Efficiency improvement in proton dose calculations with an equivalent restricted stopping power formalism

NASA Astrophysics Data System (ADS)

Maneval, Daniel; Bouchard, Hugo; Ozell, Benoît; Després, Philippe

2018-01-01

The equivalent restricted stopping power formalism is introduced for proton mean energy loss calculations under the continuous slowing down approximation. The objective is the acceleration of Monte Carlo dose calculations by allowing larger steps while preserving accuracy. The fractional energy loss per step length ɛ was obtained with a secant method and a Gauss-Kronrod quadrature estimation of the integral equation relating the mean energy loss to the step length. The midpoint rule of the Newton-Cotes formulae was then used to solve this equation, allowing the creation of a lookup table linking ɛ to the equivalent restricted stopping power L eq, used here as a key physical quantity. The mean energy loss for any step length was simply defined as the product of the step length with L eq. Proton inelastic collisions with electrons were added to GPUMCD, a GPU-based Monte Carlo dose calculation code. The proton continuous slowing-down was modelled with the L eq formalism. GPUMCD was compared to Geant4 in a validation study where ionization processes alone were activated and a voxelized geometry was used. The energy straggling was first switched off to validate the L eq formalism alone. Dose differences between Geant4 and GPUMCD were smaller than 0.31% for the L eq formalism. The mean error and the standard deviation were below 0.035% and 0.038% respectively. 99.4 to 100% of GPUMCD dose points were consistent with a 0.3% dose tolerance. GPUMCD 80% falloff positions (R80 ) matched Geant’s R80 within 1 μm. With the energy straggling, dose differences were below 2.7% in the Bragg peak falloff and smaller than 0.83% elsewhere. The R80 positions matched within 100 μm. The overall computation times to transport one million protons with GPUMCD were 31-173 ms. Under similar conditions, Geant4 computation times were 1.4-20 h. The L eq formalism led to an intrinsic efficiency gain factor ranging between 30-630, increasing with the prescribed accuracy of simulations. The L eq formalism allows larger steps leading to a O(constant) algorithmic time complexity. It significantly accelerates Monte Carlo proton transport while preserving accuracy. It therefore constitutes a promising variance reduction technique for computing proton dose distributions in a clinical context.

Developing an eLearning tool formalizing in YAWL the guidelines used in a transfusion medicine service.

PubMed

Russo, Paola; Piazza, Miriam; Leonardi, Giorgio; Roncoroni, Layla; Russo, Carlo; Spadaro, Salvatore; Quaglini, Silvana

2012-01-01

The blood transfusion is a complex activity subject to a high risk of eventually fatal errors. The development and application of computer-based systems could help reducing the error rate, playing a fundamental role in the improvement of the quality of care. This poster presents an under development eLearning tool formalizing the guidelines of the transfusion process. This system, implemented in YAWL (Yet Another Workflow Language), will be used to train the personnel in order to improve the efficiency of care and to reduce errors.

Morphological computation and morphological control: steps toward a formal theory and applications.

PubMed

Füchslin, Rudolf M; Dzyakanchuk, Andrej; Flumini, Dandolo; Hauser, Helmut; Hunt, Kenneth J; Luchsinger, Rolf H; Reller, Benedikt; Scheidegger, Stephan; Walker, Richard

2013-01-01

Morphological computation can be loosely defined as the exploitation of the shape, material properties, and physical dynamics of a physical system to improve the efficiency of a computation. Morphological control is the application of morphological computing to a control task. In its theoretical part, this article sharpens and extends these definitions by suggesting new formalized definitions and identifying areas in which the definitions we propose are still inadequate. We go on to describe three ongoing studies, in which we are applying morphological control to problems in medicine and in chemistry. The first involves an inflatable support system for patients with impaired movement, and is based on macroscopic physics and concepts already tested in robotics. The two other case studies (self-assembly of chemical microreactors; models of induced cell repair in radio-oncology) describe processes and devices on the micrometer scale, in which the emergent dynamics of the underlying physical system (e.g., phase transitions) are dominated by stochastic processes such as diffusion.

Efficient calculation of beyond RPA correlation energies in the dielectric matrix formalism

NASA Astrophysics Data System (ADS)

Beuerle, Matthias; Graf, Daniel; Schurkus, Henry F.; Ochsenfeld, Christian

2018-05-01

We present efficient methods to calculate beyond random phase approximation (RPA) correlation energies for molecular systems with up to 500 atoms. To reduce the computational cost, we employ the resolution-of-the-identity and a double-Laplace transform of the non-interacting polarization propagator in conjunction with an atomic orbital formalism. Further improvements are achieved using integral screening and the introduction of Cholesky decomposed densities. Our methods are applicable to the dielectric matrix formalism of RPA including second-order screened exchange (RPA-SOSEX), the RPA electron-hole time-dependent Hartree-Fock (RPA-eh-TDHF) approximation, and RPA renormalized perturbation theory using an approximate exchange kernel (RPA-AXK). We give an application of our methodology by presenting RPA-SOSEX benchmark results for the L7 test set of large, dispersion dominated molecules, yielding a mean absolute error below 1 kcal/mol. The present work enables calculating beyond RPA correlation energies for significantly larger molecules than possible to date, thereby extending the applicability of these methods to a wider range of chemical systems.

Rigorous modal analysis of plasmonic nanoresonators

NASA Astrophysics Data System (ADS)

Yan, Wei; Faggiani, Rémi; Lalanne, Philippe

2018-05-01

The specificity of modal-expansion formalisms is their capabilities to model the physical properties in the natural resonance-state basis of the system in question, leading to a transparent interpretation of the numerical results. In electromagnetism, modal-expansion formalisms are routinely used for optical waveguides. In contrast, they are much less mature for analyzing open non-Hermitian systems, such as micro- and nanoresonators. Here, by accounting for material dispersion with auxiliary fields, we considerably extend the capabilities of these formalisms, in terms of computational effectiveness, number of states handled, and range of validity. We implement an efficient finite-element solver to compute the resonance states, and derive closed-form expressions of the modal excitation coefficients for reconstructing the scattered fields. Together, these two achievements allow us to perform rigorous modal analysis of complicated plasmonic resonators, being not limited to a few resonance states, with straightforward physical interpretations and remarkable computation speeds. We particularly show that, when the number of states retained in the expansion increases, convergence toward accurate predictions is achieved, offering a solid theoretical foundation for analyzing important issues, e.g., Fano interference, quenching, and coupling with the continuum, which are critical in nanophotonic research.

KARL: A Knowledge-Assisted Retrieval Language. M.S. Thesis Final Report, 1 Jul. 1985 - 31 Dec. 1987

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Triantafyllopoulos, Spiros

1985-01-01

Data classification and storage are tasks typically performed by application specialists. In contrast, information users are primarily non-computer specialists who use information in their decision-making and other activities. Interaction efficiency between such users and the computer is often reduced by machine requirements and resulting user reluctance to use the system. This thesis examines the problems associated with information retrieval for non-computer specialist users, and proposes a method for communicating in restricted English that uses knowledge of the entities involved, relationships between entities, and basic English language syntax and semantics to translate the user requests into formal queries. The proposed method includes an intelligent dictionary, syntax and semantic verifiers, and a formal query generator. In addition, the proposed system has a learning capability that can improve portability and performance. With the increasing demand for efficient human-machine communication, the significance of this thesis becomes apparent. As human resources become more valuable, software systems that will assist in improving the human-machine interface will be needed and research addressing new solutions will be of utmost importance. This thesis presents an initial design and implementation as a foundation for further research and development into the emerging field of natural language database query systems.

A Robust and Effective Smart-Card-Based Remote User Authentication Mechanism Using Hash Function

PubMed Central

Odelu, Vanga; Goswami, Adrijit

2014-01-01

In a remote user authentication scheme, a remote server verifies whether a login user is genuine and trustworthy, and also for mutual authentication purpose a login user validates whether the remote server is genuine and trustworthy. Several remote user authentication schemes using the password, the biometrics, and the smart card have been proposed in the literature. However, most schemes proposed in the literature are either computationally expensive or insecure against several known attacks. In this paper, we aim to propose a new robust and effective password-based remote user authentication scheme using smart card. Our scheme is efficient, because our scheme uses only efficient one-way hash function and bitwise XOR operations. Through the rigorous informal and formal security analysis, we show that our scheme is secure against possible known attacks. We perform the simulation for the formal security analysis using the widely accepted AVISPA (Automated Validation Internet Security Protocols and Applications) tool to ensure that our scheme is secure against passive and active attacks. Furthermore, our scheme supports efficiently the password change phase always locally without contacting the remote server and correctly. In addition, our scheme performs significantly better than other existing schemes in terms of communication, computational overheads, security, and features provided by our scheme. PMID:24892078

A robust and effective smart-card-based remote user authentication mechanism using hash function.

PubMed

Das, Ashok Kumar; Odelu, Vanga; Goswami, Adrijit

2014-01-01

In a remote user authentication scheme, a remote server verifies whether a login user is genuine and trustworthy, and also for mutual authentication purpose a login user validates whether the remote server is genuine and trustworthy. Several remote user authentication schemes using the password, the biometrics, and the smart card have been proposed in the literature. However, most schemes proposed in the literature are either computationally expensive or insecure against several known attacks. In this paper, we aim to propose a new robust and effective password-based remote user authentication scheme using smart card. Our scheme is efficient, because our scheme uses only efficient one-way hash function and bitwise XOR operations. Through the rigorous informal and formal security analysis, we show that our scheme is secure against possible known attacks. We perform the simulation for the formal security analysis using the widely accepted AVISPA (Automated Validation Internet Security Protocols and Applications) tool to ensure that our scheme is secure against passive and active attacks. Furthermore, our scheme supports efficiently the password change phase always locally without contacting the remote server and correctly. In addition, our scheme performs significantly better than other existing schemes in terms of communication, computational overheads, security, and features provided by our scheme.

Dendritic nonlinearities are tuned for efficient spike-based computations in cortical circuits.

PubMed

Ujfalussy, Balázs B; Makara, Judit K; Branco, Tiago; Lengyel, Máté

2015-12-24

Cortical neurons integrate thousands of synaptic inputs in their dendrites in highly nonlinear ways. It is unknown how these dendritic nonlinearities in individual cells contribute to computations at the level of neural circuits. Here, we show that dendritic nonlinearities are critical for the efficient integration of synaptic inputs in circuits performing analog computations with spiking neurons. We developed a theory that formalizes how a neuron's dendritic nonlinearity that is optimal for integrating synaptic inputs depends on the statistics of its presynaptic activity patterns. Based on their in vivo preynaptic population statistics (firing rates, membrane potential fluctuations, and correlations due to ensemble dynamics), our theory accurately predicted the responses of two different types of cortical pyramidal cells to patterned stimulation by two-photon glutamate uncaging. These results reveal a new computational principle underlying dendritic integration in cortical neurons by suggesting a functional link between cellular and systems--level properties of cortical circuits.

User's Guide for Computer Program that Routes Signal Traces

NASA Technical Reports Server (NTRS)

Hedgley, David R., Jr.

2000-01-01

This disk contains both a FORTRAN computer program and the corresponding user's guide that facilitates both its incorporation into your system and its utility. The computer program represents an efficient algorithm that routes signal traces on layers of a printed circuit with both through-pins and surface mounts. The computer program included is an implementation of the ideas presented in the theoretical paper titled "A Formal Algorithm for Routing Signal Traces on a Printed Circuit Board", NASA TP-3639 published in 1996. The computer program in the "connects" file can be read with a FORTRAN compiler and readily integrated into software unique to each particular environment where it might be used.

Acceleration of FDTD mode solver by high-performance computing techniques.

PubMed

Han, Lin; Xi, Yanping; Huang, Wei-Ping

2010-06-21

A two-dimensional (2D) compact finite-difference time-domain (FDTD) mode solver is developed based on wave equation formalism in combination with the matrix pencil method (MPM). The method is validated for calculation of both real guided and complex leaky modes of typical optical waveguides against the bench-mark finite-difference (FD) eigen mode solver. By taking advantage of the inherent parallel nature of the FDTD algorithm, the mode solver is implemented on graphics processing units (GPUs) using the compute unified device architecture (CUDA). It is demonstrated that the high-performance computing technique leads to significant acceleration of the FDTD mode solver with more than 30 times improvement in computational efficiency in comparison with the conventional FDTD mode solver running on CPU of a standard desktop computer. The computational efficiency of the accelerated FDTD method is in the same order of magnitude of the standard finite-difference eigen mode solver and yet require much less memory (e.g., less than 10%). Therefore, the new method may serve as an efficient, accurate and robust tool for mode calculation of optical waveguides even when the conventional eigen value mode solvers are no longer applicable due to memory limitation.

Habitual control of goal selection in humans

PubMed Central

Cushman, Fiery; Morris, Adam

2015-01-01

Humans choose actions based on both habit and planning. Habitual control is computationally frugal but adapts slowly to novel circumstances, whereas planning is computationally expensive but can adapt swiftly. Current research emphasizes the competition between habits and plans for behavioral control, yet many complex tasks instead favor their integration. We consider a hierarchical architecture that exploits the computational efficiency of habitual control to select goals while preserving the flexibility of planning to achieve those goals. We formalize this mechanism in a reinforcement learning setting, illustrate its costs and benefits, and experimentally demonstrate its spontaneous application in a sequential decision-making task. PMID:26460050

A survey of the computer literacy of undergraduate dental students at a University Dental School in Ireland during the academic year 1997-98.

PubMed

Ray, N J; Hannigan, A

1999-05-01

As dental practice management becomes more computer-based, the efficient functioning of the dentist will become dependent on adequate computer literacy. A survey has been carried out into the computer literacy of a cohort of 140 undergraduate dental students at a University Dental School in Ireland (years 1-5), in the academic year 1997-98. Aspects investigated by anonymous questionnaire were: (1) keyboard skills; (2) computer skills; (3) access to computer facilities; (4) software competencies and (5) use of medical library computer facilities. The students are relatively unfamiliar with basic computer hardware and software: 51.1% considered their expertise with computers as "poor"; 34.3% had taken a formal typewriting or computer keyboarding course; 7.9% had taken a formal computer course at university level and 67.2% were without access to computer facilities at their term-time residences. A majority of students had never used either word-processing, spreadsheet, or graphics programs. Programs relating to "informatics" were more popular, such as literature searching, accessing the Internet and the use of e-mail which represent the major use of the computers in the medical library. The lack of experience with computers may be addressed by including suitable computing courses at the secondary level (age 13-18 years) and/or tertiary level (FE/HE) education programmes. Such training may promote greater use of generic softwares, particularly in the library, with a more electronic-based approach to data handling.

Unified Approach To Control Of Motions Of Mobile Robots

NASA Technical Reports Server (NTRS)

Seraji, Homayoun

1995-01-01

Improved computationally efficient scheme developed for on-line coordinated control of both manipulation and mobility of robots that include manipulator arms mounted on mobile bases. Present scheme similar to one described in "Coordinated Control of Mobile Robotic Manipulators" (NPO-19109). Both schemes based on configuration-control formalism. Present one incorporates explicit distinction between holonomic and nonholonomic constraints. Several other prior articles in NASA Tech Briefs discussed aspects of configuration-control formalism. These include "Increasing the Dexterity of Redundant Robots" (NPO-17801), "Redundant Robot Can Avoid Obstacles" (NPO-17852), "Configuration-Control Scheme Copes with Singularities" (NPO-18556), "More Uses for Configuration Control of Robots" (NPO-18607/NPO-18608).

An intermediate level of abstraction for computational systems chemistry.

PubMed

Andersen, Jakob L; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F

2017-12-28

Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, because precise information on the molecular composition, the dominant reaction chemistry and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with large-scale reaction systems. The formalization of chemical reactions as graph grammars provides a generative system, well grounded in category theory, at the right level of abstraction for the analysis of large and complex reaction networks. An extension of the basic formalism into the realm of integer hyperflows allows for the identification of complex reaction patterns, such as autocatalysis, in large reaction networks using optimization techniques.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Author(s).

Combinatorial solutions to integrable hierarchies

NASA Astrophysics Data System (ADS)

Kazarian, M. E.; Lando, S. K.

2015-06-01

This paper reviews modern approaches to the construction of formal solutions to integrable hierarchies of mathematical physics whose coefficients are answers to various enumerative problems. The relationship between these approaches and the combinatorics of symmetric groups and their representations is explained. Applications of the results to the construction of efficient computations in problems related to models of quantum field theories are described. Bibliography: 34 titles.

A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation and Retrieval.

PubMed

Lee, Chia-Ju; Devine, Beth; Tarczy-Hornoch, Peter

2017-01-01

Pharmacogenomics holds promise as a critical component of precision medicine. Yet, the use of pharmacogenomics in routine clinical care is minimal, partly due to the lack of efficient and effective use of existing evidence. This paper describes the design, development, implementation and evaluation of a knowledge-based system that fulfills three critical features: a) providing clinically relevant evidence, b) applying an evidence-based approach, and c) using semantically computable formalism, to facilitate efficient evidence assessment to support timely decisions on adoption of pharmacogenomics in clinical care. To illustrate functionality, the system was piloted in the context of clopidogrel and warfarin pharmacogenomics. In contrast to existing pharmacogenomics knowledge bases, the developed system is the first to exploit the expressivity and reasoning power of logic-based representation formalism to enable unambiguous expression and automatic retrieval of pharmacogenomics evidence to support systematic review with meta-analysis.

On the Equivalence of Formal Grammars and Machines.

ERIC Educational Resources Information Center

Lund, Bruce

1991-01-01

Explores concepts of formal language and automata theory underlying computational linguistics. A computational formalism is described known as a "logic grammar," with which computational systems process linguistic data, with examples in declarative and procedural semantics and definite clause grammars. (13 references) (CB)

The changing landscape of astrostatistics and astroinformatics

NASA Astrophysics Data System (ADS)

Feigelson, Eric D.

2017-06-01

The history and current status of the cross-disciplinary fields of astrostatistics and astroinformatics are reviewed. Astronomers need a wide range of statistical methods for both data reduction and science analysis. With the proliferation of high-throughput telescopes, efficient large scale computational methods are also becoming essential. However, astronomers receive only weak training in these fields during their formal education. Interest in the fields is rapidly growing with conferences organized by scholarly societies, textbooks and tutorial workshops, and research studies pushing the frontiers of methodology. R, the premier language of statistical computing, can provide an important software environment for the incorporation of advanced statistical and computational methodology into the astronomical community.

Lattice dynamics calculations based on density-functional perturbation theory in real space

NASA Astrophysics Data System (ADS)

Shang, Honghui; Carbogno, Christian; Rinke, Patrick; Scheffler, Matthias

2017-06-01

A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered orbitals as basis functions is demonstrated exemplarily for the all-electron Fritz Haber Institute ab initio molecular simulations (FHI-aims) package. The convergence of the calculations with respect to numerical parameters is carefully investigated and a systematic comparison with finite-difference approaches is performed both for finite (molecules) and extended (periodic) systems. Finally, the scaling tests and scalability tests on massively parallel computer systems demonstrate the computational efficiency.

A direct method for unfolding the resolution function from measurements of neutron induced reactions

NASA Astrophysics Data System (ADS)

Žugec, P.; Colonna, N.; Sabate-Gilarte, M.; Vlachoudis, V.; Massimi, C.; Lerendegui-Marco, J.; Stamatopoulos, A.; Bacak, M.; Warren, S. G.; n TOF Collaboration

2017-12-01

The paper explores the numerical stability and the computational efficiency of a direct method for unfolding the resolution function from the measurements of the neutron induced reactions. A detailed resolution function formalism is laid out, followed by an overview of challenges present in a practical implementation of the method. A special matrix storage scheme is developed in order to facilitate both the memory management of the resolution function matrix, and to increase the computational efficiency of the matrix multiplication and decomposition procedures. Due to its admirable computational properties, a Cholesky decomposition is at the heart of the unfolding procedure. With the smallest but necessary modification of the matrix to be decomposed, the method is successfully applied to system of 105 × 105. However, the amplification of the uncertainties during the direct inversion procedures limits the applicability of the method to high-precision measurements of neutron induced reactions.

