisted Approaches to Multiattribute Decision Making.
ERIC Educational Resources Information Center
Radcliff, Benjamin
1986-01-01
This article evaluates three general types of computer-assisted approaches to multicriteria decision problems in which criteria are attributes as opposed to objectives. Several programs specifically designed for multiattribute problems, as well as spreadsheets and decision-free software, are discussed. (Author/BS)
New Theoretical Approaches for Human-Computer Interaction.
ERIC Educational Resources Information Center
Rogers, Yvonne
2004-01-01
Presents a critique of recent theoretical developments in the field of human-computer interaction (HCI) together with an overview of HCI practice. This chapter discusses why theoretically based approaches have had little impact on the practice of interaction design and suggests mechanisms to enable designers and researchers to better articulate…
Tsygankov, Denis; Bilancia, Colleen G; Vitriol, Eric A; Hahn, Klaus M; Peifer, Mark; Elston, Timothy C
2014-02-01
Cell biologists increasingly rely on computer-aided image analysis, allowing them to collect precise, unbiased quantitative results. However, despite great progress in image processing and computer vision, current computational approaches fail to address many key aspects of cell behavior, including the cell protrusions that guide cell migration and drive morphogenesis. We developed the open source MATLAB application CellGeo, a user-friendly computational platform to allow simultaneous, automated tracking and analysis of dynamic changes in cell shape, including protrusions ranging from filopodia to lamellipodia. Our method maps an arbitrary cell shape onto a tree graph that, unlike traditional skeletonization algorithms, preserves complex boundary features. CellGeo allows rigorous but flexible definition and accurate automated detection and tracking of geometric features of interest. We demonstrate CellGeo's utility by deriving new insights into (a) the roles of Diaphanous, Enabled, and Capping protein in regulating filopodia and lamellipodia dynamics in Drosophila melanogaster cells and (b) the dynamic properties of growth cones in catecholaminergic a-differentiated neuroblastoma cells. PMID:24493591
ERIC Educational Resources Information Center
Fisher, Merrill Edgar
The purposes of this study were (1) to identify and compare the effect on student achievement of an individualized computer-managed geometry course, built on behavioral objectives, with traditional instructional methods; and (2) to identify how selected individual aptitudes interact with the two instructional modes. The subjects were…
ERIC Educational Resources Information Center
Ruthven, Kenneth
2008-01-01
This article examines three important facets of the incorporation of new technologies into educational practice, focusing on emergent usages of the mathematical tools of computer algebra and dynamic geometry. First, it illustrates the interpretative flexibility of these tools, highlighting important differences in ways of conceptualizing and…
Connecting Geometry and Chemistry: A Three-Step Approach to Three-Dimensional Thinking
ERIC Educational Resources Information Center
Donaghy, Kelley J.; Saxton, Kathleen J.
2012-01-01
A three-step active-learning approach is described to enhance the spatial abilities of general chemistry students with respect to three-dimensional molecular drawing and visualization. These activities are used in a medium-sized lecture hall with approximately 150 students in the first semester of the general chemistry course. The first activity…
ERIC Educational Resources Information Center
New York State Education Dept., Albany. Bureau of Elementary Curriculum Development.
This guide describes activities and materials which can be used in a mathematics laboratory approach to a basic mathematics program for grades 1-6. Thirty-five activities pertaining to geometric concepts are described in terms of purpose, suggested grade levels, materials needed, and procedures. Some concepts included in the guide are: basic…
Diversifying Our Perspectives on Mathematics about Space and Geometry: An Ecocultural Approach
ERIC Educational Resources Information Center
Owens, Kay
2014-01-01
School mathematics tends to have developed from the major cultures of Asia, the Mediterranean and Europe. However, indigenous cultures in particular may have distinctly different systematic ways of referring to space and thinking mathematically about spatial activity. Their approaches are based on the close link between the environment and…
Cloud computing approaches to accelerate drug discovery value chain.
Garg, Vibhav; Arora, Suchir; Gupta, Chitra
2011-12-01
Continued advancements in the area of technology have helped high throughput screening (HTS) evolve from a linear to parallel approach by performing system level screening. Advanced experimental methods used for HTS at various steps of drug discovery (i.e. target identification, target validation, lead identification and lead validation) can generate data of the order of terabytes. As a consequence, there is pressing need to store, manage, mine and analyze this data to identify informational tags. This need is again posing challenges to computer scientists to offer the matching hardware and software infrastructure, while managing the varying degree of desired computational power. Therefore, the potential of "On-Demand Hardware" and "Software as a Service (SAAS)" delivery mechanisms cannot be denied. This on-demand computing, largely referred to as Cloud Computing, is now transforming the drug discovery research. Also, integration of Cloud computing with parallel computing is certainly expanding its footprint in the life sciences community. The speed, efficiency and cost effectiveness have made cloud computing a 'good to have tool' for researchers, providing them significant flexibility, allowing them to focus on the 'what' of science and not the 'how'. Once reached to its maturity, Discovery-Cloud would fit best to manage drug discovery and clinical development data, generated using advanced HTS techniques, hence supporting the vision of personalized medicine. PMID:21843145
Euclidean Geometry via Programming.