Dendritic nonlinearities are tuned for efficient spike-based computations in cortical circuits

PubMed Central

Ujfalussy, Balázs B; Makara, Judit K; Branco, Tiago; Lengyel, Máté

2015-01-01

Cortical neurons integrate thousands of synaptic inputs in their dendrites in highly nonlinear ways. It is unknown how these dendritic nonlinearities in individual cells contribute to computations at the level of neural circuits. Here, we show that dendritic nonlinearities are critical for the efficient integration of synaptic inputs in circuits performing analog computations with spiking neurons. We developed a theory that formalizes how a neuron's dendritic nonlinearity that is optimal for integrating synaptic inputs depends on the statistics of its presynaptic activity patterns. Based on their in vivo preynaptic population statistics (firing rates, membrane potential fluctuations, and correlations due to ensemble dynamics), our theory accurately predicted the responses of two different types of cortical pyramidal cells to patterned stimulation by two-photon glutamate uncaging. These results reveal a new computational principle underlying dendritic integration in cortical neurons by suggesting a functional link between cellular and systems--level properties of cortical circuits. DOI: http://dx.doi.org/10.7554/eLife.10056.001 PMID:26705334

Infinities in Quantum Field Theory and in Classical Computing: Renormalization Program

NASA Astrophysics Data System (ADS)

Manin, Yuri I.

Introduction. The main observable quantities in Quantum Field Theory, correlation functions, are expressed by the celebrated Feynman path integrals. A mathematical definition of them involving a measure and actual integration is still lacking. Instead, it is replaced by a series of ad hoc but highly efficient and suggestive heuristic formulas such as perturbation formalism. The latter interprets such an integral as a formal series of finite-dimensional but divergent integrals, indexed by Feynman graphs, the list of which is determined by the Lagrangian of the theory. Renormalization is a prescription that allows one to systematically "subtract infinities" from these divergent terms producing an asymptotic series for quantum correlation functions. On the other hand, graphs treated as "flowcharts", also form a combinatorial skeleton of the abstract computation theory. Partial recursive functions that according to Church's thesis exhaust the universe of (semi)computable maps are generally not everywhere defined due to potentially infinite searches and loops. In this paper I argue that such infinities can be addressed in the same way as Feynman divergences. More details can be found in [9,10].

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Path integrals with higher order actions: Application to realistic chemical systems

NASA Astrophysics Data System (ADS)

Lindoy, Lachlan P.; Huang, Gavin S.; Jordan, Meredith J. T.

2018-02-01

Quantum thermodynamic parameters can be determined using path integral Monte Carlo (PIMC) simulations. These simulations, however, become computationally demanding as the quantum nature of the system increases, although their efficiency can be improved by using higher order approximations to the thermal density matrix, specifically the action. Here we compare the standard, primitive approximation to the action (PA) and three higher order approximations, the Takahashi-Imada action (TIA), the Suzuki-Chin action (SCA) and the Chin action (CA). The resulting PIMC methods are applied to two realistic potential energy surfaces, for H2O and HCN-HNC, both of which are spectroscopically accurate and contain three-body interactions. We further numerically optimise, for each potential, the SCA parameter and the two free parameters in the CA, obtaining more significant improvements in efficiency than seen previously in the literature. For both H2O and HCN-HNC, accounting for all required potential and force evaluations, the optimised CA formalism is approximately twice as efficient as the TIA formalism and approximately an order of magnitude more efficient than the PA. The optimised SCA formalism shows similar efficiency gains to the CA for HCN-HNC but has similar efficiency to the TIA for H2O at low temperature. In H2O and HCN-HNC systems, the optimal value of the a1 CA parameter is approximately 1/3 , corresponding to an equal weighting of all force terms in the thermal density matrix, and similar to previous studies, the optimal α parameter in the SCA was ˜0.31. Importantly, poor choice of parameter significantly degrades the performance of the SCA and CA methods. In particular, for the CA, setting a1 = 0 is not efficient: the reduction in convergence efficiency is not offset by the lower number of force evaluations. We also find that the harmonic approximation to the CA parameters, whilst providing a fourth order approximation to the action, is not optimal for these realistic potentials: numerical optimisation leads to better approximate cancellation of the fifth order terms, with deviation between the harmonic and numerically optimised parameters more marked in the more quantum H2O system. This suggests that numerically optimising the CA or SCA parameters, which can be done at high temperature, will be important in fully realising the efficiency gains of these formalisms for realistic potentials.

Application of the Convolution Formalism to the Ocean Tide Potential: Results from the Gravity and Recovery and Climate Experiment (GRACE)

NASA Technical Reports Server (NTRS)

Desai, S. D.; Yuan, D. -N.

2006-01-01

A computationally efficient approach to reducing omission errors in ocean tide potential models is derived and evaluated using data from the Gravity Recovery and Climate Experiment (GRACE) mission. Ocean tide height models are usually explicitly available at a few frequencies, and a smooth unit response is assumed to infer the response across the tidal spectrum. The convolution formalism of Munk and Cartwright (1966) models this response function with a Fourier series. This allows the total ocean tide height, and therefore the total ocean tide potential, to be modeled as a weighted sum of past, present, and future values of the tide-generating potential. Previous applications of the convolution formalism have usually been limited to tide height models, but we extend it to ocean tide potential models. We use luni-solar ephemerides to derive the required tide-generating potential so that the complete spectrum of the ocean tide potential is efficiently represented. In contrast, the traditionally adopted harmonic model of the ocean tide potential requires the explicit sum of the contributions from individual tidal frequencies. It is therefore subject to omission errors from neglected frequencies and is computationally more intensive. Intersatellite range rate data from the GRACE mission are used to compare convolution and harmonic models of the ocean tide potential. The monthly range rate residual variance is smaller by 4-5%, and the daily residual variance is smaller by as much as 15% when using the convolution model than when using a harmonic model that is defined by twice the number of parameters.

Bypassing the malfunction junction in warm dense matter simulations

NASA Astrophysics Data System (ADS)

Cangi, Attila; Pribram-Jones, Aurora

2015-03-01

Simulation of warm dense matter requires computational methods that capture both quantum and classical behavior efficiently under high-temperature and high-density conditions. The state-of-the-art approach to model electrons and ions under those conditions is density functional theory molecular dynamics, but this method's computational cost skyrockets as temperatures and densities increase. We propose finite-temperature potential functional theory as an in-principle-exact alternative that suffers no such drawback. In analogy to the zero-temperature theory developed previously, we derive an orbital-free free energy approximation through a coupling-constant formalism. Our density approximation and its associated free energy approximation demonstrate the method's accuracy and efficiency. A.C. has been partially supported by NSF Grant CHE-1112442. A.P.J. is supported by DOE Grant DE-FG02-97ER25308.

Delayed Slater determinant update algorithms for high efficiency quantum Monte Carlo

DOE PAGES

McDaniel, Tyler; D’Azevedo, Ed F.; Li, Ying Wai; ...

2017-11-07

Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is therefore formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with applicationmore » of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. Here this procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi- core CPUs and GPUs.« less

Delayed Slater determinant update algorithms for high efficiency quantum Monte Carlo

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDaniel, Tyler; D’Azevedo, Ed F.; Li, Ying Wai

Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is therefore formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with applicationmore » of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. Here this procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi- core CPUs and GPUs.« less

Delayed Slater determinant update algorithms for high efficiency quantum Monte Carlo.

PubMed

McDaniel, T; D'Azevedo, E F; Li, Y W; Wong, K; Kent, P R C

2017-11-07

Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is, therefore, formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with an application of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. This procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo, where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi-core central processing units and graphical processing units.

Delayed Slater determinant update algorithms for high efficiency quantum Monte Carlo

NASA Astrophysics Data System (ADS)

McDaniel, T.; D'Azevedo, E. F.; Li, Y. W.; Wong, K.; Kent, P. R. C.

2017-11-01

Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is, therefore, formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with an application of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. This procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo, where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi-core central processing units and graphical processing units.

Hybrid-dual-fourier tomographic algorithm for a fast three-dimensionial optical image reconstruction in turbid media

NASA Technical Reports Server (NTRS)

Alfano, Robert R. (Inventor); Cai, Wei (Inventor)

2007-01-01

A reconstruction technique for reducing computation burden in the 3D image processes, wherein the reconstruction procedure comprises an inverse and a forward model. The inverse model uses a hybrid dual Fourier algorithm that combines a 2D Fourier inversion with a 1D matrix inversion to thereby provide high-speed inverse computations. The inverse algorithm uses a hybrid transfer to provide fast Fourier inversion for data of multiple sources and multiple detectors. The forward model is based on an analytical cumulant solution of a radiative transfer equation. The accurate analytical form of the solution to the radiative transfer equation provides an efficient formalism for fast computation of the forward model.

An Introduction to the BFS Method and Its Use to Model Binary NiAl Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Noebe, Ronald D.; Ferrante, J.; Amador, C.

1998-01-01

We introduce the Bozzolo-Ferrante-Smith (BFS) method for alloys as a computationally efficient tool for aiding in the process of alloy design. An intuitive description of the BFS method is provided, followed by a formal discussion of its implementation. The method is applied to the study of the defect structure of NiAl binary alloys. The groundwork is laid for a detailed progression to higher order NiAl-based alloys linking theoretical calculations and computer simulations based on the BFS method and experimental work validating each step of the alloy design process.

Computational neural learning formalisms for manipulator inverse kinematics

NASA Technical Reports Server (NTRS)

Gulati, Sandeep; Barhen, Jacob; Iyengar, S. Sitharama

1989-01-01

An efficient, adaptive neural learning paradigm for addressing the inverse kinematics of redundant manipulators is presented. The proposed methodology exploits the infinite local stability of terminal attractors - a new class of mathematical constructs which provide unique information processing capabilities to artificial neural systems. For robotic applications, synaptic elements of such networks can rapidly acquire the kinematic invariances embedded within the presented samples. Subsequently, joint-space configurations, required to follow arbitrary end-effector trajectories, can readily be computed. In a significant departure from prior neuromorphic learning algorithms, this methodology provides mechanisms for incorporating an in-training skew to handle kinematics and environmental constraints.

Genomic region operation kit for flexible processing of deep sequencing data.

PubMed

Ovaska, Kristian; Lyly, Lauri; Sahu, Biswajyoti; Jänne, Olli A; Hautaniemi, Sampsa

2013-01-01

Computational analysis of data produced in deep sequencing (DS) experiments is challenging due to large data volumes and requirements for flexible analysis approaches. Here, we present a mathematical formalism based on set algebra for frequently performed operations in DS data analysis to facilitate translation of biomedical research questions to language amenable for computational analysis. With the help of this formalism, we implemented the Genomic Region Operation Kit (GROK), which supports various DS-related operations such as preprocessing, filtering, file conversion, and sample comparison. GROK provides high-level interfaces for R, Python, Lua, and command line, as well as an extension C++ API. It supports major genomic file formats and allows storing custom genomic regions in efficient data structures such as red-black trees and SQL databases. To demonstrate the utility of GROK, we have characterized the roles of two major transcription factors (TFs) in prostate cancer using data from 10 DS experiments. GROK is freely available with a user guide from >http://csbi.ltdk.helsinki.fi/grok/.

Software Validation via Model Animation

NASA Technical Reports Server (NTRS)

Dutle, Aaron M.; Munoz, Cesar A.; Narkawicz, Anthony J.; Butler, Ricky W.

2015-01-01

This paper explores a new approach to validating software implementations that have been produced from formally-verified algorithms. Although visual inspection gives some confidence that the implementations faithfully reflect the formal models, it does not provide complete assurance that the software is correct. The proposed approach, which is based on animation of formal specifications, compares the outputs computed by the software implementations on a given suite of input values to the outputs computed by the formal models on the same inputs, and determines if they are equal up to a given tolerance. The approach is illustrated on a prototype air traffic management system that computes simple kinematic trajectories for aircraft. Proofs for the mathematical models of the system's algorithms are carried out in the Prototype Verification System (PVS). The animation tool PVSio is used to evaluate the formal models on a set of randomly generated test cases. Output values computed by PVSio are compared against output values computed by the actual software. This comparison improves the assurance that the translation from formal models to code is faithful and that, for example, floating point errors do not greatly affect correctness and safety properties.

A brief overview of NASA Langley's research program in formal methods

NASA Technical Reports Server (NTRS)

1992-01-01

An overview of NASA Langley's research program in formal methods is presented. The major goal of this work is to bring formal methods technology to a sufficiently mature level for use by the United States aerospace industry. Towards this goal, work is underway to design and formally verify a fault-tolerant computing platform suitable for advanced flight control applications. Also, several direct technology transfer efforts have been initiated that apply formal methods to critical subsystems of real aerospace computer systems. The research team consists of six NASA civil servants and contractors from Boeing Military Aircraft Company, Computational Logic Inc., Odyssey Research Associates, SRI International, University of California at Davis, and Vigyan Inc.

Systems, methods and apparatus for implementation of formal specifications derived from informal requirements

NASA Technical Reports Server (NTRS)

Hinchey, Michael G. (Inventor); Rouff, Christopher A. (Inventor); Rash, James L. (Inventor); Erickson, John D. (Inventor); Gracinin, Denis (Inventor)

2010-01-01

Systems, methods and apparatus are provided through which in some embodiments an informal specification is translated without human intervention into a formal specification. In some embodiments the formal specification is a process-based specification. In some embodiments, the formal specification is translated into a high-level computer programming language which is further compiled into a set of executable computer instructions.

Proceedings of the Second NASA Formal Methods Symposium

NASA Technical Reports Server (NTRS)

Munoz, Cesar (Editor)

2010-01-01

This publication contains the proceedings of the Second NASA Formal Methods Symposium sponsored by the National Aeronautics and Space Administration and held in Washington D.C. April 13-15, 2010. Topics covered include: Decision Engines for Software Analysis using Satisfiability Modulo Theories Solvers; Verification and Validation of Flight-Critical Systems; Formal Methods at Intel -- An Overview; Automatic Review of Abstract State Machines by Meta Property Verification; Hardware-independent Proofs of Numerical Programs; Slice-based Formal Specification Measures -- Mapping Coupling and Cohesion Measures to Formal Z; How Formal Methods Impels Discovery: A Short History of an Air Traffic Management Project; A Machine-Checked Proof of A State-Space Construction Algorithm; Automated Assume-Guarantee Reasoning for Omega-Regular Systems and Specifications; Modeling Regular Replacement for String Constraint Solving; Using Integer Clocks to Verify the Timing-Sync Sensor Network Protocol; Can Regulatory Bodies Expect Efficient Help from Formal Methods?; Synthesis of Greedy Algorithms Using Dominance Relations; A New Method for Incremental Testing of Finite State Machines; Verification of Faulty Message Passing Systems with Continuous State Space in PVS; Phase Two Feasibility Study for Software Safety Requirements Analysis Using Model Checking; A Prototype Embedding of Bluespec System Verilog in the PVS Theorem Prover; SimCheck: An Expressive Type System for Simulink; Coverage Metrics for Requirements-Based Testing: Evaluation of Effectiveness; Software Model Checking of ARINC-653 Flight Code with MCP; Evaluation of a Guideline by Formal Modelling of Cruise Control System in Event-B; Formal Verification of Large Software Systems; Symbolic Computation of Strongly Connected Components Using Saturation; Towards the Formal Verification of a Distributed Real-Time Automotive System; Slicing AADL Specifications for Model Checking; Model Checking with Edge-valued Decision Diagrams; and Data-flow based Model Analysis.

Quantified Event Automata: Towards Expressive and Efficient Runtime Monitors

NASA Technical Reports Server (NTRS)

Barringer, Howard; Falcone, Ylies; Havelund, Klaus; Reger, Giles; Rydeheard, David

2012-01-01

Runtime verification is the process of checking a property on a trace of events produced by the execution of a computational system. Runtime verification techniques have recently focused on parametric specifications where events take data values as parameters. These techniques exist on a spectrum inhabited by both efficient and expressive techniques. These characteristics are usually shown to be conflicting - in state-of-the-art solutions, efficiency is obtained at the cost of loss of expressiveness and vice-versa. To seek a solution to this conflict we explore a new point on the spectrum by defining an alternative runtime verification approach.We introduce a new formalism for concisely capturing expressive specifications with parameters. Our technique is more expressive than the currently most efficient techniques while at the same time allowing for optimizations.

Generalized Bondi-Sachs equations for characteristic formalism of numerical relativity

NASA Astrophysics Data System (ADS)

Cao, Zhoujian; He, Xiaokai

2013-11-01

The Cauchy formalism of numerical relativity has been successfully applied to simulate various dynamical spacetimes without any symmetry assumption. But discovering how to set a mathematically consistent and physically realistic boundary condition is still an open problem for Cauchy formalism. In addition, the numerical truncation error and finite region ambiguity affect the accuracy of gravitational wave form calculation. As to the finite region ambiguity issue, the characteristic extraction method helps much. But it does not solve all of the above issues. Besides the above problems for Cauchy formalism, the computational efficiency is another problem. Although characteristic formalism of numerical relativity suffers the difficulty from caustics in the inner near zone, it has advantages in relation to all of the issues listed above. Cauchy-characteristic matching (CCM) is a possible way to take advantage of characteristic formalism regarding these issues and treat the inner caustics at the same time. CCM has difficulty treating the gauge difference between the Cauchy part and the characteristic part. We propose generalized Bondi-Sachs equations for characteristic formalism for the Cauchy-characteristic matching end. Our proposal gives out a possible same numerical evolution scheme for both the Cauchy part and the characteristic part. And our generalized Bondi-Sachs equations have one adjustable gauge freedom which can be used to relate the gauge used in the Cauchy part. Then these equations can make the Cauchy part and the characteristic part share a consistent gauge condition. So our proposal gives a possible new starting point for Cauchy-characteristic matching.

Formalisms for user interface specification and design

NASA Technical Reports Server (NTRS)

Auernheimer, Brent J.

1989-01-01

The application of formal methods to the specification and design of human-computer interfaces is described. A broad outline of human-computer interface problems, a description of the field of cognitive engineering and two relevant research results, the appropriateness of formal specification techniques, and potential NASA application areas are described.

Information Technology and Literacy Assessment.

ERIC Educational Resources Information Center

Balajthy, Ernest

2002-01-01

Compares technology predictions from around 1989 with the technology of 2002. Discusses the place of computer-based assessment today, computer-scored testing, computer-administered formal assessment, Internet-based formal assessment, computerized adaptive tests, placement tests, informal assessment, electronic portfolios, information management,…

Fully relativistic pseudopotential formalism under an atomic orbital basis: spin-orbit splittings and magnetic anisotropies.

PubMed

Cuadrado, R; Cerdá, J I

2012-02-29

We present an efficient implementation of the spin-orbit coupling within the density functional theory based SIESTA code (2002 J. Phys.: Condens. Matter 14 2745) using the fully relativistic and totally separable pseudopotential formalism of Hemstreet et al (1993 Phys. Rev. B 47 4238). First, we obtain the spin-orbit splittings for several systems ranging from isolated atoms to bulk metals and semiconductors as well as the Au(111) surface state. Next, and after extensive tests on the accuracy of the formalism, we also demonstrate its capability to yield reliable values for the magnetic anisotropy energy in magnetic systems. In particular, we focus on the L1(0) binary alloys and on two large molecules: Mn(6)O(2)(H -sao)(6)(O(2)CH)(2)(CH(3)OH)(4) and Co(4)(hmp)(4)(CH(3)OH)(4)Cl(4). In all cases our calculated anisotropies are in good agreement with those obtained with full-potential methods, despite the latter being, in general, computationally more demanding.

The effect of dephasing on the thermoelectric efficiency of molecular junctions.

PubMed

Zimbovskaya, Natalya A

2014-07-09

In this work we report the results of theoretical analysis of the effect of the thermal environment on the thermoelectric efficiency of molecular junctions. The environment is represented by two thermal phonon baths associated with the electrodes, which are kept at different temperatures. The analysis is carried out using the Buttiker model within the scattering matrix formalism to compute electron transmission through the system. This approach is further developed so that the dephasing parameters are expressed in terms of relevant energies, including the thermal energy, strengths of coupling between the molecular bridge and the electrodes and characteristic energies of electron-phonon interactions. It is shown that the latter significantly affect thermoelectric efficiency by destroying the coherency of electron transport through the considered system.

Adjoint shape optimization for fluid-structure interaction of ducted flows

NASA Astrophysics Data System (ADS)

Heners, J. P.; Radtke, L.; Hinze, M.; Düster, A.

2018-03-01

Based on the coupled problem of time-dependent fluid-structure interaction, equations for an appropriate adjoint problem are derived by the consequent use of the formal Lagrange calculus. Solutions of both primal and adjoint equations are computed in a partitioned fashion and enable the formulation of a surface sensitivity. This sensitivity is used in the context of a steepest descent algorithm for the computation of the required gradient of an appropriate cost functional. The efficiency of the developed optimization approach is demonstrated by minimization of the pressure drop in a simple two-dimensional channel flow and in a three-dimensional ducted flow surrounded by a thin-walled structure.

Efficient and Scalable Cross-Matching of (Very) Large Catalogs

NASA Astrophysics Data System (ADS)

Pineau, F.-X.; Boch, T.; Derriere, S.

2011-07-01

Whether it be for building multi-wavelength datasets from independent surveys, studying changes in objects luminosities, or detecting moving objects (stellar proper motions, asteroids), cross-catalog matching is a technique widely used in astronomy. The need for efficient, reliable and scalable cross-catalog matching is becoming even more pressing with forthcoming projects which will produce huge catalogs in which astronomers will dig for rare objects, perform statistical analysis and classification, or real-time transients detection. We have developed a formalism and the corresponding technical framework to address the challenge of fast cross-catalog matching. Our formalism supports more than simple nearest-neighbor search, and handles elliptical positional errors. Scalability is improved by partitioning the sky using the HEALPix scheme, and processing independently each sky cell. The use of multi-threaded two-dimensional kd-trees adapted to managing equatorial coordinates enables efficient neighbor search. The whole process can run on a single computer, but could also use clusters of machines to cross-match future very large surveys such as GAIA or LSST in reasonable times. We already achieve performances where the 2MASS (˜470M sources) and SDSS DR7 (˜350M sources) can be matched on a single machine in less than 10 minutes. We aim at providing astronomers with a catalog cross-matching service, available on-line and leveraging on the catalogs present in the VizieR database. This service will allow users both to access pre-computed cross-matches across some very large catalogs, and to run customized cross-matching operations. It will also support VO protocols for synchronous or asynchronous queries.

Formal Techniques for Synchronized Fault-Tolerant Systems

NASA Technical Reports Server (NTRS)

DiVito, Ben L.; Butler, Ricky W.

1992-01-01

We present the formal verification of synchronizing aspects of the Reliable Computing Platform (RCP), a fault-tolerant computing system for digital flight control applications. The RCP uses NMR-style redundancy to mask faults and internal majority voting to purge the effects of transient faults. The system design has been formally specified and verified using the EHDM verification system. Our formalization is based on an extended state machine model incorporating snapshots of local processors clocks.

Formal Operations and Learning Style Predict Success in Statistics and Computer Science Courses.

ERIC Educational Resources Information Center

Hudak, Mary A.; Anderson, David E.

1990-01-01

Studies 94 undergraduate students in introductory statistics and computer science courses. Applies Formal Operations Reasoning Test (FORT) and Kolb's Learning Style Inventory (LSI). Finds that substantial numbers of students have not achieved the formal operation level of cognitive maturity. Emphasizes need to examine students learning style and…

Self-Organized Service Negotiation for Collaborative Decision Making

PubMed Central

Zhang, Bo; Zheng, Ziming

2014-01-01

This paper proposes a self-organized service negotiation method for CDM in intelligent and automatic manners. It mainly includes three phases: semantic-based capacity evaluation for the CDM sponsor, trust computation of the CDM organization, and negotiation selection of the decision-making service provider (DMSP). In the first phase, the CDM sponsor produces the formal semantic description of the complex decision task for DMSP and computes the capacity evaluation values according to participator instructions from different DMSPs. In the second phase, a novel trust computation approach is presented to compute the subjective belief value, the objective reputation value, and the recommended trust value. And in the third phase, based on the capacity evaluation and trust computation, a negotiation mechanism is given to efficiently implement the service selection. The simulation experiment results show that our self-organized service negotiation method is feasible and effective for CDM. PMID:25243228

Self-organized service negotiation for collaborative decision making.

PubMed

Zhang, Bo; Huang, Zhenhua; Zheng, Ziming

2014-01-01

This paper proposes a self-organized service negotiation method for CDM in intelligent and automatic manners. It mainly includes three phases: semantic-based capacity evaluation for the CDM sponsor, trust computation of the CDM organization, and negotiation selection of the decision-making service provider (DMSP). In the first phase, the CDM sponsor produces the formal semantic description of the complex decision task for DMSP and computes the capacity evaluation values according to participator instructions from different DMSPs. In the second phase, a novel trust computation approach is presented to compute the subjective belief value, the objective reputation value, and the recommended trust value. And in the third phase, based on the capacity evaluation and trust computation, a negotiation mechanism is given to efficiently implement the service selection. The simulation experiment results show that our self-organized service negotiation method is feasible and effective for CDM.

Computing generalized Langevin equations and generalized Fokker-Planck equations.

PubMed

Darve, Eric; Solomon, Jose; Kia, Amirali

2009-07-07

The Mori-Zwanzig formalism is an effective tool to derive differential equations describing the evolution of a small number of resolved variables. In this paper we present its application to the derivation of generalized Langevin equations and generalized non-Markovian Fokker-Planck equations. We show how long time scales rates and metastable basins can be extracted from these equations. Numerical algorithms are proposed to discretize these equations. An important aspect is the numerical solution of the orthogonal dynamics equation which is a partial differential equation in a high dimensional space. We propose efficient numerical methods to solve this orthogonal dynamics equation. In addition, we present a projection formalism of the Mori-Zwanzig type that is applicable to discrete maps. Numerical applications are presented from the field of Hamiltonian systems.

On the effect of tilted roof reflectors in Martin-Puplett spectrometers

NASA Astrophysics Data System (ADS)

Schillaci, Alessandro; de Bernardis, Paolo

2012-01-01

In this paper we analyze theoretically and experimentally the effect of tilt of the roof mirrors in a double pendulum Martin-Puplett Polarizing Interferometer (MPI), focusing on the polarization of the interfering beams. In principle, the tilt affects the efficiency and polarimetric properties of the interferometer. The case of a moderate resolution spectrometer is analysed in detail. Using the Stokes formalism we recover the analytical expressions for the orientation angle and the ellipticity of the beam reflected from a metallic surface, and we compute these quantities for the roof-mirror of a MPI. We find that the polarization rotation and depolarization are small. Using the Jones formalism we propagate their effect on the measured interferogram and spectrum, and demonstrate that the performance degradation is small compared to other systematic effects.

Provable Transient Recovery for Frame-Based, Fault-Tolerant Computing Systems

NASA Technical Reports Server (NTRS)

DiVito, Ben L.; Butler, Ricky W.

1992-01-01

We present a formal verification of the transient fault recovery aspects of the Reliable Computing Platform (RCP), a fault-tolerant computing system architecture for digital flight control applications. The RCP uses NMR-style redundancy to mask faults and internal majority voting to purge the effects of transient faults. The system design has been formally specified and verified using the EHDM verification system. Our formalization accommodates a wide variety of voting schemes for purging the effects of transients.

Efficient and anonymous two-factor user authentication in wireless sensor networks: achieving user anonymity with lightweight sensor computation.

PubMed

Nam, Junghyun; Choo, Kim-Kwang Raymond; Han, Sangchul; Kim, Moonseong; Paik, Juryon; Won, Dongho

2015-01-01

A smart-card-based user authentication scheme for wireless sensor networks (hereafter referred to as a SCA-WSN scheme) is designed to ensure that only users who possess both a smart card and the corresponding password are allowed to gain access to sensor data and their transmissions. Despite many research efforts in recent years, it remains a challenging task to design an efficient SCA-WSN scheme that achieves user anonymity. The majority of published SCA-WSN schemes use only lightweight cryptographic techniques (rather than public-key cryptographic techniques) for the sake of efficiency, and have been demonstrated to suffer from the inability to provide user anonymity. Some schemes employ elliptic curve cryptography for better security but require sensors with strict resource constraints to perform computationally expensive scalar-point multiplications; despite the increased computational requirements, these schemes do not provide user anonymity. In this paper, we present a new SCA-WSN scheme that not only achieves user anonymity but also is efficient in terms of the computation loads for sensors. Our scheme employs elliptic curve cryptography but restricts its use only to anonymous user-to-gateway authentication, thereby allowing sensors to perform only lightweight cryptographic operations. Our scheme also enjoys provable security in a formal model extended from the widely accepted Bellare-Pointcheval-Rogaway (2000) model to capture the user anonymity property and various SCA-WSN specific attacks (e.g., stolen smart card attacks, node capture attacks, privileged insider attacks, and stolen verifier attacks).

Efficient and Anonymous Two-Factor User Authentication in Wireless Sensor Networks: Achieving User Anonymity with Lightweight Sensor Computation

PubMed Central

Nam, Junghyun; Choo, Kim-Kwang Raymond; Han, Sangchul; Kim, Moonseong; Paik, Juryon; Won, Dongho

2015-01-01

A smart-card-based user authentication scheme for wireless sensor networks (hereafter referred to as a SCA-WSN scheme) is designed to ensure that only users who possess both a smart card and the corresponding password are allowed to gain access to sensor data and their transmissions. Despite many research efforts in recent years, it remains a challenging task to design an efficient SCA-WSN scheme that achieves user anonymity. The majority of published SCA-WSN schemes use only lightweight cryptographic techniques (rather than public-key cryptographic techniques) for the sake of efficiency, and have been demonstrated to suffer from the inability to provide user anonymity. Some schemes employ elliptic curve cryptography for better security but require sensors with strict resource constraints to perform computationally expensive scalar-point multiplications; despite the increased computational requirements, these schemes do not provide user anonymity. In this paper, we present a new SCA-WSN scheme that not only achieves user anonymity but also is efficient in terms of the computation loads for sensors. Our scheme employs elliptic curve cryptography but restricts its use only to anonymous user-to-gateway authentication, thereby allowing sensors to perform only lightweight cryptographic operations. Our scheme also enjoys provable security in a formal model extended from the widely accepted Bellare-Pointcheval-Rogaway (2000) model to capture the user anonymity property and various SCA-WSN specific attacks (e.g., stolen smart card attacks, node capture attacks, privileged insider attacks, and stolen verifier attacks). PMID:25849359

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Kuang; Libisch, Florian; Carter, Emily A., E-mail: eac@princeton.edu

We report a new implementation of the density functional embedding theory (DFET) in the VASP code, using the projector-augmented-wave (PAW) formalism. Newly developed algorithms allow us to efficiently perform optimized effective potential optimizations within PAW. The new algorithm generates robust and physically correct embedding potentials, as we verified using several test systems including a covalently bound molecule, a metal surface, and bulk semiconductors. We show that with the resulting embedding potential, embedded cluster models can reproduce the electronic structure of point defects in bulk semiconductors, thereby demonstrating the validity of DFET in semiconductors for the first time. Compared to ourmore » previous version, the new implementation of DFET within VASP affords use of all features of VASP (e.g., a systematic PAW library, a wide selection of functionals, a more flexible choice of U correction formalisms, and faster computational speed) with DFET. Furthermore, our results are fairly robust with respect to both plane-wave and Gaussian type orbital basis sets in the embedded cluster calculations. This suggests that the density functional embedding method is potentially an accurate and efficient way to study properties of isolated defects in semiconductors.« less

Protection - Principles and practice.

NASA Technical Reports Server (NTRS)

Graham, G. S.; Denning, P. J.

1972-01-01

The protection mechanisms of computer systems control the access to objects, especially information objects. The principles of protection system design are formalized as a model (theory) of protection. Each process has a unique identification number which is attached by the system to each access attempted by the process. Details of system implementation are discussed, taking into account the storing of the access matrix, aspects of efficiency, and the selection of subjects and objects. Two systems which have protection features incorporating all the elements of the model are described.

Directly executable formal models of middleware for MANET and Cloud Networking and Computing

NASA Astrophysics Data System (ADS)

Pashchenko, D. V.; Sadeq Jaafar, Mustafa; Zinkin, S. A.; Trokoz, D. A.; Pashchenko, T. U.; Sinev, M. P.

2016-04-01

The article considers some “directly executable” formal models that are suitable for the specification of computing and networking in the cloud environment and other networks which are similar to wireless networks MANET. These models can be easily programmed and implemented on computer networks.

Integrated analysis of engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1981-01-01

The need for light, durable, fuel efficient, cost effective aircraft requires the development of engine structures which are flexible, made from advaced materials (including composites), resist higher temperatures, maintain tighter clearances and have lower maintenance costs. The formal quantification of any or several of these requires integrated computer programs (multilevel and/or interdisciplinary analysis programs interconnected) for engine structural analysis/design. Several integrated analysis computer prorams are under development at Lewis Reseach Center. These programs include: (1) COBSTRAN-Composite Blade Structural Analysis, (2) CODSTRAN-Composite Durability Structural Analysis, (3) CISTRAN-Composite Impact Structural Analysis, (4) STAEBL-StruTailoring of Engine Blades, and (5) ESMOSS-Engine Structures Modeling Software System. Three other related programs, developed under Lewis sponsorship, are described.

Spectral-based propagation schemes for time-dependent quantum systems with application to carbon nanotubes

NASA Astrophysics Data System (ADS)

Chen, Zuojing; Polizzi, Eric

2010-11-01

Effective modeling and numerical spectral-based propagation schemes are proposed for addressing the challenges in time-dependent quantum simulations of systems ranging from atoms, molecules, and nanostructures to emerging nanoelectronic devices. While time-dependent Hamiltonian problems can be formally solved by propagating the solutions along tiny simulation time steps, a direct numerical treatment is often considered too computationally demanding. In this paper, however, we propose to go beyond these limitations by introducing high-performance numerical propagation schemes to compute the solution of the time-ordered evolution operator. In addition to the direct Hamiltonian diagonalizations that can be efficiently performed using the new eigenvalue solver FEAST, we have designed a Gaussian propagation scheme and a basis-transformed propagation scheme (BTPS) which allow to reduce considerably the simulation times needed by time intervals. It is outlined that BTPS offers the best computational efficiency allowing new perspectives in time-dependent simulations. Finally, these numerical schemes are applied to study the ac response of a (5,5) carbon nanotube within a three-dimensional real-space mesh framework.

Formal design and verification of a reliable computing platform for real-time control. Phase 2: Results

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Divito, Ben L.

1992-01-01

The design and formal verification of the Reliable Computing Platform (RCP), a fault tolerant computing system for digital flight control applications is presented. The RCP uses N-Multiply Redundant (NMR) style redundancy to mask faults and internal majority voting to flush the effects of transient faults. The system is formally specified and verified using the Ehdm verification system. A major goal of this work is to provide the system with significant capability to withstand the effects of High Intensity Radiated Fields (HIRF).

A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

PubMed Central

Bazinet, Adam L.; Zwickl, Derrick J.; Cummings, Michael P.

2014-01-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.] PMID:24789072

Algorithms in the historical emergence of word senses.

PubMed

Ramiro, Christian; Srinivasan, Mahesh; Malt, Barbara C; Xu, Yang

2018-03-06

Human language relies on a finite lexicon to express a potentially infinite set of ideas. A key result of this tension is that words acquire novel senses over time. However, the cognitive processes that underlie the historical emergence of new word senses are poorly understood. Here, we present a computational framework that formalizes competing views of how new senses of a word might emerge by attaching to existing senses of the word. We test the ability of the models to predict the temporal order in which the senses of individual words have emerged, using an historical lexicon of English spanning the past millennium. Our findings suggest that word senses emerge in predictable ways, following an historical path that reflects cognitive efficiency, predominantly through a process of nearest-neighbor chaining. Our work contributes a formal account of the generative processes that underlie lexical evolution.

An efficient method for removing point sources from full-sky radio interferometric maps

NASA Astrophysics Data System (ADS)

Berger, Philippe; Oppermann, Niels; Pen, Ue-Li; Shaw, J. Richard

2017-12-01

A new generation of wide-field radio interferometers designed for 21-cm surveys is being built as drift scan instruments allowing them to observe large fractions of the sky. With large numbers of antennas and frequency channels, the enormous instantaneous data rates of these telescopes require novel, efficient, data management and analysis techniques. The m-mode formalism exploits the periodicity of such data with the sidereal day, combined with the assumption of statistical isotropy of the sky, to achieve large computational savings and render optimal analysis methods computationally tractable. We present an extension to that work that allows us to adopt a more realistic sky model and treat objects such as bright point sources. We develop a linear procedure for deconvolving maps, using a Wiener filter reconstruction technique, which simultaneously allows filtering of these unwanted components. We construct an algorithm, based on the Sherman-Morrison-Woodbury formula, to efficiently invert the data covariance matrix, as required for any optimal signal-to-noise ratio weighting. The performance of our algorithm is demonstrated using simulations of a cylindrical transit telescope.

Quantum dynamical framework for Brownian heat engines

NASA Astrophysics Data System (ADS)

Agarwal, G. S.; Chaturvedi, S.

2013-07-01

We present a self-contained formalism modeled after the Brownian motion of a quantum harmonic oscillator for describing the performance of microscopic Brownian heat engines such as Carnot, Stirling, and Otto engines. Our theory, besides reproducing the standard thermodynamics results in the steady state, enables us to study the role dissipation plays in determining the efficiency of Brownian heat engines under actual laboratory conditions. In particular, we analyze in detail the dynamics associated with decoupling a system in equilibrium with one bath and recoupling it to another bath and obtain exact analytical results, which are shown to have significant ramifications on the efficiencies of engines involving such a step. We also develop a simple yet powerful technique for computing corrections to the steady state results arising from finite operation time and use it to arrive at the thermodynamic complementarity relations for various operating conditions and also to compute the efficiencies of the three engines cited above at maximum power. Some of the methods and exactly solvable models presented here are interesting in their own right and could find useful applications in other contexts as well.

A Mutual Authentication Framework for Wireless Medical Sensor Networks.