ERIC Educational Resources Information Center
Filimonov, Rossen; Kreith, Kurt
1992-01-01
Describes the Plane Geometry System computer software developed at the Educational Computer Systems laboratory in Sofia, Bulgaria. The system enables students to use the concept of "algorithm" to correspond to the process of "deductive proof" in the development of plane geometry. Provides an example of the software's capability and compares it to…
Thallmair, Sebastian; Roos, Matthias K; de Vivie-Riedle, Regina
2016-06-21
Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence. PMID:27334151
NASA Astrophysics Data System (ADS)
Thallmair, Sebastian; Roos, Matthias K.; de Vivie-Riedle, Regina
2016-06-01
Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.
Energy Science and Technology Software Center (ESTSC)
1990-04-25
Version 00 TPTRIA calculates reactivity, effective delayed neutron fractions and mean generation time for two-dimensional triangular geometry on the basis of neutron transport perturbation theory. DIAMANT2 (also designated as CCC-414), is a multigroup two-dimensional discrete ordinates transport code system for triangular and hexagonal geometry which calculates direct and adjoint angular fluxes.
Analytical and Computational Properties of Distributed Approaches to MDO
NASA Technical Reports Server (NTRS)
Alexandrov, Natalia M.; Lewis, Robert Michael
2000-01-01
Historical evolution of engineering disciplines and the complexity of the MDO problem suggest that disciplinary autonomy is a desirable goal in formulating and solving MDO problems. We examine the notion of disciplinary autonomy and discuss the analytical properties of three approaches to formulating and solving MDO problems that achieve varying degrees of autonomy by distributing the problem along disciplinary lines. Two of the approaches-Optimization by Linear Decomposition and Collaborative Optimization-are based on bi-level optimization and reflect what we call a structural perspective. The third approach, Distributed Analysis Optimization, is a single-level approach that arises from what we call an algorithmic perspective. The main conclusion of the paper is that disciplinary autonomy may come at a price: in the bi-level approaches, the system-level constraints introduced to relax the interdisciplinary coupling and enable disciplinary autonomy can cause analytical and computational difficulties for optimization algorithms. The single-level alternative we discuss affords a more limited degree of autonomy than that of the bi-level approaches, but without the computational difficulties of the bi-level methods. Key Words: Autonomy, bi-level optimization, distributed optimization, multidisciplinary optimization, multilevel optimization, nonlinear programming, problem integration, system synthesis
Kerschbamer, Rudolf
2015-01-01
This paper proposes a geometric delineation of distributional preference types and a non-parametric approach for their identification in a two-person context. It starts with a small set of assumptions on preferences and shows that this set (i) naturally results in a taxonomy of distributional archetypes that nests all empirically relevant types considered in previous work; and (ii) gives rise to a clean experimental identification procedure – the Equality Equivalence Test – that discriminates between archetypes according to core features of preferences rather than properties of specific modeling variants. As a by-product the test yields a two-dimensional index of preference intensity. PMID:26089571
Inness, Emma K; Moutrie, Vaughan; Charles, Paul H
2014-06-01
A computed tomography number to relative electron density (CT-RED) calibration is performed when commissioning a radiotherapy CT scanner by imaging a calibration phantom with inserts of specified RED and recording the CT number displayed. In this work, CT-RED calibrations were generated using several commercially available phantoms to observe the effect of phantom geometry on conversion to electron density and, ultimately, the dose calculation in a treatment planning system. Using an anthropomorphic phantom as a gold standard, the CT number of a material was found to depend strongly on the amount and type of scattering material surrounding the volume of interest, with the largest variation observed for the highest density material tested, cortical bone. Cortical bone gave a maximum CT number difference of 1,110 when a cylindrical insert of diameter 28 mm scanned free in air was compared to that in the form of a 30 × 30 cm(2) slab. The effect of using each CT-RED calibration on planned dose to a patient was quantified using a commercially available treatment planning system. When all calibrations were compared to the anthropomorphic calibration, the largest percentage dose difference was 4.2 % which occurred when the CT-RED calibration curve was acquired with heterogeneity inserts removed from the phantom and scanned free in air. The maximum dose difference observed between two dedicated CT-RED phantoms was ±2.1 %. A phantom that is to be used for CT-RED calibrations must have sufficient water equivalent scattering material surrounding the heterogeneous objects that are to be used for calibration. PMID:24760737
Protein Engineering by Combined Computational and In Vitro Evolution Approaches.