PubMed

Srinivas, Jangirala; Mishra, Dheerendra; Mukhopadhyay, Sourav

2017-05-01

Wireless medical sensor networks (WMSN) comprise of distributed sensors, which can sense human physiological signs and monitor the health condition of the patient. It is observed that providing privacy to the patient's data is an important issue and can be challenging. The information passing is done via the public channel in WMSN. Thus, the patient, sensitive information can be obtained by eavesdropping or by unauthorized use of handheld devices which the health professionals use in monitoring the patient. Therefore, there is an essential need of restricting the unauthorized access to the patient's medical information. Hence, the efficient authentication scheme for the healthcare applications is needed to preserve the privacy of the patients' vital signs. To ensure secure and authorized communication in WMSN, we design a symmetric key based authentication protocol for WMSN environment. The proposed protocol uses only computationally efficient operations to achieve lightweight attribute. We analyze the security of the proposed protocol. We use a formal security proof algorithm to show the scheme security against known attacks. We also use the Automated Validation of Internet Security Protocols and Applications (AVISPA) simulator to show protocol secure against man-in-the-middle attack and replay attack. Additionally, we adopt an informal analysis to discuss the key attributes of the proposed scheme. From the formal proof of security, we can see that an attacker has a negligible probability of breaking the protocol security. AVISPA simulator also demonstrates the proposed scheme security against active attacks, namely, man-in-the-middle attack and replay attack. Additionally, through the comparison of computational efficiency and security attributes with several recent results, proposed scheme seems to be battered.

From Three-Photon Greenberger-Horne-Zeilinger States to Ballistic Universal Quantum Computation.

PubMed

Gimeno-Segovia, Mercedes; Shadbolt, Pete; Browne, Dan E; Rudolph, Terry

2015-07-10

Single photons, manipulated using integrated linear optics, constitute a promising platform for universal quantum computation. A series of increasingly efficient proposals have shown linear-optical quantum computing to be formally scalable. However, existing schemes typically require extensive adaptive switching, which is experimentally challenging and noisy, thousands of photon sources per renormalized qubit, and/or large quantum memories for repeat-until-success strategies. Our work overcomes all these problems. We present a scheme to construct a cluster state universal for quantum computation, which uses no adaptive switching, no large memories, and which is at least an order of magnitude more resource efficient than previous passive schemes. Unlike previous proposals, it is constructed entirely from loss-detecting gates and offers a robustness to photon loss. Even without the use of an active loss-tolerant encoding, our scheme naturally tolerates a total loss rate ∼1.6% in the photons detected in the gates. This scheme uses only 3 Greenberger-Horne-Zeilinger states as a resource, together with a passive linear-optical network. We fully describe and model the iterative process of cluster generation, including photon loss and gate failure. This demonstrates that building a linear-optical quantum computer needs to be less challenging than previously thought.

Formal specification of human-computer interfaces

NASA Technical Reports Server (NTRS)

Auernheimer, Brent

1990-01-01

A high-level formal specification of a human computer interface is described. Previous work is reviewed and the ASLAN specification language is described. Top-level specifications written in ASLAN for a library and a multiwindow interface are discussed.

Formal ontologies in biomedical knowledge representation.

PubMed

Schulz, S; Jansen, L

2013-01-01

Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are often misinterpreted to encode all kinds of statements, including those which are not ontological. We distinguish four kinds of statements needed to comprehensively represent domain knowledge: universal statements, terminological statements, statements about particulars and contingent statements. We argue that the task of formal ontologies is solely to represent universal statements, while the non-ontological kinds of statements can nevertheless be connected with ontological representations. To illustrate these four types of representations, we use a running example from parasitology. We finally formulate recommendations for semantically adequate ontologies that can efficiently be used as a stable framework for more context-dependent biomedical knowledge representation and reasoning applications like clinical decision support systems.

Molecular properties of excited electronic state: Formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, Qiao; Liang, WanZhen, E-mail: liangwz@xmu.edu.cn; Liu, Jie

2014-05-14

This work extends our previous works [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011); J. Liu and W. Z. Liang, J. Chem. Phys. 135, 184111 (2011)] on analytical excited-state energy Hessian within the framework of time-dependent density functional theory (TDDFT) to couple with molecular mechanics (MM). The formalism, implementation, and applications of analytical first and second energy derivatives of TDDFT/MM excited state with respect to the nuclear and electric perturbations are presented. Their performances are demonstrated by the calculations of adiabatic excitation energies, and excited-state geometries, harmonic vibrational frequencies, and infrared intensities for a number ofmore » benchmark systems. The consistent results with the full quantum mechanical method and other hybrid theoretical methods indicate the reliability of the current numerical implementation of developed algorithms. The computational accuracy and efficiency of the current analytical approach are also checked and the computational efficient strategies are suggested to speed up the calculations of complex systems with many MM degrees of freedom. Finally, we apply the current analytical approach in TDDFT/MM to a realistic system, a red fluorescent protein chromophore together with part of its nearby protein matrix. The calculated results indicate that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the large Stokes shift.« less

An effective and secure key-management scheme for hierarchical access control in E-medicine system.

PubMed

Odelu, Vanga; Das, Ashok Kumar; Goswami, Adrijit

2013-04-01

Recently several hierarchical access control schemes are proposed in the literature to provide security of e-medicine systems. However, most of them are either insecure against 'man-in-the-middle attack' or they require high storage and computational overheads. Wu and Chen proposed a key management method to solve dynamic access control problems in a user hierarchy based on hybrid cryptosystem. Though their scheme improves computational efficiency over Nikooghadam et al.'s approach, it suffers from large storage space for public parameters in public domain and computational inefficiency due to costly elliptic curve point multiplication. Recently, Nikooghadam and Zakerolhosseini showed that Wu-Chen's scheme is vulnerable to man-in-the-middle attack. In order to remedy this security weakness in Wu-Chen's scheme, they proposed a secure scheme which is again based on ECC (elliptic curve cryptography) and efficient one-way hash function. However, their scheme incurs huge computational cost for providing verification of public information in the public domain as their scheme uses ECC digital signature which is costly when compared to symmetric-key cryptosystem. In this paper, we propose an effective access control scheme in user hierarchy which is only based on symmetric-key cryptosystem and efficient one-way hash function. We show that our scheme reduces significantly the storage space for both public and private domains, and computational complexity when compared to Wu-Chen's scheme, Nikooghadam-Zakerolhosseini's scheme, and other related schemes. Through the informal and formal security analysis, we further show that our scheme is secure against different attacks and also man-in-the-middle attack. Moreover, dynamic access control problems in our scheme are also solved efficiently compared to other related schemes, making our scheme is much suitable for practical applications of e-medicine systems.

Digital and biological computing in organizations.

PubMed

Kampfner, Roberto R

2002-01-01

Michael Conrad unveiled many of the fundamental characteristics of biological computing. Underlying the behavioral variability and the adaptability of biological systems are these characteristics, including the ability of biological information processing to exploit quantum features at the atomic level, the powerful 3-D pattern recognition capabilities of macromolecules, the computational efficiency, and the ability to support biological function. Among many other things, Conrad formalized and explicated the underlying principles of biological adaptability, characterized the differences between biological and digital computing in terms of a fundamental tradeoff between adaptability and programmability of information processing, and discussed the challenges of interfacing digital computers and human society. This paper is about the encounter of biological and digital computing. The focus is on the nature of the biological information processing infrastructure of organizations and how it can be extended effectively with digital computing. In order to achieve this goal effectively, however, we need to embed properly digital computing into the information processing aspects of human and social behavior and intelligence, which are fundamentally biological. Conrad's legacy provides a firm, strong, and inspiring foundation for this endeavor.

Computational logic: its origins and applications.

PubMed

Paulson, Lawrence C

2018-02-01

Computational logic is the use of computers to establish facts in a logical formalism. Originating in nineteenth century attempts to understand the nature of mathematical reasoning, the subject now comprises a wide variety of formalisms, techniques and technologies. One strand of work follows the 'logic for computable functions (LCF) approach' pioneered by Robin Milner, where proofs can be constructed interactively or with the help of users' code (which does not compromise correctness). A refinement of LCF, called Isabelle, retains these advantages while providing flexibility in the choice of logical formalism and much stronger automation. The main application of these techniques has been to prove the correctness of hardware and software systems, but increasingly researchers have been applying them to mathematics itself.

Great Computational Intelligence in the Formal Sciences via Analogical Reasoning

DTIC Science & Technology

2017-05-08

computational harnessing of traditional mathematical statistics (as e.g. covered in Hogg, Craig & McKean 2005) is used to power statistical learning techniques...AFRL-AFOSR-VA-TR-2017-0099 Great Computational Intelligence in the Formal Sciences via Analogical Reasoning Selmer Bringsjord RENSSELAER POLYTECHNIC...08-05-2017 2. REPORT TYPE Final Performance 3. DATES COVERED (From - To) 15 Oct 2011 to 31 Dec 2016 4. TITLE AND SUBTITLE Great Computational

New Computational Approach to Electron Transport in Irregular Graphene Nanostructures

NASA Astrophysics Data System (ADS)

Mason, Douglas; Heller, Eric; Prendergast, David; Neaton, Jeffrey

2009-03-01

For novel graphene devices of nanoscale-to-macroscopic scale, many aspects of their transport properties are not easily understood due to difficulties in fabricating devices with regular edges. Here we develop a framework to efficiently calculate and potentially screen electronic transport properties of arbitrary nanoscale graphene device structures. A generalization of the established recursive Green's function method is presented, providing access to arbitrary device and lead geometries with substantial computer-time savings. Using single-orbital nearest-neighbor tight-binding models and the Green's function-Landauer scattering formalism, we will explore the transmission function of irregular two-dimensional graphene-based nanostructures with arbitrary lead orientation. Prepared by LBNL under contract DE-AC02-05CH11231 and supported by the U.S. Dept. of Energy Computer Science Graduate Fellowship under grant DE-FG02-97ER25308.

ADCIS Conference Proceedings. Computer-Based Instruction (28th, Washington, D.C., November 10-13, 1986).

ERIC Educational Resources Information Center

Association for the Development of Computer-based Instructional Systems.

This volume is divided into full formal paper manuscripts and 200-word abstracts of presentations that were made without submitting formal papers. The 73 papers presented in full represent recent research and applications in the field of computer-based instruction. They are organized into 13 sections by special interest group: (1) Computer-Based…

Efficiently computing and deriving topological relation matrices between complex regions with broad boundaries

NASA Astrophysics Data System (ADS)

Du, Shihong; Guo, Luo; Wang, Qiao; Qin, Qimin

The extended 9-intersection matrix is used to formalize topological relations between uncertain regions while it is designed to satisfy the requirements at a concept level, and to deal with the complex regions with broad boundaries (CBBRs) as a whole without considering their hierarchical structures. In contrast to simple regions with broad boundaries, CBBRs have complex hierarchical structures. Therefore, it is necessary to take into account the complex hierarchical structure and to represent the topological relations between all regions in CBBRs as a relation matrix, rather than using the extended 9-intersection matrix to determine topological relations. In this study, a tree model is first used to represent the intrinsic configuration of CBBRs hierarchically. Then, the reasoning tables are presented for deriving topological relations between child, parent and sibling regions from the relations between two given regions in CBBRs. Finally, based on the reasoning, efficient methods are proposed to compute and derive the topological relation matrix. The proposed methods can be incorporated into spatial databases to facilitate geometric-oriented applications.

A Novel Latin Hypercube Algorithm via Translational Propagation

PubMed Central

Pan, Guang; Ye, Pengcheng

2014-01-01

Metamodels have been widely used in engineering design to facilitate analysis and optimization of complex systems that involve computationally expensive simulation programs. The accuracy of metamodels is directly related to the experimental designs used. Optimal Latin hypercube designs are frequently used and have been shown to have good space-filling and projective properties. However, the high cost in constructing them limits their use. In this paper, a methodology for creating novel Latin hypercube designs via translational propagation and successive local enumeration algorithm (TPSLE) is developed without using formal optimization. TPSLE algorithm is based on the inspiration that a near optimal Latin Hypercube design can be constructed by a simple initial block with a few points generated by algorithm SLE as a building block. In fact, TPSLE algorithm offers a balanced trade-off between the efficiency and sampling performance. The proposed algorithm is compared to two existing algorithms and is found to be much more efficient in terms of the computation time and has acceptable space-filling and projective properties. PMID:25276844

Seed robustness of oriented relative fuzzy connectedness: core computation and its applications

NASA Astrophysics Data System (ADS)

Tavares, Anderson C. M.; Bejar, Hans H. C.; Miranda, Paulo A. V.

2017-02-01

In this work, we present a formal definition and an efficient algorithm to compute the cores of Oriented Relative Fuzzy Connectedness (ORFC), a recent seed-based segmentation technique. The core is a region where the seed can be moved without altering the segmentation, an important aspect for robust techniques and reduction of user effort. We show how ORFC cores can be used to build a powerful hybrid image segmentation approach. We also provide some new theoretical relations between ORFC and Oriented Image Foresting Transform (OIFT), as well as their cores. Experimental results among several methods show that the hybrid approach conserves high accuracy, avoids the shrinking problem and provides robustness to seed placement inside the desired object due to the cores properties.

Hemispherical reflectance model for passive images in an outdoor environment.

PubMed

Kim, Charles C; Thai, Bea; Yamaoka, Neil; Aboutalib, Omar

2015-05-01

We present a hemispherical reflectance model for simulating passive images in an outdoor environment where illumination is provided by natural sources such as the sun and the clouds. While the bidirectional reflectance distribution function (BRDF) accurately produces radiance from any objects after the illumination, using the BRDF in calculating radiance requires double integration. Replacing the BRDF by hemispherical reflectance under the natural sources transforms the double integration into a multiplication. This reduces both storage space and computation time. We present the formalism for the radiance of the scene using hemispherical reflectance instead of BRDF. This enables us to generate passive images in an outdoor environment taking advantage of the computational and storage efficiencies. We show some examples for illustration.

A Semantic Approach for Geospatial Information Extraction from Unstructured Documents

NASA Astrophysics Data System (ADS)

Sallaberry, Christian; Gaio, Mauro; Lesbegueries, Julien; Loustau, Pierre

Local cultural heritage document collections are characterized by their content, which is strongly attached to a territory and its land history (i.e., geographical references). Our contribution aims at making the content retrieval process more efficient whenever a query includes geographic criteria. We propose a core model for a formal representation of geographic information. It takes into account characteristics of different modes of expression, such as written language, captures of drawings, maps, photographs, etc. We have developed a prototype that fully implements geographic information extraction (IE) and geographic information retrieval (IR) processes. All PIV prototype processing resources are designed as Web Services. We propose a geographic IE process based on semantic treatment as a supplement to classical IE approaches. We implement geographic IR by using intersection computing algorithms that seek out any intersection between formal geocoded representations of geographic information in a user query and similar representations in document collection indexes.

Computational logic: its origins and applications

PubMed Central

2018-01-01

Computational logic is the use of computers to establish facts in a logical formalism. Originating in nineteenth century attempts to understand the nature of mathematical reasoning, the subject now comprises a wide variety of formalisms, techniques and technologies. One strand of work follows the ‘logic for computable functions (LCF) approach’ pioneered by Robin Milner, where proofs can be constructed interactively or with the help of users’ code (which does not compromise correctness). A refinement of LCF, called Isabelle, retains these advantages while providing flexibility in the choice of logical formalism and much stronger automation. The main application of these techniques has been to prove the correctness of hardware and software systems, but increasingly researchers have been applying them to mathematics itself. PMID:29507522

Hierarchical Parallelism in Finite Difference Analysis of Heat Conduction

NASA Technical Reports Server (NTRS)

Padovan, Joseph; Krishna, Lala; Gute, Douglas

1997-01-01

Based on the concept of hierarchical parallelism, this research effort resulted in highly efficient parallel solution strategies for very large scale heat conduction problems. Overall, the method of hierarchical parallelism involves the partitioning of thermal models into several substructured levels wherein an optimal balance into various associated bandwidths is achieved. The details are described in this report. Overall, the report is organized into two parts. Part 1 describes the parallel modelling methodology and associated multilevel direct, iterative and mixed solution schemes. Part 2 establishes both the formal and computational properties of the scheme.

Kuang's Semi-Classical Formalism for Calculating Electron Capture Cross Sections: A Space- Physics Application

NASA Technical Reports Server (NTRS)

Barghouty, A. F.

2014-01-01

Accurate estimates of electroncapture cross sections at energies relevant to the modeling of the transport, acceleration, and interaction of energetic neutral atoms (ENA) in space (approximately few MeV per nucleon) and especially for multi-electron ions must rely on detailed, but computationally expensive, quantum-mechanical description of the collision process. Kuang's semi-classical approach is an elegant and efficient way to arrive at these estimates. Motivated by ENA modeling efforts for apace applications, we shall briefly present this approach along with sample applications and report on current progress.

DEVELOPMENTS IN GRworkbench

NASA Astrophysics Data System (ADS)

Moylan, Andrew; Scott, Susan M.; Searle, Anthony C.

2006-02-01

The software tool GRworkbench is an ongoing project in visual, numerical General Relativity at The Australian National University. Recently, GRworkbench has been significantly extended to facilitate numerical experimentation in analytically-defined space-times. The numerical differential geometric engine has been rewritten using functional programming techniques, enabling objects which are normally defined as functions in the formalism of differential geometry and General Relativity to be directly represented as function variables in the C++ code of GRworkbench. The new functional differential geometric engine allows for more accurate and efficient visualisation of objects in space-times and makes new, efficient computational techniques available. Motivated by the desire to investigate a recent scientific claim using GRworkbench, new tools for numerical experimentation have been implemented, allowing for the simulation of complex physical situations.

Exploring Experienced Professionals' Reflections on Computing Education

ERIC Educational Resources Information Center

Exter, Marisa; Turnage, Nichole

2012-01-01

This exploratory qualitative study examines computing professional's memories of their own formal and non-formal educational experiences, their reflections on how these have prepared them for their professional roles, and their recommendations for an "ideal" undergraduate degree program. Data was collected through semi-structured interviews of…

Machine Learning-based Intelligent Formal Reasoning and Proving System

NASA Astrophysics Data System (ADS)

Chen, Shengqing; Huang, Xiaojian; Fang, Jiaze; Liang, Jia

2018-03-01

The reasoning system can be used in many fields. How to improve reasoning efficiency is the core of the design of system. Through the formal description of formal proof and the regular matching algorithm, after introducing the machine learning algorithm, the system of intelligent formal reasoning and verification has high efficiency. The experimental results show that the system can verify the correctness of propositional logic reasoning and reuse the propositional logical reasoning results, so as to obtain the implicit knowledge in the knowledge base and provide the basic reasoning model for the construction of intelligent system.

Scattering of Airy elastic sheets by a cylindrical cavity in a solid.

PubMed

Mitri, F G

2017-11-01

The prediction of the elastic scattering by voids (and cracks) in materials is an important process in structural health monitoring, phononic crystals, metamaterials and non-destructive evaluation/imaging to name a few examples. Earlier analytical theories and numerical computations considered the elastic scattering by voids in plane waves of infinite extent. However, current research suggesting the use of (limited-diffracting, accelerating and self-healing) Airy acoustical-sheet beams for non-destructive evaluation or imaging applications in elastic solids requires the development of an improved analytical formalism to predict the scattering efficiency used as a priori information in quantitative material characterization. Based on the definition of the time-averaged scattered power flow density, an analytical expression for the scattering efficiency of a cylindrical empty cavity (i.e., void) encased in an elastic medium is derived for compressional and normally-polarized shear-wave Airy beams. The multipole expansion method using cylindrical wave functions is utilized. Numerical computations for the scattering energy efficiency factors for compressional and shear waves illustrate the analysis with particular emphasis on the Airy beam parameters and the non-dimensional frequency, for various elastic materials surrounding the cavity. The ratio of the compressional to the shear wave speed stimulates the generation of elastic resonances, which are manifested as a series of peaks in the scattering efficiency plots. The present analysis provides an improved method for the computations of the scattering energy efficiency factors using compressional and shear-wave Airy beams in elastic materials as opposed to plane waves of infinite extent. Copyright © 2017 Elsevier B.V. All rights reserved.

Proceedings of the Seminar on the DOD Computer Security Initiative (4th) Held at the National Bureau of Standards, Gaithersburg, Maryland on August 10-12, 1981.

DTIC Science & Technology

1981-01-01

comparison of formal and informal design methodologies will show how we think they are converging. Lastly, I will describe our involvement with the DoD...computer security must begin with the design methodology , with the objective being provability. The idea ofa formal evaluation and on-the-shelf... Methodologies ] Here we can compare the formal design methodologies with those used by informal practitioners like Control Data. Obviously, both processes

Spin density and orbital optimization in open shell systems: A rational and computationally efficient proposal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giner, Emmanuel, E-mail: gnrmnl@unife.it; Angeli, Celestino, E-mail: anc@unife.it

2016-03-14

The present work describes a new method to compute accurate spin densities for open shell systems. The proposed approach follows two steps: first, it provides molecular orbitals which correctly take into account the spin delocalization; second, a proper CI treatment allows to account for the spin polarization effect while keeping a restricted formalism and avoiding spin contamination. The main idea of the optimization procedure is based on the orbital relaxation of the various charge transfer determinants responsible for the spin delocalization. The algorithm is tested and compared to other existing methods on a series of organic and inorganic open shellmore » systems. The results reported here show that the new approach (almost black-box) provides accurate spin densities at a reasonable computational cost making it suitable for a systematic study of open shell systems.« less

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

2015-12-07

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

PubMed

Bazinet, Adam L; Zwickl, Derrick J; Cummings, Michael P

2014-09-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Labeled trees and the efficient computation of derivations

NASA Technical Reports Server (NTRS)

Grossman, Robert; Larson, Richard G.

1989-01-01

The effective parallel symbolic computation of operators under composition is discussed. Examples include differential operators under composition and vector fields under the Lie bracket. Data structures consisting of formal linear combinations of rooted labeled trees are discussed. A multiplication on rooted labeled trees is defined, thereby making the set of these data structures into an associative algebra. An algebra homomorphism is defined from the original algebra of operators into this algebra of trees. An algebra homomorphism from the algebra of trees into the algebra of differential operators is then described. The cancellation which occurs when noncommuting operators are expressed in terms of commuting ones occurs naturally when the operators are represented using this data structure. This leads to an algorithm which, for operators which are derivations, speeds up the computation exponentially in the degree of the operator. It is shown that the algebra of trees leads naturally to a parallel version of the algorithm.

Discovery of Boolean metabolic networks: integer linear programming based approach.

PubMed

Qiu, Yushan; Jiang, Hao; Ching, Wai-Ki; Cheng, Xiaoqing

2018-04-11

Traditional drug discovery methods focused on the efficacy of drugs rather than their toxicity. However, toxicity and/or lack of efficacy are produced when unintended targets are affected in metabolic networks. Thus, identification of biological targets which can be manipulated to produce the desired effect with minimum side-effects has become an important and challenging topic. Efficient computational methods are required to identify the drug targets while incurring minimal side-effects. In this paper, we propose a graph-based computational damage model that summarizes the impact of enzymes on compounds in metabolic networks. An efficient method based on Integer Linear Programming formalism is then developed to identify the optimal enzyme-combination so as to minimize the side-effects. The identified target enzymes for known successful drugs are then verified by comparing the results with those in the existing literature. Side-effects reduction plays a crucial role in the study of drug development. A graph-based computational damage model is proposed and the theoretical analysis states the captured problem is NP-completeness. The proposed approaches can therefore contribute to the discovery of drug targets. Our developed software is available at " http://hkumath.hku.hk/~wkc/APBC2018-metabolic-network.zip ".

Combining Archetypes, Ontologies and Formalization Enables Automated Computation of Quality Indicators.

PubMed

Legaz-García, María Del Carmen; Dentler, Kathrin; Fernández-Breis, Jesualdo Tomás; Cornet, Ronald

2017-01-01

ArchMS is a framework that represents clinical information and knowledge using ontologies in OWL, which facilitates semantic interoperability and thereby the exploitation and secondary use of clinical data. However, it does not yet support the automated assessment of quality of care. CLIF is a stepwise method to formalize quality indicators. The method has been implemented in the CLIF tool which supports its users in generating computable queries based on a patient data model which can be based on archetypes. To enable the automated computation of quality indicators using ontologies and archetypes, we tested whether ArchMS and the CLIF tool can be integrated. We successfully automated the process of generating SPARQL queries from quality indicators that have been formalized with CLIF and integrated them into ArchMS. Hence, ontologies and archetypes can be combined for the execution of formalized quality indicators.

The Formal Semantics of PVS

NASA Technical Reports Server (NTRS)

Owre, Sam; Shankar, Natarajan

1999-01-01

A specification language is a medium for expressing what is computed rather than how it is computed. Specification languages share some features with programming languages but are also different in several important ways. For our purpose, a specification language is a logic within which the behavior of computational systems can be formalized. Although a specification can be used to simulate the behavior of such systems, we mainly use specifications to state and prove system properties with mechanical assistance. We present the formal semantics of the specification language of SRI's Prototype Verification System (PVS). This specification language is based on the simply typed lambda calculus. The novelty in PVS is that it contains very expressive language features whose static analysis (e.g., typechecking) requires the assistance of a theorem prover. The formal semantics illuminates several of the design considerations underlying PVS, the interaction between theorem proving and typechecking.

Fast and robust generation of feature maps for region-based visual attention.

PubMed

Aziz, Muhammad Zaheer; Mertsching, Bärbel

2008-05-01

Visual attention is one of the important phenomena in biological vision which can be followed to achieve more efficiency, intelligence, and robustness in artificial vision systems. This paper investigates a region-based approach that performs pixel clustering prior to the processes of attention in contrast to late clustering as done by contemporary methods. The foundation steps of feature map construction for the region-based attention model are proposed here. The color contrast map is generated based upon the extended findings from the color theory, the symmetry map is constructed using a novel scanning-based method, and a new algorithm is proposed to compute a size contrast map as a formal feature channel. Eccentricity and orientation are computed using the moments of obtained regions and then saliency is evaluated using the rarity criteria. The efficient design of the proposed algorithms allows incorporating five feature channels while maintaining a processing rate of multiple frames per second. Another salient advantage over the existing techniques is the reusability of the salient regions in the high-level machine vision procedures due to preservation of their shapes and precise locations. The results indicate that the proposed model has the potential to efficiently integrate the phenomenon of attention into the main stream of machine vision and systems with restricted computing resources such as mobile robots can benefit from its advantages.

Knowledge acquisition, semantic text mining, and security risks in health and biomedical informatics

PubMed Central

Huang, Jingshan; Dou, Dejing; Dang, Jiangbo; Pardue, J Harold; Qin, Xiao; Huan, Jun; Gerthoffer, William T; Tan, Ming

2012-01-01

Computational techniques have been adopted in medical and biological systems for a long time. There is no doubt that the development and application of computational methods will render great help in better understanding biomedical and biological functions. Large amounts of datasets have been produced by biomedical and biological experiments and simulations. In order for researchers to gain knowledge from original data, nontrivial transformation is necessary, which is regarded as a critical link in the chain of knowledge acquisition, sharing, and reuse. Challenges that have been encountered include: how to efficiently and effectively represent human knowledge in formal computing models, how to take advantage of semantic text mining techniques rather than traditional syntactic text mining, and how to handle security issues during the knowledge sharing and reuse. This paper summarizes the state-of-the-art in these research directions. We aim to provide readers with an introduction of major computing themes to be applied to the medical and biological research. PMID:22371823

A Formal Construction of Term Classes. Technical Report No. TR73-18.

ERIC Educational Resources Information Center

Yu, Clement T.

The computational complexity of a formal process for the construction of term classes for information retrieval is examined. While the process is proven to be difficult computationally, heuristic methods are applied. Experimental results are obtained to illustrate the maximum possible improvement in system performance of retrieval using the formal…

Correlation energy functional within the GW -RPA: Exact forms, approximate forms, and challenges

NASA Astrophysics Data System (ADS)

Ismail-Beigi, Sohrab

2010-05-01

In principle, the Luttinger-Ward Green’s-function formalism allows one to compute simultaneously the total energy and the quasiparticle band structure of a many-body electronic system from first principles. We present approximate and exact expressions for the correlation energy within the GW -random-phase approximation that are more amenable to computation and allow for developing efficient approximations to the self-energy operator and correlation energy. The exact form is a sum over differences between plasmon and interband energies. The approximate forms are based on summing over screened interband transitions. We also demonstrate that blind extremization of such functionals leads to unphysical results: imposing physical constraints on the allowed solutions (Green’s functions) is necessary. Finally, we present some relevant numerical results for atomic systems.

Weighted Flow Algorithms (WFA) for stochastic particle coagulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeVille, R.E.L., E-mail: rdeville@illinois.edu; Riemer, N., E-mail: nriemer@illinois.edu; West, M., E-mail: mwest@illinois.edu

2011-09-20

Stochastic particle-resolved methods are a useful way to compute the time evolution of the multi-dimensional size distribution of atmospheric aerosol particles. An effective approach to improve the efficiency of such models is the use of weighted computational particles. Here we introduce particle weighting functions that are power laws in particle size to the recently-developed particle-resolved model PartMC-MOSAIC and present the mathematical formalism of these Weighted Flow Algorithms (WFA) for particle coagulation and growth. We apply this to an urban plume scenario that simulates a particle population undergoing emission of different particle types, dilution, coagulation and aerosol chemistry along a Lagrangianmore » trajectory. We quantify the performance of the Weighted Flow Algorithm for number and mass-based quantities of relevance for atmospheric sciences applications.« less

Survivable algorithms and redundancy management in NASA's distributed computing systems

NASA Technical Reports Server (NTRS)

Malek, Miroslaw

1992-01-01

The design of survivable algorithms requires a solid foundation for executing them. While hardware techniques for fault-tolerant computing are relatively well understood, fault-tolerant operating systems, as well as fault-tolerant applications (survivable algorithms), are, by contrast, little understood, and much more work in this field is required. We outline some of our work that contributes to the foundation of ultrareliable operating systems and fault-tolerant algorithm design. We introduce our consensus-based framework for fault-tolerant system design. This is followed by a description of a hierarchical partitioning method for efficient consensus. A scheduler for redundancy management is introduced, and application-specific fault tolerance is described. We give an overview of our hybrid algorithm technique, which is an alternative to the formal approach given.

Efficient searching in meshfree methods

NASA Astrophysics Data System (ADS)

Olliff, James; Alford, Brad; Simkins, Daniel C.

2018-04-01

Meshfree methods such as the Reproducing Kernel Particle Method and the Element Free Galerkin method have proven to be excellent choices for problems involving complex geometry, evolving topology, and large deformation, owing to their ability to model the problem domain without the constraints imposed on the Finite Element Method (FEM) meshes. However, meshfree methods have an added computational cost over FEM that come from at least two sources: increased cost of shape function evaluation and the determination of adjacency or connectivity. The focus of this paper is to formally address the types of adjacency information that arises in various uses of meshfree methods; a discussion of available techniques for computing the various adjacency graphs; propose a new search algorithm and data structure; and finally compare the memory and run time performance of the methods.

Weighted Flow Algorithms (WFA) for stochastic particle coagulation

NASA Astrophysics Data System (ADS)

DeVille, R. E. L.; Riemer, N.; West, M.

2011-09-01

Stochastic particle-resolved methods are a useful way to compute the time evolution of the multi-dimensional size distribution of atmospheric aerosol particles. An effective approach to improve the efficiency of such models is the use of weighted computational particles. Here we introduce particle weighting functions that are power laws in particle size to the recently-developed particle-resolved model PartMC-MOSAIC and present the mathematical formalism of these Weighted Flow Algorithms (WFA) for particle coagulation and growth. We apply this to an urban plume scenario that simulates a particle population undergoing emission of different particle types, dilution, coagulation and aerosol chemistry along a Lagrangian trajectory. We quantify the performance of the Weighted Flow Algorithm for number and mass-based quantities of relevance for atmospheric sciences applications.

Combining Modeling and Gaming for Predictive Analytics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riensche, Roderick M.; Whitney, Paul D.

2012-08-22

Many of our most significant challenges involve people. While human behavior has long been studied, there are recent advances in computational modeling of human behavior. With advances in computational capabilities come increases in the volume and complexity of data that humans must understand in order to make sense of and capitalize on these modeling advances. Ultimately, models represent an encapsulation of human knowledge. One inherent challenge in modeling is efficient and accurate transfer of knowledge from humans to models, and subsequent retrieval. The simulated real-world environment of games presents one avenue for these knowledge transfers. In this paper we describemore » our approach of combining modeling and gaming disciplines to develop predictive capabilities, using formal models to inform game development, and using games to provide data for modeling.« less

Shielding from space radiations

NASA Technical Reports Server (NTRS)

Chang, C. Ken; Badavi, Forooz F.; Tripathi, Ram K.

1993-01-01

This Progress Report covering the period of December 1, 1992 to June 1, 1993 presents the development of an analytical solution to the heavy ion transport equation in terms of Green's function formalism. The mathematical development results are recasted into a highly efficient computer code for space applications. The efficiency of this algorithm is accomplished by a nonperturbative technique of extending the Green's function over the solution domain. The code may also be applied to accelerator boundary conditions to allow code validation in laboratory experiments. Results from the isotopic version of the code with 59 isotopes present for a single layer target material, for the case of an iron beam projectile at 600 MeV/nucleon in water is presented. A listing of the single layer isotopic version of the code is included.

Two-dimensional radiative transfer. I - Planar geometry. [in stellar atmospheres

NASA Technical Reports Server (NTRS)

Mihalas, D.; Auer, L. H.; Mihalas, B. R.

1978-01-01

Differential-equation methods for solving the transfer equation in two-dimensional planar geometries are developed. One method, which uses a Hermitian integration formula on ray segments through grid points, proves to be extremely well suited to velocity-dependent problems. An efficient elimination scheme is developed for which the computing time scales linearly with the number of angles and frequencies; problems with large velocity amplitudes can thus be treated accurately. A very accurate and efficient method for performing a formal solution is also presented. A discussion is given of several examples of periodic media and free-standing slabs, both in static cases and with velocity fields. For the free-standing slabs, two-dimensional transport effects are significant near boundaries, but no important effects were found in any of the periodic cases studied.

Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism

NASA Astrophysics Data System (ADS)

Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; Nicholson, D. M.; Johnson, Duane D.

2014-11-01

The Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an efficient site-centered, electronic-structure technique for addressing an assembly of N scatterers. Wave functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax=(l,mmax), while scattering matrices, which determine spectral properties, are truncated at Lt r=(l,mt r) where phase shifts δl >ltr are negligible. Historically, Lmax is set equal to Lt r, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax>Lt r with δl >ltr set to zero [X.-G. Zhang and W. H. Butler, Phys. Rev. B 46, 7433 (1992), 10.1103/PhysRevB.46.7433]. We present a numerically efficient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N (ltr+1 ) 2 ] and includes higher-L contributions via linear algebra [R2 process with rank N (lmax+1) 2 ]. The augmented-KKR approach yields properly normalized wave functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe, and L 1 0 CoPt and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Lt r.

A semi-Lagrangian transport method for kinetic problems with application to dense-to-dilute polydisperse reacting spray flows

NASA Astrophysics Data System (ADS)

Doisneau, François; Arienti, Marco; Oefelein, Joseph C.

2017-01-01

For sprays, as described by a kinetic disperse phase model strongly coupled to the Navier-Stokes equations, the resolution strategy is constrained by accuracy objectives, robustness needs, and the computing architecture. In order to leverage the good properties of the Eulerian formalism, we introduce a deterministic particle-based numerical method to solve transport in physical space, which is simple to adapt to the many types of closures and moment systems. The method is inspired by the semi-Lagrangian schemes, developed for Gas Dynamics. We show how semi-Lagrangian formulations are relevant for a disperse phase far from equilibrium and where the particle-particle coupling barely influences the transport; i.e., when particle pressure is negligible. The particle behavior is indeed close to free streaming. The new method uses the assumption of parcel transport and avoids to compute fluxes and their limiters, which makes it robust. It is a deterministic resolution method so that it does not require efforts on statistical convergence, noise control, or post-processing. All couplings are done among data under the form of Eulerian fields, which allows one to use efficient algorithms and to anticipate the computational load. This makes the method both accurate and efficient in the context of parallel computing. After a complete verification of the new transport method on various academic test cases, we demonstrate the overall strategy's ability to solve a strongly-coupled liquid jet with fine spatial resolution and we apply it to the case of high-fidelity Large Eddy Simulation of a dense spray flow. A fuel spray is simulated after atomization at Diesel engine combustion chamber conditions. The large, parallel, strongly coupled computation proves the efficiency of the method for dense, polydisperse, reacting spray flows.

A semi-Lagrangian transport method for kinetic problems with application to dense-to-dilute polydisperse reacting spray flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doisneau, François, E-mail: fdoisne@sandia.gov; Arienti, Marco, E-mail: marient@sandia.gov; Oefelein, Joseph C., E-mail: oefelei@sandia.gov

For sprays, as described by a kinetic disperse phase model strongly coupled to the Navier–Stokes equations, the resolution strategy is constrained by accuracy objectives, robustness needs, and the computing architecture. In order to leverage the good properties of the Eulerian formalism, we introduce a deterministic particle-based numerical method to solve transport in physical space, which is simple to adapt to the many types of closures and moment systems. The method is inspired by the semi-Lagrangian schemes, developed for Gas Dynamics. We show how semi-Lagrangian formulations are relevant for a disperse phase far from equilibrium and where the particle–particle coupling barelymore » influences the transport; i.e., when particle pressure is negligible. The particle behavior is indeed close to free streaming. The new method uses the assumption of parcel transport and avoids to compute fluxes and their limiters, which makes it robust. It is a deterministic resolution method so that it does not require efforts on statistical convergence, noise control, or post-processing. All couplings are done among data under the form of Eulerian fields, which allows one to use efficient algorithms and to anticipate the computational load. This makes the method both accurate and efficient in the context of parallel computing. After a complete verification of the new transport method on various academic test cases, we demonstrate the overall strategy's ability to solve a strongly-coupled liquid jet with fine spatial resolution and we apply it to the case of high-fidelity Large Eddy Simulation of a dense spray flow. A fuel spray is simulated after atomization at Diesel engine combustion chamber conditions. The large, parallel, strongly coupled computation proves the efficiency of the method for dense, polydisperse, reacting spray flows.« less

Formal specification and verification of a fault-masking and transient-recovery model for digital flight-control systems

NASA Technical Reports Server (NTRS)

Rushby, John

1991-01-01

The formal specification and mechanically checked verification for a model of fault-masking and transient-recovery among the replicated computers of digital flight-control systems are presented. The verification establishes, subject to certain carefully stated assumptions, that faults among the component computers are masked so that commands sent to the actuators are the same as those that would be sent by a single computer that suffers no failures.