Rosenfeld, Lior; Heyne, Michael; Shifman, Julia M; Papo, Niv
2016-05-01
Two alternative strategies are commonly used to study protein-protein interactions (PPIs) and to engineer protein-based inhibitors. In one approach, binders are selected experimentally from combinatorial libraries of protein mutants that are displayed on a cell surface. In the other approach, computational modeling is used to explore an astronomically large number of protein sequences to select a small number of sequences for experimental testing. While both approaches have some limitations, their combination produces superior results in various protein engineering applications. Such applications include the design of novel binders and inhibitors, the enhancement of affinity and specificity, and the mapping of binding epitopes. The combination of these approaches also aids in the understanding of the specificity profiles of various PPIs. PMID:27061494
Computational modeling approaches to the dynamics of oncolytic viruses.
Wodarz, Dominik
2016-05-01
Replicating oncolytic viruses represent a promising treatment approach against cancer, specifically targeting the tumor cells. Significant progress has been made through experimental and clinical studies. Besides these approaches, however, mathematical models can be useful when analyzing the dynamics of virus spread through tumors, because the interactions between a growing tumor and a replicating virus are complex and nonlinear, making them difficult to understand by experimentation alone. Mathematical models have provided significant biological insight into the field of virus dynamics, and similar approaches can be adopted to study oncolytic viruses. The review discusses this approach and highlights some of the challenges that need to be overcome in order to build mathematical and computation models that are clinically predictive. WIREs Syst Biol Med 2016, 8:242-252. doi: 10.1002/wsbm.1332 For further resources related to this article, please visit the WIREs website. PMID:27001049
SU-C-207-01: Four-Dimensional Inverse Geometry Computed Tomography: Concept and Its Validation
Kim, K; Kim, D; Kim, T; Kang, S; Cho, M; Shin, D; Suh, T
2015-06-15
Purpose: In past few years, the inverse geometry computed tomography (IGCT) system has been developed to overcome shortcomings of a conventional computed tomography (CT) system such as scatter problem induced from large detector size and cone-beam artifact. In this study, we intend to present a concept of a four-dimensional (4D) IGCT system that has positive aspects above all with temporal resolution for dynamic studies and reduction of motion artifact. Methods: Contrary to conventional CT system, projection data at a certain angle in IGCT was a group of fractionated narrow cone-beam projection data, projection group (PG), acquired from multi-source array which have extremely short time gap of sequential operation between each of sources. At this, for 4D IGCT imaging, time-related data acquisition parameters were determined by combining multi-source scanning time for collecting one PG with conventional 4D CBCT data acquisition sequence. Over a gantry rotation, acquired PGs from multi-source array were tagged time and angle for 4D image reconstruction. Acquired PGs were sorted into 10 phase and image reconstructions were independently performed at each phase. Image reconstruction algorithm based upon filtered-backprojection was used in this study. Results: The 4D IGCT had uniform image without cone-beam artifact on the contrary to 4D CBCT image. In addition, the 4D IGCT images of each phase had no significant artifact induced from motion compared with 3D CT. Conclusion: The 4D IGCT image seems to give relatively accurate dynamic information of patient anatomy based on the results were more endurable than 3D CT about motion artifact. From this, it will be useful for dynamic study and respiratory-correlated radiation therapy. This work was supported by the Industrial R&D program of MOTIE/KEIT [10048997, Development of the core technology for integrated therapy devices based on real-time MRI guided tumor tracking] and the Mid-career Researcher Program (2014R1A2A1A
Style: A Computational and Conceptual Blending-Based Approach
NASA Astrophysics Data System (ADS)
Goguen, Joseph A.; Harrell, D. Fox
This chapter proposes a new approach to style, arising from our work on computational media using structural blending, which enriches the conceptual blending of cognitive linguistics with structure building operations in order to encompass syntax and narrative as well as metaphor. We have implemented both conceptual and structural blending, and conducted initial experiments with poetry, including interactive multimedia poetry, although the approach generalizes to other media. The central idea is to generate multimedia content and analyze style in terms of blending principles, based on our finding that different principles from those of common sense blending are often needed for some contemporary poetic metaphors.