A Formal Specification and Verification Method for the Prevention of Denial of Service in Ada Services

DTIC Science & Technology

1988-03-01

Mechanism; Computer Security. 16. PRICE CODE 17. SECURITY CLASSIFICATION IS. SECURITY CLASSIFICATION 19. SECURITY CLASSIFICATION 20. UMrrATION OF ABSTRACT...denial of service. This paper assumes that the reader is a computer science or engineering professional working in the area of formal specification and...recovery from such events as deadlocks and crashes can be accounted for in the computation of the waiting time for each service in the service hierarchy

Formal design and verification of a reliable computing platform for real-time control (phase 3 results)

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Divito, Ben L.; Holloway, C. Michael

1994-01-01

In this paper the design and formal verification of the lower levels of the Reliable Computing Platform (RCP), a fault-tolerant computing system for digital flight control applications, are presented. The RCP uses NMR-style redundancy to mask faults and internal majority voting to flush the effects of transient faults. Two new layers of the RCP hierarchy are introduced: the Minimal Voting refinement (DA_minv) of the Distributed Asynchronous (DA) model and the Local Executive (LE) Model. Both the DA_minv model and the LE model are specified formally and have been verified using the Ehdm verification system. All specifications and proofs are available electronically via the Internet using anonymous FTP or World Wide Web (WWW) access.

Analyzing thresholds and efficiency with hierarchical Bayesian logistic regression.

PubMed

Houpt, Joseph W; Bittner, Jennifer L

2018-07-01

Ideal observer analysis is a fundamental tool used widely in vision science for analyzing the efficiency with which a cognitive or perceptual system uses available information. The performance of an ideal observer provides a formal measure of the amount of information in a given experiment. The ratio of human to ideal performance is then used to compute efficiency, a construct that can be directly compared across experimental conditions while controlling for the differences due to the stimuli and/or task specific demands. In previous research using ideal observer analysis, the effects of varying experimental conditions on efficiency have been tested using ANOVAs and pairwise comparisons. In this work, we present a model that combines Bayesian estimates of psychometric functions with hierarchical logistic regression for inference about both unadjusted human performance metrics and efficiencies. Our approach improves upon the existing methods by constraining the statistical analysis using a standard model connecting stimulus intensity to human observer accuracy and by accounting for variability in the estimates of human and ideal observer performance scores. This allows for both individual and group level inferences. Copyright © 2018 Elsevier Ltd. All rights reserved.

Automatically Grading Customer Confidence in a Formal Specification.

ERIC Educational Resources Information Center

Shukur, Zarina; Burke, Edmund; Foxley, Eric

1999-01-01

Describes an automatic grading system for a formal methods computer science course that is able to evaluate a formal specification written in the Z language. Quality is measured by considering first, specification correctness (syntax, semantics, and satisfaction of customer requirements), and second, specification maintainability (comparison of…

Increasing horizontal resolution in numerical weather prediction and climate simulations: illusion or panacea?

PubMed

Wedi, Nils P

2014-06-28

The steady path of doubling the global horizontal resolution approximately every 8 years in numerical weather prediction (NWP) at the European Centre for Medium Range Weather Forecasts may be substantially altered with emerging novel computing architectures. It coincides with the need to appropriately address and determine forecast uncertainty with increasing resolution, in particular, when convective-scale motions start to be resolved. Blunt increases in the model resolution will quickly become unaffordable and may not lead to improved NWP forecasts. Consequently, there is a need to accordingly adjust proven numerical techniques. An informed decision on the modelling strategy for harnessing exascale, massively parallel computing power thus also requires a deeper understanding of the sensitivity to uncertainty--for each part of the model--and ultimately a deeper understanding of multi-scale interactions in the atmosphere and their numerical realization in ultra-high-resolution NWP and climate simulations. This paper explores opportunities for substantial increases in the forecast efficiency by judicious adjustment of the formal accuracy or relative resolution in the spectral and physical space. One path is to reduce the formal accuracy by which the spectral transforms are computed. The other pathway explores the importance of the ratio used for the horizontal resolution in gridpoint space versus wavenumbers in spectral space. This is relevant for both high-resolution simulations as well as ensemble-based uncertainty estimation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Non-additive non-interacting kinetic energy of rare gas dimers

NASA Astrophysics Data System (ADS)

Jiang, Kaili; Nafziger, Jonathan; Wasserman, Adam

2018-03-01

Approximations of the non-additive non-interacting kinetic energy (NAKE) as an explicit functional of the density are the basis of several electronic structure methods that provide improved computational efficiency over standard Kohn-Sham calculations. However, within most fragment-based formalisms, there is no unique exact NAKE, making it difficult to develop general, robust approximations for it. When adjustments are made to the embedding formalisms to guarantee uniqueness, approximate functionals may be more meaningfully compared to the exact unique NAKE. We use numerically accurate inversions to study the exact NAKE of several rare-gas dimers within partition density functional theory, a method that provides the uniqueness for the exact NAKE. We find that the NAKE decreases nearly exponentially with atomic separation for the rare-gas dimers. We compute the logarithmic derivative of the NAKE with respect to the bond length for our numerically accurate inversions as well as for several approximate NAKE functionals. We show that standard approximate NAKE functionals do not reproduce the correct behavior for this logarithmic derivative and propose two new NAKE functionals that do. The first of these is based on a re-parametrization of a conjoint Perdew-Burke-Ernzerhof (PBE) functional. The second is a simple, physically motivated non-decomposable NAKE functional that matches the asymptotic decay constant without fitting.

Dose rate calculations around 192Ir brachytherapy sources using a Sievert integration model

NASA Astrophysics Data System (ADS)

Karaiskos, P.; Angelopoulos, A.; Baras, P.; Rozaki-Mavrouli, H.; Sandilos, P.; Vlachos, L.; Sakelliou, L.

2000-02-01

The classical Sievert integral method is a valuable tool for dose rate calculations around brachytherapy sources, combining simplicity with reasonable computational times. However, its accuracy in predicting dose rate anisotropy around 192 Ir brachytherapy sources has been repeatedly put into question. In this work, we used a primary and scatter separation technique to improve an existing modification of the Sievert integral (Williamson's isotropic scatter model) that determines dose rate anisotropy around commercially available 192 Ir brachytherapy sources. The proposed Sievert formalism provides increased accuracy while maintaining the simplicity and computational time efficiency of the Sievert integral method. To describe transmission within the materials encountered, the formalism makes use of narrow beam attenuation coefficients which can be directly and easily calculated from the initially emitted 192 Ir spectrum. The other numerical parameters required for its implementation, once calculated with the aid of our home-made Monte Carlo simulation code, can be used for any 192 Ir source design. Calculations of dose rate and anisotropy functions with the proposed Sievert expression, around commonly used 192 Ir high dose rate sources and other 192 Ir elongated source designs, are in good agreement with corresponding accurate Monte Carlo results which have been reported by our group and other authors.

A simple, robust and efficient high-order accurate shock-capturing scheme for compressible flows: Towards minimalism

NASA Astrophysics Data System (ADS)

Ohwada, Taku; Shibata, Yuki; Kato, Takuma; Nakamura, Taichi

2018-06-01

Developed is a high-order accurate shock-capturing scheme for the compressible Euler/Navier-Stokes equations; the formal accuracy is 5th order in space and 4th order in time. The performance and efficiency of the scheme are validated in various numerical tests. The main ingredients of the scheme are nothing special; they are variants of the standard numerical flux, MUSCL, the usual Lagrange's polynomial and the conventional Runge-Kutta method. The scheme can compute a boundary layer accurately with a rational resolution and capture a stationary contact discontinuity sharply without inner points. And yet it is endowed with high resistance against shock anomalies (carbuncle phenomenon, post-shock oscillations, etc.). A good balance between high robustness and low dissipation is achieved by blending three types of numerical fluxes according to physical situation in an intuitively easy-to-understand way. The performance of the scheme is largely comparable to that of WENO5-Rusanov, while its computational cost is 30-40% less than of that of the advanced scheme.

Development of the 3DHZETRN code for space radiation protection

NASA Astrophysics Data System (ADS)

Wilson, John; Badavi, Francis; Slaba, Tony; Reddell, Brandon; Bahadori, Amir; Singleterry, Robert

Space radiation protection requires computationally efficient shield assessment methods that have been verified and validated. The HZETRN code is the engineering design code used for low Earth orbit dosimetric analysis and astronaut record keeping with end-to-end validation to twenty percent in Space Shuttle and International Space Station operations. HZETRN treated diffusive leakage only at the distal surface limiting its application to systems with a large radius of curvature. A revision of HZETRN that included forward and backward diffusion allowed neutron leakage to be evaluated at both the near and distal surfaces. That revision provided a deterministic code of high computational efficiency that was in substantial agreement with Monte Carlo (MC) codes in flat plates (at least to the degree that MC codes agree among themselves). In the present paper, the 3DHZETRN formalism capable of evaluation in general geometry is described. Benchmarking will help quantify uncertainty with MC codes (Geant4, FLUKA, MCNP6, and PHITS) in simple shapes such as spheres within spherical shells and boxes. Connection of the 3DHZETRN to general geometry will be discussed.

A Formal Valuation Framework for Emotions and Their Control.

PubMed

Huys, Quentin J M; Renz, Daniel

2017-09-15

Computational psychiatry aims to apply mathematical and computational techniques to help improve psychiatric care. To achieve this, the phenomena under scrutiny should be within the scope of formal methods. As emotions play an important role across many psychiatric disorders, such computational methods must encompass emotions. Here, we consider formal valuation accounts of emotions. We focus on the fact that the flexibility of emotional responses and the nature of appraisals suggest the need for a model-based valuation framework for emotions. However, resource limitations make plain model-based valuation impossible and require metareasoning strategies to apportion cognitive resources adaptively. We argue that emotions may implement such metareasoning approximations by restricting the range of behaviors and states considered. We consider the processes that guide the deployment of the approximations, discerning between innate, model-free, heuristic, and model-based controllers. A formal valuation and metareasoning framework may thus provide a principled approach to examining emotions. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Reconfigurable Hardware Adapts to Changing Mission Demands

NASA Technical Reports Server (NTRS)

2003-01-01

A new class of computing architectures and processing systems, which use reconfigurable hardware, is creating a revolutionary approach to implementing future spacecraft systems. With the increasing complexity of electronic components, engineers must design next-generation spacecraft systems with new technologies in both hardware and software. Derivation Systems, Inc., of Carlsbad, California, has been working through NASA s Small Business Innovation Research (SBIR) program to develop key technologies in reconfigurable computing and Intellectual Property (IP) soft cores. Founded in 1993, Derivation Systems has received several SBIR contracts from NASA s Langley Research Center and the U.S. Department of Defense Air Force Research Laboratories in support of its mission to develop hardware and software for high-assurance systems. Through these contracts, Derivation Systems began developing leading-edge technology in formal verification, embedded Java, and reconfigurable computing for its PF3100, Derivational Reasoning System (DRS ), FormalCORE IP, FormalCORE PCI/32, FormalCORE DES, and LavaCORE Configurable Java Processor, which are designed for greater flexibility and security on all space missions.

From Slow Repetition to Awkward Omission: Economic, Efficient, and Precise Language Use in Bilingual Formal Meetings

ERIC Educational Resources Information Center

Koskela, Merja; Pilke, Nina

2016-01-01

This article explores how linguistic resources from two local languages, Finnish and Swedish, are used in expert presentations in bilingual formal meetings and how they function with respect to the three ideal criteria of professional communication: economy, efficiency, and precision. Based on the results, the article suggests a typology of…

Algorithmic Mechanism Design of Evolutionary Computation.

PubMed

Pei, Yan

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

Algorithmic Mechanism Design of Evolutionary Computation

PubMed Central

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

Collision-induced absorption with exchange effects and anisotropic interactions: theory and application to H2 - H2.

PubMed

Karman, Tijs; van der Avoird, Ad; Groenenboom, Gerrit C

2015-02-28

We discuss three quantum mechanical formalisms for calculating collision-induced absorption spectra. First, we revisit the established theory of collision-induced absorption, assuming distinguishable molecules which interact isotropically. Then, the theory is rederived incorporating exchange effects between indistinguishable molecules. It is shown that the spectrum can no longer be written as an incoherent sum of the contributions of the different spherical components of the dipole moment. Finally, we derive an efficient method to include the effects of anisotropic interactions in the computation of the absorption spectrum. This method calculates the dipole coupling on-the-fly, which allows for the uncoupled treatment of the initial and final states without the explicit reconstruction of the many-component wave functions. The three formalisms are applied to the collision-induced rotation-translation spectra of hydrogen molecules in the far-infrared. Good agreement with experimental data is obtained. Significant effects of anisotropic interactions are observed in the far wing.

The connection-set algebra--a novel formalism for the representation of connectivity structure in neuronal network models.

PubMed

Djurfeldt, Mikael

2012-07-01

The connection-set algebra (CSA) is a novel and general formalism for the description of connectivity in neuronal network models, from small-scale to large-scale structure. The algebra provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. CSA is expressive enough to describe a wide range of connection patterns, including multiple types of random and/or geometrically dependent connectivity, and can serve as a concise notation for network structure in scientific writing. CSA implementations allow for scalable and efficient representation of connectivity in parallel neuronal network simulators and could even allow for avoiding explicit representation of connections in computer memory. The expressiveness of CSA makes prototyping of network structure easy. A C+ + version of the algebra has been implemented and used in a large-scale neuronal network simulation (Djurfeldt et al., IBM J Res Dev 52(1/2):31-42, 2008b) and an implementation in Python has been publicly released.

Formal Methods for Life-Critical Software

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Johnson, Sally C.

1993-01-01

The use of computer software in life-critical applications, such as for civil air transports, demands the use of rigorous formal mathematical verification procedures. This paper demonstrates how to apply formal methods to the development and verification of software by leading the reader step-by-step through requirements analysis, design, implementation, and verification of an electronic phone book application. The current maturity and limitations of formal methods tools and techniques are then discussed, and a number of examples of the successful use of formal methods by industry are cited.

Review of Estelle and LOTOS with respect to critical computer applications

NASA Technical Reports Server (NTRS)

Bown, Rodney L.

1991-01-01

Man rated NASA space vehicles seem to represent a set of ultimate critical computer applications. These applications require a high degree of security, integrity, and safety. A variety of formal and/or precise modeling techniques are becoming available for the designer of critical systems. The design phase of the software engineering life cycle includes the modification of non-development components. A review of the Estelle and LOTOS formal description languages is presented. Details of the languages and a set of references are provided. The languages were used to formally describe some of the Open System Interconnect (OSI) protocols.

Weaving a Formal Methods Education with Problem-Based Learning

NASA Astrophysics Data System (ADS)

Gibson, J. Paul

The idea of weaving formal methods through computing (or software engineering) degrees is not a new one. However, there has been little success in developing and implementing such a curriculum. Formal methods continue to be taught as stand-alone modules and students, in general, fail to see how fundamental these methods are to the engineering of software. A major problem is one of motivation — how can the students be expected to enthusiastically embrace a challenging subject when the learning benefits, beyond passing an exam and achieving curriculum credits, are not clear? Problem-based learning has gradually moved from being an innovative pedagogique technique, commonly used to better-motivate students, to being widely adopted in the teaching of many different disciplines, including computer science and software engineering. Our experience shows that a good problem can be re-used throughout a student's academic life. In fact, the best computing problems can be used with children (young and old), undergraduates and postgraduates. In this paper we present a process for weaving formal methods through a University curriculum that is founded on the application of problem-based learning and a library of good software engineering problems, where students learn about formal methods without sitting a traditional formal methods module. The process of constructing good problems and integrating them into the curriculum is shown to be analagous to the process of engineering software. This approach is not intended to replace more traditional formal methods modules: it will better prepare students for such specialised modules and ensure that all students have an understanding and appreciation for formal methods even if they do not go on to specialise in them.

Parallel peak pruning for scalable SMP contour tree computation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carr, Hamish A.; Weber, Gunther H.; Sewell, Christopher M.

As data sets grow to exascale, automated data analysis and visualisation are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this formmore » of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Here in this paper, we report the first shared SMP algorithm for fully parallel contour tree computation, withfor-mal guarantees of O(lgnlgt) parallel steps and O(n lgn) work, and implementations with up to 10x parallel speed up in OpenMP and up to 50x speed up in NVIDIA Thrust.« less

Semi-implicit finite difference methods for three-dimensional shallow water flow

USGS Publications Warehouse

Casulli, Vincenzo; Cheng, Ralph T.

1992-01-01

A semi-implicit finite difference method for the numerical solution of three-dimensional shallow water flows is presented and discussed. The governing equations are the primitive three-dimensional turbulent mean flow equations where the pressure distribution in the vertical has been assumed to be hydrostatic. In the method of solution a minimal degree of implicitness has been adopted in such a fashion that the resulting algorithm is stable and gives a maximal computational efficiency at a minimal computational cost. At each time step the numerical method requires the solution of one large linear system which can be formally decomposed into a set of small three-diagonal systems coupled with one five-diagonal system. All these linear systems are symmetric and positive definite. Thus the existence and uniquencess of the numerical solution are assured. When only one vertical layer is specified, this method reduces as a special case to a semi-implicit scheme for solving the corresponding two-dimensional shallow water equations. The resulting two- and three-dimensional algorithm has been shown to be fast, accurate and mass-conservative and can also be applied to simulate flooding and drying of tidal mud-flats in conjunction with three-dimensional flows. Furthermore, the resulting algorithm is fully vectorizable for an efficient implementation on modern vector computers.

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions.

PubMed

Paliwal, Himanshu; Shirts, Michael R

2013-11-12

Multistate reweighting methods such as the multistate Bennett acceptance ratio (MBAR) can predict free energies and expectation values of thermodynamic observables at poorly sampled or unsampled thermodynamic states using simulations performed at only a few sampled states combined with single point energy reevaluations of these samples at the unsampled states. In this study, we demonstrate the power of this general reweighting formalism by exploring the effect of simulation parameters controlling Coulomb and Lennard-Jones cutoffs on free energy calculations and other observables. Using multistate reweighting, we can quickly identify, with very high sensitivity, the computationally least expensive nonbonded parameters required to obtain a specified accuracy in observables compared to the answer obtained using an expensive "gold standard" set of parameters. We specifically examine free energy estimates of three molecular transformations in a benchmark molecular set as well as the enthalpy of vaporization of TIP3P. The results demonstrates the power of this multistate reweighting approach for measuring changes in free energy differences or other estimators with respect to simulation or model parameters with very high precision and/or very low computational effort. The results also help to identify which simulation parameters affect free energy calculations and provide guidance to determine which simulation parameters are both appropriate and computationally efficient in general.

A Quantitative Approach to the Formal Verification of Real-Time Systems.

DTIC Science & Technology

1996-09-01

Computer Science A Quantitative Approach to the Formal Verification of Real - Time Systems Sergio Vale Aguiar Campos September 1996 CMU-CS-96-199...ptisiic raieaiSI v Diambimos Lboiamtad _^ A Quantitative Approach to the Formal Verification of Real - Time Systems Sergio Vale Aguiar Campos...implied, of NSF, the Semiconduc- tor Research Corporation, ARPA or the U.S. government. Keywords: real - time systems , formal verification, symbolic

Contrasting lexical similarity and formal definitions in SNOMED CT: consistency and implications.

PubMed

Agrawal, Ankur; Elhanan, Gai

2014-02-01

To quantify the presence of and evaluate an approach for detection of inconsistencies in the formal definitions of SNOMED CT (SCT) concepts utilizing a lexical method. Utilizing SCT's Procedure hierarchy, we algorithmically formulated similarity sets: groups of concepts with similar lexical structure of their fully specified name. We formulated five random samples, each with 50 similarity sets, based on the same parameter: number of parents, attributes, groups, all the former as well as a randomly selected control sample. All samples' sets were reviewed for types of formal definition inconsistencies: hierarchical, attribute assignment, attribute target values, groups, and definitional. For the Procedure hierarchy, 2111 similarity sets were formulated, covering 18.1% of eligible concepts. The evaluation revealed that 38 (Control) to 70% (Different relationships) of similarity sets within the samples exhibited significant inconsistencies. The rate of inconsistencies for the sample with different relationships was highly significant compared to Control, as well as the number of attribute assignment and hierarchical inconsistencies within their respective samples. While, at this time of the HITECH initiative, the formal definitions of SCT are only a minor consideration, in the grand scheme of sophisticated, meaningful use of captured clinical data, they are essential. However, significant portion of the concepts in the most semantically complex hierarchy of SCT, the Procedure hierarchy, are modeled inconsistently in a manner that affects their computability. Lexical methods can efficiently identify such inconsistencies and possibly allow for their algorithmic resolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Anaphora and Logical Form: On Formal Meaning Representations for Natural Language. Technical Report No. 36.

ERIC Educational Resources Information Center

Nash-Webber, Bonnie; Reiter, Raymond

This paper describes a computational approach to certain problems of anaphora in natural language and argues in favor of formal meaning representation languages (MRLs) for natural language. After presenting arguments in favor of formal meaning representation languages, appropriate MRLs are discussed. Minimal requirements include provisions for…

An Educational Development Tool Based on Principles of Formal Ontology

ERIC Educational Resources Information Center

Guzzi, Rodolfo; Scarpanti, Stefano; Ballista, Giovanni; Di Nicolantonio, Walter

2005-01-01

Computer science provides with virtual laboratories, places where one can merge real experiments with the formalism of algorithms and mathematics and where, with the advent of multimedia, sounds and movies can also be added. In this paper we present a method, based on principles of formal ontology, allowing one to develop interactive educational…

Algorithmics - Is There Hope for a Unified Theory?

NASA Astrophysics Data System (ADS)

Hromkovič, Juraj

Computer science was born with the formal definition of the notion of an algorithm. This definition provides clear limits of automatization, separating problems into algorithmically solvable problems and algorithmically unsolvable ones. The second big bang of computer science was the development of the concept of computational complexity. People recognized that problems that do not admit efficient algorithms are not solvable in practice. The search for a reasonable, clear and robust definition of the class of practically solvable algorithmic tasks started with the notion of the class {P} and of {NP}-completeness. In spite of the fact that this robust concept is still fundamental for judging the hardness of computational problems, a variety of approaches was developed for solving instances of {NP}-hard problems in many applications. Our 40-years short attempt to fix the fuzzy border between the practically solvable problems and the practically unsolvable ones partially reminds of the never-ending search for the definition of "life" in biology or for the definitions of matter and energy in physics. Can the search for the formal notion of "practical solvability" also become a never-ending story or is there hope for getting a well-accepted, robust definition of it? Hopefully, it is not surprising that we are not able to answer this question in this invited talk. But to deal with this question is of crucial importance, because only due to enormous effort scientists get a better and better feeling of what the fundamental notions of science like life and energy mean. In the flow of numerous technical results, we must not forget the fact that most of the essential revolutionary contributions to science were done by defining new concepts and notions.

Integrating Research and Education at the National Center for Atmospheric Research at the Interface of Formal and Informal Education

NASA Astrophysics Data System (ADS)

Johnson, R.; Foster, S.

2005-12-01

The National Center for Atmospheric Research (NCAR) in Boulder, Colorado, is a leading institution in scientific research, education and service associated with exploring and understanding our atmosphere and its interactions with the Sun, the oceans, the biosphere, and human society. NCAR draws thousands of public and scientific visitors from around the world to its Mesa Laboratory facility annually for educational as well as research purposes. Public visitors include adult visitors, clubs, and families on an informal visit to NCAR and its exhibits, as well as classroom and summer camp groups. Additionally, NCAR provides extensive computational and visualization services, which can be used not only for scientific, but also public informational purposes. As such, NCAR's audience provides an opportunity to address both formal and informal education through the programs that we offer. The University Corporation for Atmospheric Research (UCAR) Office of Education and Outreach works with NCAR to develop and implement a highly-integrated strategy for reaching both formal and informal audiences through programs that range from events and exhibits to professional development (for scientists and educators) and bilingual distance learning. The hallmarks of our program include close collaboration with scientists, multi-purposing resources where appropriate for maximum efficiency, and a commitment to engage populations historically underrepresented in science in the geosciences.

Applying Evidence-Based Medicine in Telehealth: An Interactive Pattern Recognition Approximation

PubMed Central

Fernández-Llatas, Carlos; Meneu, Teresa; Traver, Vicente; Benedi, José-Miguel

2013-01-01

Born in the early nineteen nineties, evidence-based medicine (EBM) is a paradigm intended to promote the integration of biomedical evidence into the physicians daily practice. This paradigm requires the continuous study of diseases to provide the best scientific knowledge for supporting physicians in their diagnosis and treatments in a close way. Within this paradigm, usually, health experts create and publish clinical guidelines, which provide holistic guidance for the care for a certain disease. The creation of these clinical guidelines requires hard iterative processes in which each iteration supposes scientific progress in the knowledge of the disease. To perform this guidance through telehealth, the use of formal clinical guidelines will allow the building of care processes that can be interpreted and executed directly by computers. In addition, the formalization of clinical guidelines allows for the possibility to build automatic methods, using pattern recognition techniques, to estimate the proper models, as well as the mathematical models for optimizing the iterative cycle for the continuous improvement of the guidelines. However, to ensure the efficiency of the system, it is necessary to build a probabilistic model of the problem. In this paper, an interactive pattern recognition approach to support professionals in evidence-based medicine is formalized. PMID:24185841

An Efficient Mutual Authentication Framework for Healthcare System in Cloud Computing.

PubMed

Kumar, Vinod; Jangirala, Srinivas; Ahmad, Musheer

2018-06-28

The increasing role of Telecare Medicine Information Systems (TMIS) makes its accessibility for patients to explore medical treatment, accumulate and approach medical data through internet connectivity. Security and privacy preservation is necessary for medical data of the patient in TMIS because of the very perceptive purpose. Recently, Mohit et al.'s proposed a mutual authentication protocol for TMIS in the cloud computing environment. In this work, we reviewed their protocol and found that it is not secure against stolen verifier attack, many logged in patient attack, patient anonymity, impersonation attack, and fails to protect session key. For enhancement of security level, we proposed a new mutual authentication protocol for the similar environment. The presented framework is also more capable in terms of computation cost. In addition, the security evaluation of the protocol protects resilience of all possible security attributes, and we also explored formal security evaluation based on random oracle model. The performance of the proposed protocol is much better in comparison to the existing protocol.

Global Sensory Qualities and Aesthetic Experience in Music.

PubMed

Brattico, Pauli; Brattico, Elvira; Vuust, Peter

2017-01-01

A well-known tradition in the study of visual aesthetics holds that the experience of visual beauty is grounded in global computational or statistical properties of the stimulus, for example, scale-invariant Fourier spectrum or self-similarity. Some approaches rely on neural mechanisms, such as efficient computation, processing fluency, or the responsiveness of the cells in the primary visual cortex. These proposals are united by the fact that the contributing factors are hypothesized to be global (i.e., they concern the percept as a whole), formal or non-conceptual (i.e., they concern form instead of content), computational and/or statistical, and based on relatively low-level sensory properties. Here we consider that the study of aesthetic responses to music could benefit from the same approach. Thus, along with local features such as pitch, tuning, consonance/dissonance, harmony, timbre, or beat, also global sonic properties could be viewed as contributing toward creating an aesthetic musical experience. Several such properties are discussed and their neural implementation is reviewed in the light of recent advances in neuroaesthetics.

Maximal aggregation of polynomial dynamical systems

PubMed Central

Cardelli, Luca; Tschaikowski, Max

2017-01-01

Ordinary differential equations (ODEs) with polynomial derivatives are a fundamental tool for understanding the dynamics of systems across many branches of science, but our ability to gain mechanistic insight and effectively conduct numerical evaluations is critically hindered when dealing with large models. Here we propose an aggregation technique that rests on two notions of equivalence relating ODE variables whenever they have the same solution (backward criterion) or if a self-consistent system can be written for describing the evolution of sums of variables in the same equivalence class (forward criterion). A key feature of our proposal is to encode a polynomial ODE system into a finitary structure akin to a formal chemical reaction network. This enables the development of a discrete algorithm to efficiently compute the largest equivalence, building on approaches rooted in computer science to minimize basic models of computation through iterative partition refinements. The physical interpretability of the aggregation is shown on polynomial ODE systems for biochemical reaction networks, gene regulatory networks, and evolutionary game theory. PMID:28878023

A linear decomposition method for large optimization problems. Blueprint for development

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, J.

1982-01-01

A method is proposed for decomposing large optimization problems encountered in the design of engineering systems such as an aircraft into a number of smaller subproblems. The decomposition is achieved by organizing the problem and the subordinated subproblems in a tree hierarchy and optimizing each subsystem separately. Coupling of the subproblems is accounted for by subsequent optimization of the entire system based on sensitivities of the suboptimization problem solutions at each level of the tree to variables of the next higher level. A formalization of the procedure suitable for computer implementation is developed and the state of readiness of the implementation building blocks is reviewed showing that the ingredients for the development are on the shelf. The decomposition method is also shown to be compatible with the natural human organization of the design process of engineering systems. The method is also examined with respect to the trends in computer hardware and software progress to point out that its efficiency can be amplified by network computing using parallel processors.

Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes.

PubMed

Sedwards, Sean; Mazza, Tommaso

2007-10-15

Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. While it is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, few, if any, explicitly model the topology of the membranes themselves. Discrete stochastic simulation potentially offers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described at the lowest level, i.e. by mass action. Simulation is a form of computer-aided analysis, relying on human interpretation to derive meaning. To improve efficiency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties. We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner, outer and integral layer. The underlying model is based on formal language theory and has been shown to have decidable properties (Cavaliere and Sedwards, 2006), allowing formal analysis in addition to simulation. The simulator provides variable levels of abstraction via arbitrary chemical kinetics which link to ordinary differential equations. In addition to its compact native syntax, Cyto-Sim currently supports models described as Petri nets, can import all versions of SBML and can export SBML and MATLAB m-files. Cyto-Sim is available free, either as an applet or a stand-alone Java program via the web page (http://www.cosbi.eu/Rpty_Soft_CytoSim.php). Other versions can be made available upon request.

Inflationary dynamics and preheating of the nonminimally coupled inflaton field in the metric and Palatini formalisms

NASA Astrophysics Data System (ADS)

Fu, Chengjie; Wu, Puxun; Yu, Hongwei

2017-11-01

The inflationary dynamics and preheating in a model with a nonminimally coupled inflaton field in the metric and Palatini formalisms are studied in this paper. We find that in both formalisms, irrespective of the initial conditions, our Universe will evolve into a slow-roll inflationary era and then the scalar field rolls into an oscillating phase. The value of the scalar field at the end of the inflation in the Palatini formalism is always larger than that in the metric one, which becomes more and more obvious with the increase of the absolute value of the coupling parameter |ξ |. During the preheating, we find that the inflaton quanta are produced explosively due to the parameter resonance and the growth of inflaton quanta will be terminated by the backreaction. With the increase of |ξ |, the resonance bands gradually close to the zero momentum (k =0 ), and the structure of resonance changes and becomes broader and broader in the metric formalism, while it remains to be narrow in the Palatini formalism. The energy transfer from the inflaton field to the fluctuation becomes more and more efficient with the increase of |ξ |, and in the metric formalism the growth of the efficiency of energy transfer is much faster than that in the Palatini formalism. Therefore, the inflation and preheating show different characteristics in different formalisms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solis, John Hector

In this paper, we present a modular framework for constructing a secure and efficient program obfuscation scheme. Our approach, inspired by the obfuscation with respect to oracle machines model of [4], retains an interactive online protocol with an oracle, but relaxes the original computational and storage restrictions. We argue this is reasonable given the computational resources of modern personal devices. Furthermore, we relax the information-theoretic security requirement for computational security to utilize established cryptographic primitives. With this additional flexibility we are free to explore different cryptographic buildingblocks. Our approach combines authenticated encryption with private information retrieval to construct a securemore » program obfuscation framework. We give a formal specification of our framework, based on desired functionality and security properties, and provide an example instantiation. In particular, we implement AES in Galois/Counter Mode for authenticated encryption and the Gentry-Ramzan [13]constant communication-rate private information retrieval scheme. We present our implementation results and show that non-trivial sized programs can be realized, but scalability is quickly limited by computational overhead. Finally, we include a discussion on security considerations when instantiating specific modules.« less

The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

PubMed

Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

2012-01-01

Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

Formal Assurance Arguments: A Solution In Search of a Problem?

NASA Technical Reports Server (NTRS)

Graydon, Patrick J.

2015-01-01

An assurance case comprises evidence and argument showing how that evidence supports assurance claims (e.g., about safety or security). It is unsurprising that some computer scientists have proposed formalizing assurance arguments: most associate formality with rigor. But while engineers can sometimes prove that source code refines a formal specification, it is not clear that formalization will improve assurance arguments or that this benefit is worth its cost. For example, formalization might reduce the benefits of argumentation by limiting the audience to people who can read formal logic. In this paper, we present (1) a systematic survey of the literature surrounding formal assurance arguments, (2) an analysis of errors that formalism can help to eliminate, (3) a discussion of existing evidence, and (4) suggestions for experimental work to definitively answer the question.

General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

NASA Astrophysics Data System (ADS)

Nagai, Tetsuro

2017-01-01

Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.

Comparison of nonmesonic hypernuclear decay rates computed in laboratory and center-of-mass coordinates

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Conti, C.; Barbero, C.; Galeão, A. P.

In this work we compute the one-nucleon-induced nonmesonic hypernuclear decay rates of {sub Λ}{sup 5}He, {sub Λ}{sup 12}C and {sub Λ}{sup 13}C using a formalism based on the independent particle shell model in terms of laboratory coordinates. To ascertain the correctness and precision of the method, these results are compared with those obtained using a formalism in terms of center-of-mass coordinates, which has been previously reported in the literature. The formalism in terms of laboratory coordinates will be useful in the shell-model approach to two-nucleon-induced transitions.

Efficient and accurate modeling of electron photoemission in nanostructures with TDDFT

NASA Astrophysics Data System (ADS)

Wopperer, Philipp; De Giovannini, Umberto; Rubio, Angel

2017-03-01

We derive and extend the time-dependent surface-flux method introduced in [L. Tao, A. Scrinzi, New J. Phys. 14, 013021 (2012)] within a time-dependent density-functional theory (TDDFT) formalism and use it to calculate photoelectron spectra and angular distributions of atoms and molecules when excited by laser pulses. We present other, existing computational TDDFT methods that are suitable for the calculation of electron emission in compact spatial regions, and compare their results. We illustrate the performance of the new method by simulating strong-field ionization of C60 fullerene and discuss final state effects in the orbital reconstruction of planar organic molecules.

Numerical studies of edge localized instabilities in tokamaks

NASA Astrophysics Data System (ADS)

Wilson, H. R.; Snyder, P. B.; Huysmans, G. T. A.; Miller, R. L.

2002-04-01

A new computational tool, edge localized instabilities in tokamaks equilibria (ELITE), has been developed to help our understanding of short wavelength instabilities close to the edge of tokamak plasmas. Such instabilities may be responsible for the edge localized modes observed in high confinement H-mode regimes, which are a serious concern for next step tokamaks because of the high transient power loads which they can impose on divertor target plates. ELITE uses physical insight gained from analytic studies of peeling and ballooning modes to provide an efficient way of calculating the edge ideal magnetohydrodynamic stability properties of tokamaks. This paper describes the theoretical formalism which forms the basis for the code.

F-Nets and Software Cabling: Deriving a Formal Model and Language for Portable Parallel Programming

NASA Technical Reports Server (NTRS)

DiNucci, David C.; Saini, Subhash (Technical Monitor)

1998-01-01

Parallel programming is still being based upon antiquated sequence-based definitions of the terms "algorithm" and "computation", resulting in programs which are architecture dependent and difficult to design and analyze. By focusing on obstacles inherent in existing practice, a more portable model is derived here, which is then formalized into a model called Soviets which utilizes a combination of imperative and functional styles. This formalization suggests more general notions of algorithm and computation, as well as insights into the meaning of structured programming in a parallel setting. To illustrate how these principles can be applied, a very-high-level graphical architecture-independent parallel language, called Software Cabling, is described, with many of the features normally expected from today's computer languages (e.g. data abstraction, data parallelism, and object-based programming constructs).

Computing biological functions using BioΨ, a formal description of biological processes based on elementary bricks of actions

PubMed Central

Pérès, Sabine; Felicori, Liza; Rialle, Stéphanie; Jobard, Elodie; Molina, Franck

2010-01-01

Motivation: In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes. Results: We present a formalism that uses the BioΨ concepts to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure–function relationships, etc.). We illustrate its application with two examples: the functional comparison of proteases and the functional description of the glycolysis network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation. Availability: www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/ Contact: sabine.peres@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20448138

Computational attributes of the integral form of the equation of transfer

NASA Technical Reports Server (NTRS)

Frankel, J. I.

1991-01-01

Difficulties can arise in radiative and neutron transport calculations when a highly anisotropic scattering phase function is present. In the presence of anisotropy, currently used numerical solutions are based on the integro-differential form of the linearized Boltzmann transport equation. This paper, departs from classical thought and presents an alternative numerical approach based on application of the integral form of the transport equation. Use of the integral formalism facilitates the following steps: a reduction in dimensionality of the system prior to discretization, the use of symbolic manipulation to augment the computational procedure, and the direct determination of key physical quantities which are derivable through the various Legendre moments of the intensity. The approach is developed in the context of radiative heat transfer in a plane-parallel geometry, and results are presented and compared with existing benchmark solutions. Encouraging results are presented to illustrate the potential of the integral formalism for computation. The integral formalism appears to possess several computational attributes which are well-suited to radiative and neutron transport calculations.

Computational models of epileptiform activity.

PubMed

Wendling, Fabrice; Benquet, Pascal; Bartolomei, Fabrice; Jirsa, Viktor

2016-02-15

We reviewed computer models that have been developed to reproduce and explain epileptiform activity. Unlike other already-published reviews on computer models of epilepsy, the proposed overview starts from the various types of epileptiform activity encountered during both interictal and ictal periods. Computational models proposed so far in the context of partial and generalized epilepsies are classified according to the following taxonomy: neural mass, neural field, detailed network and formal mathematical models. Insights gained about interictal epileptic spikes and high-frequency oscillations, about fast oscillations at seizure onset, about seizure initiation and propagation, about spike-wave discharges and about status epilepticus are described. This review shows the richness and complementarity of the various modeling approaches as well as the fruitful contribution of the computational neuroscience community in the field of epilepsy research. It shows that models have progressively gained acceptance and are now considered as an efficient way of integrating structural, functional and pathophysiological data about neural systems into "coherent and interpretable views". The advantages, limitations and future of modeling approaches are discussed. Perspectives in epilepsy research and clinical epileptology indicate that very promising directions are foreseen, like model-guided experiments or model-guided therapeutic strategy, among others. Copyright © 2015 Elsevier B.V. All rights reserved.

Computer Learning Through Piaget's Eyes.

ERIC Educational Resources Information Center

Huber, Leonard N.

1985-01-01

Discusses Piaget's pre-operational, concrete operational, and formal operational stages and shows how this information sheds light on how children approach computers and computing, particularly with the LOGO programming language. (JN)

Standardized development of computer software. Part 1: Methods

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1976-01-01

This work is a two-volume set on standards for modern software engineering methodology. This volume presents a tutorial and practical guide to the efficient development of reliable computer software, a unified and coordinated discipline for design, coding, testing, documentation, and project organization and management. The aim of the monograph is to provide formal disciplines for increasing the probability of securing software that is characterized by high degrees of initial correctness, readability, and maintainability, and to promote practices which aid in the consistent and orderly development of a total software system within schedule and budgetary constraints. These disciplines are set forth as a set of rules to be applied during software development to drastically reduce the time traditionally spent in debugging, to increase documentation quality, to foster understandability among those who must come in contact with it, and to facilitate operations and alterations of the program as requirements on the program environment change.

Tolerant (parallel) Programming

NASA Technical Reports Server (NTRS)

DiNucci, David C.; Bailey, David H. (Technical Monitor)

1997-01-01

In order to be truly portable, a program must be tolerant of a wide range of development and execution environments, and a parallel program is just one which must be tolerant of a very wide range. This paper first defines the term "tolerant programming", then describes many layers of tools to accomplish it. The primary focus is on F-Nets, a formal model for expressing computation as a folded partial-ordering of operations, thereby providing an architecture-independent expression of tolerant parallel algorithms. For implementing F-Nets, Cooperative Data Sharing (CDS) is a subroutine package for implementing communication efficiently in a large number of environments (e.g. shared memory and message passing). Software Cabling (SC), a very-high-level graphical programming language for building large F-Nets, possesses many of the features normally expected from today's computer languages (e.g. data abstraction, array operations). Finally, L2(sup 3) is a CASE tool which facilitates the construction, compilation, execution, and debugging of SC programs.

Homeostatic reinforcement learning for integrating reward collection and physiological stability.

PubMed

Keramati, Mehdi; Gutkin, Boris

2014-12-02

Efficient regulation of internal homeostasis and defending it against perturbations requires adaptive behavioral strategies. However, the computational principles mediating the interaction between homeostatic and associative learning processes remain undefined. Here we use a definition of primary rewards, as outcomes fulfilling physiological needs, to build a normative theory showing how learning motivated behaviors may be modulated by internal states. Within this framework, we mathematically prove that seeking rewards is equivalent to the fundamental objective of physiological stability, defining the notion of physiological rationality of behavior. We further suggest a formal basis for temporal discounting of rewards by showing that discounting motivates animals to follow the shortest path in the space of physiological variables toward the desired setpoint. We also explain how animals learn to act predictively to preclude prospective homeostatic challenges, and several other behavioral patterns. Finally, we suggest a computational role for interaction between hypothalamus and the brain reward system.

Enhancing Team Composition in Professional Networks: Problem Definitions and Fast Solutions

PubMed Central

Li, Liangyue; Tong, Hanghang; Cao, Nan; Ehrlich, Kate; Lin, Yu-Ru; Buchler, Norbou

2017-01-01

In this paper, we study ways to enhance the composition of teams based on new requirements in a collaborative environment. We focus on recommending team members who can maintain the team’s performance by minimizing changes to the team’s skills and social structure. Our recommendations are based on computing team-level similarity, which includes skill similarity, structural similarity as well as the synergy between the two. Current heuristic approaches are one-dimensional and not comprehensive, as they consider the two aspects independently. To formalize team-level similarity, we adopt the notion of graph kernel of attributed graphs to encompass the two aspects and their interaction. To tackle the computational challenges, we propose a family of fast algorithms by (a) designing effective pruning strategies, and (b) exploring the smoothness between the existing and the new team structures. Extensive empirical evaluations on real world datasets validate the effectiveness and efficiency of our algorithms. PMID:29104408

Modeling biological pathway dynamics with timed automata.

PubMed

Schivo, Stefano; Scholma, Jetse; Wanders, Brend; Urquidi Camacho, Ricardo A; van der Vet, Paul E; Karperien, Marcel; Langerak, Rom; van de Pol, Jaco; Post, Janine N

2014-05-01

Living cells are constantly subjected to a plethora of environmental stimuli that require integration into an appropriate cellular response. This integration takes place through signal transduction events that form tightly interconnected networks. The understanding of these networks requires capturing their dynamics through computational support and models. ANIMO (analysis of Networks with Interactive Modeling) is a tool that enables the construction and exploration of executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analyzed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signaling pathways, contributing to the integration of isolated signaling events into complex network models. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic behavior of the network of interest. A user-friendly interface hides the use of Timed Automata from the user, while keeping the expressive power intact. Abstraction to single-parameter kinetics speeds up construction of models that remain faithful enough to provide meaningful insight. The resulting dynamic behavior of the network components is displayed graphically, allowing for an intuitive and interactive modeling experience.

Microscopic derivation of particle-based coarse-grained dynamics: Exact expression for memory function

NASA Astrophysics Data System (ADS)

Izvekov, Sergei

2017-03-01

We consider the generalized Langevin equations of motion describing exactly the particle-based coarse-grained dynamics in the classical microscopic ensemble that were derived recently within the Mori-Zwanzig formalism based on new projection operators [S. Izvekov, J. Chem. Phys. 138(13), 134106 (2013)]. The fundamental difference between the new family of projection operators and the standard Zwanzig projection operator used in the past to derive the coarse-grained equations of motion is that the new operators average out the explicit irrelevant trajectories leading to the possibility of solving the projected dynamics exactly. We clarify the definition of the projection operators and revisit the formalism to compute the projected dynamics exactly for the microscopic system in equilibrium. The resulting expression for the projected force is in the form of a "generalized additive fluctuating force" describing the departure of the generalized microscopic force associated with the coarse-grained coordinate from its projection. Starting with this key expression, we formulate a new exact formula for the memory function in terms of microscopic and coarse-grained conservative forces. We conclude by studying two independent limiting cases of practical importance: the Markov limit (vanishing correlations of projected force) and the limit of weak dependence of the memory function on the particle momenta. We present computationally affordable expressions which can be efficiently evaluated from standard molecular dynamics simulations.

Magnetic field oscillations of the critical current in long ballistic graphene Josephson junctions

NASA Astrophysics Data System (ADS)

Rakyta, Péter; Kormányos, Andor; Cserti, József

2016-06-01

We study the Josephson current in long ballistic superconductor-monolayer graphene-superconductor junctions. As a first step, we have developed an efficient computational approach to calculate the Josephson current in tight-binding systems. This approach can be particularly useful in the long-junction limit, which has hitherto attracted less theoretical interest but has recently become experimentally relevant. We use this computational approach to study the dependence of the critical current on the junction geometry, doping level, and an applied perpendicular magnetic field B . In zero magnetic field we find a good qualitative agreement with the recent experiment of M. Ben Shalom et al. [Nat. Phys. 12, 318 (2016), 10.1038/nphys3592] for the length dependence of the critical current. For highly doped samples our numerical calculations show a broad agreement with the results of the quasiclassical formalism. In this case the critical current exhibits Fraunhofer-like oscillations as a function of B . However, for lower doping levels, where the cyclotron orbit becomes comparable to the characteristic geometrical length scales of the system, deviations from the results of the quasiclassical formalism appear. We argue that due to the exceptional tunability and long mean free path of graphene systems a new regime can be explored where geometrical and dynamical effects are equally important to understand the magnetic field dependence of the critical current.

Deep first formal concept search.

PubMed

Zhang, Tao; Li, Hui; Hong, Wenxue; Yuan, Xiamei; Wei, Xinyu

2014-01-01

The calculation of formal concepts is a very important part in the theory of formal concept analysis (FCA); however, within the framework of FCA, computing all formal concepts is the main challenge because of its exponential complexity and difficulty in visualizing the calculating process. With the basic idea of Depth First Search, this paper presents a visualization algorithm by the attribute topology of formal context. Limited by the constraints and calculation rules, all concepts are achieved by the visualization global formal concepts searching, based on the topology degenerated with the fixed start and end points, without repetition and omission. This method makes the calculation of formal concepts precise and easy to operate and reflects the integrity of the algorithm, which enables it to be suitable for visualization analysis.

Formal logic rewrite system bachelor in teaching mathematical informatics

NASA Astrophysics Data System (ADS)

Habiballa, Hashim; Jendryscik, Radek

2017-07-01

The article presents capabilities of the formal rewrite logic system - Bachelor - for teaching theoretical computer science (mathematical informatics). The system Bachelor enables constructivist approach to teaching and therefore it may enhance the learning process in hard informatics essential disciplines. It brings not only detailed description of formal rewrite process but also it can demonstrate algorithmical principles for logic formulae manipulations.

Module Extraction for Efficient Object Queries over Ontologies with Large ABoxes

PubMed Central

Xu, Jia; Shironoshita, Patrick; Visser, Ubbo; John, Nigel; Kabuka, Mansur

2015-01-01

The extraction of logically-independent fragments out of an ontology ABox can be useful for solving the tractability problem of querying ontologies with large ABoxes. In this paper, we propose a formal definition of an ABox module, such that it guarantees complete preservation of facts about a given set of individuals, and thus can be reasoned independently w.r.t. the ontology TBox. With ABox modules of this type, isolated or distributed (parallel) ABox reasoning becomes feasible, and more efficient data retrieval from ontology ABoxes can be attained. To compute such an ABox module, we present a theoretical approach and also an approximation for SHIQ ontologies. Evaluation of the module approximation on different types of ontologies shows that, on average, extracted ABox modules are significantly smaller than the entire ABox, and the time for ontology reasoning based on ABox modules can be improved significantly. PMID:26848490

A formalism for the calculus of variations with spinors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bäckdahl, Thomas, E-mail: thobac@chalmers.se; Valiente Kroon, Juan A., E-mail: j.a.valiente-kroon@qmul.ac.uk

2016-02-15

We develop a frame and dyad gauge-independent formalism for the calculus of variations of functionals involving spinorial objects. As a part of this formalism, we define a modified variation operator which absorbs frame and spin dyad gauge terms. This formalism is applicable to both the standard spacetime (i.e., SL(2, ℂ)) 2-spinors as well as to space (i.e., SU(2, ℂ)) 2-spinors. We compute expressions for the variations of the connection and the curvature spinors.

Development of structured ICD-10 and its application to computer-assisted ICD coding.

PubMed

Imai, Takeshi; Kajino, Masayuki; Sato, Megumi; Ohe, Kazuhiko

2010-01-01

This paper presents: (1) a framework of formal representation of ICD10, which functions as a bridge between ontological information and natural language expressions; and (2) a methodology to use formally described ICD10 for computer-assisted ICD coding. First, we analyzed and structurized the meanings of categories in 15 chapters of ICD10. Then we expanded the structured ICD10 (S-ICD10) by adding subordinate concepts and labels derived from Japanese Standard Disease Names. The information model to describe formal representation was refined repeatedly. The resultant model includes 74 types of semantic links. We also developed an ICD coding module based on S-ICD10 and a 'Coding Principle,' which achieved high accuracy (>70%) for four chapters. These results not only demonstrate the basic feasibility of our coding framework but might also inform the development of the information model for formal description framework in the ICD11 revision.

Computational Psychiatry and the Challenge of Schizophrenia.

PubMed

Krystal, John H; Murray, John D; Chekroud, Adam M; Corlett, Philip R; Yang, Genevieve; Wang, Xiao-Jing; Anticevic, Alan

2017-05-01

Schizophrenia research is plagued by enormous challenges in integrating and analyzing large datasets and difficulties developing formal theories related to the etiology, pathophysiology, and treatment of this disorder. Computational psychiatry provides a path to enhance analyses of these large and complex datasets and to promote the development and refinement of formal models for features of this disorder. This presentation introduces the reader to the notion of computational psychiatry and describes discovery-oriented and theory-driven applications to schizophrenia involving machine learning, reinforcement learning theory, and biophysically-informed neural circuit models. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center 2017.

Investigations in Computer-Aided Instruction and Computer-Aided Controls. Final Report.

ERIC Educational Resources Information Center

Rosenberg, R.C.; And Others

These research projects, designed to delve into certain relationships between humans and computers, are focused on computer-assisted instruction and on man-computer interaction. One study demonstrates that within the limits of formal engineering theory, a computer simulated laboratory (Dynamic Systems Laboratory) can be built in which freshmen…

Quantum Gibbs Samplers: The Commuting Case

NASA Astrophysics Data System (ADS)

Kastoryano, Michael J.; Brandão, Fernando G. S. L.

2016-06-01

We analyze the problem of preparing quantum Gibbs states of lattice spin Hamiltonians with local and commuting terms on a quantum computer and in nature. Our central result is an equivalence between the behavior of correlations in the Gibbs state and the mixing time of the semigroup which drives the system to thermal equilibrium (the Gibbs sampler). We introduce a framework for analyzing the correlation and mixing properties of quantum Gibbs states and quantum Gibbs samplers, which is rooted in the theory of non-commutative {mathbb{L}_p} spaces. We consider two distinct classes of Gibbs samplers, one of them being the well-studied Davies generator modelling the dynamics of a system due to weak-coupling with a large Markovian environment. We show that their spectral gap is independent of system size if, and only if, a certain strong form of clustering of correlations holds in the Gibbs state. Therefore every Gibbs state of a commuting Hamiltonian that satisfies clustering of correlations in this strong sense can be prepared efficiently on a quantum computer. As concrete applications of our formalism, we show that for every one-dimensional lattice system, or for systems in lattices of any dimension at temperatures above a certain threshold, the Gibbs samplers of commuting Hamiltonians are always gapped, giving an efficient way of preparing the associated Gibbs states on a quantum computer.

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences.

PubMed

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in.

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

PubMed Central

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. Availability PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in PMID:24616564

Provably Secure Password-based Authentication in TLS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abdalla, Michel; Emmanuel, Bresson; Chevassut, Olivier

2005-12-20

In this paper, we show how to design an efficient, provably secure password-based authenticated key exchange mechanism specifically for the TLS (Transport Layer Security) protocol. The goal is to provide a technique that allows users to employ (short) passwords to securely identify themselves to servers. As our main contribution, we describe a new password-based technique for user authentication in TLS, called Simple Open Key Exchange (SOKE). Loosely speaking, the SOKE ciphersuites are unauthenticated Diffie-Hellman ciphersuites in which the client's Diffie-Hellman ephemeral public value is encrypted using a simple mask generation function. The mask is simply a constant value raised tomore » the power of (a hash of) the password.The SOKE ciphersuites, in advantage over previous pass-word-based authentication ciphersuites for TLS, combine the following features. First, SOKE has formal security arguments; the proof of security based on the computational Diffie-Hellman assumption is in the random oracle model, and holds for concurrent executions and for arbitrarily large password dictionaries. Second, SOKE is computationally efficient; in particular, it only needs operations in a sufficiently large prime-order subgroup for its Diffie-Hellman computations (no safe primes). Third, SOKE provides good protocol flexibility because the user identity and password are only required once a SOKE ciphersuite has actually been negotiated, and after the server has sent a server identity.« less

Formal design and verification of a reliable computing platform for real-time control. Phase 1: Results

NASA Technical Reports Server (NTRS)

Divito, Ben L.; Butler, Ricky W.; Caldwell, James L.

1990-01-01

A high-level design is presented for a reliable computing platform for real-time control applications. Design tradeoffs and analyses related to the development of the fault-tolerant computing platform are discussed. The architecture is formalized and shown to satisfy a key correctness property. The reliable computing platform uses replicated processors and majority voting to achieve fault tolerance. Under the assumption of a majority of processors working in each frame, it is shown that the replicated system computes the same results as a single processor system not subject to failures. Sufficient conditions are obtained to establish that the replicated system recovers from transient faults within a bounded amount of time. Three different voting schemes are examined and proved to satisfy the bounded recovery time conditions.

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

PubMed

Dahdul, Wasila M; Balhoff, James P; Engeman, Jeffrey; Grande, Terry; Hilton, Eric J; Kothari, Cartik; Lapp, Hilmar; Lundberg, John G; Midford, Peter E; Vision, Todd J; Westerfield, Monte; Mabee, Paula M

2010-05-20

The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Any Ontological Model of the Single Qubit Stabilizer Formalism must be Contextual

NASA Astrophysics Data System (ADS)

Lillystone, Piers; Wallman, Joel J.

Quantum computers allow us to easily solve some problems classical computers find hard. Non-classical improvements in computational power should be due to some non-classical property of quantum theory. Contextuality, a more general notion of non-locality, is a necessary, but not sufficient, resource for quantum speed-up. Proofs of contextuality can be constructed for the classically simulable stabilizer formalism. Previous proofs of stabilizer contextuality are known for 2 or more qubits, for example the Mermin-Peres magic square. In the work presented we extend these results and prove that any ontological model of the single qubit stabilizer theory must be contextual, as defined by R. Spekkens, and give a relation between our result and the Mermin-Peres square. By demonstrating that contextuality is present in the qubit stabilizer formalism we provide further insight into the contextuality present in quantum theory. Understanding the contextuality of classical sub-theories will allow us to better identify the physical properties of quantum theory required for computational speed up. This research was supported by CIFAR, the Government of Ontario, and the Government of Canada through NSERC and Industry Canada.

Sequential Least-Squares Using Orthogonal Transformations. [spacecraft communication/spacecraft tracking-data smoothing

NASA Technical Reports Server (NTRS)

Bierman, G. J.

1975-01-01

Square root information estimation, starting from its beginnings in least-squares parameter estimation, is considered. Special attention is devoted to discussions of sensitivity and perturbation matrices, computed solutions and their formal statistics, consider-parameters and consider-covariances, and the effects of a priori statistics. The constant-parameter model is extended to include time-varying parameters and process noise, and the error analysis capabilities are generalized. Efficient and elegant smoothing results are obtained as easy consequences of the filter formulation. The value of the techniques is demonstrated by the navigation results that were obtained for the Mariner Venus-Mercury (Mariner 10) multiple-planetary space probe and for the Viking Mars space mission.

Simulation of polymer translocation through protein channels

PubMed Central

Muthukumar, M.; Kong, C. Y.

2006-01-01

A modeling algorithm is presented to compute simultaneously polymer conformations and ionic current, as single polymer molecules undergo translocation through protein channels. The method is based on a combination of Langevin dynamics for coarse-grained models of polymers and the Poisson–Nernst–Planck formalism for ionic current. For the illustrative example of ssDNA passing through the α-hemolysin pore, vivid details of conformational fluctuations of the polymer inside the vestibule and β-barrel compartments of the protein pore, and their consequent effects on the translocation time and extent of blocked ionic current are presented. In addition to yielding insights into several experimentally reported puzzles, our simulations offer experimental strategies to sequence polymers more efficiently. PMID:16567657

High resolution x-ray CMT: Reconstruction methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, J.K.

This paper qualitatively discusses the primary characteristics of methods for reconstructing tomographic images from a set of projections. These reconstruction methods can be categorized as either {open_quotes}analytic{close_quotes} or {open_quotes}iterative{close_quotes} techniques. Analytic algorithms are derived from the formal inversion of equations describing the imaging process, while iterative algorithms incorporate a model of the imaging process and provide a mechanism to iteratively improve image estimates. Analytic reconstruction algorithms are typically computationally more efficient than iterative methods; however, analytic algorithms are available for a relatively limited set of imaging geometries and situations. Thus, the framework of iterative reconstruction methods is better suited formore » high accuracy, tomographic reconstruction codes.« less

An Overview of Computer-Based Natural Language Processing.

ERIC Educational Resources Information Center

Gevarter, William B.

Computer-based Natural Language Processing (NLP) is the key to enabling humans and their computer-based creations to interact with machines using natural languages (English, Japanese, German, etc.) rather than formal computer languages. NLP is a major research area in the fields of artificial intelligence and computational linguistics. Commercial…

Crowd Sourced Formal Verification-Augmentation (CSFV-A)

DTIC Science & Technology

2016-06-01

Formal Verification (CSFV) program built games that recast FV problems into puzzles to make these problems more accessible, increasing the manpower to...construct FV proofs. This effort supported the CSFV program by hosting the games on a public website, and analyzed the gameplay for efficiency to...provide FV proofs. 15. SUBJECT TERMS Crowd Source, Software, Formal Verification, Games 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT

OntoADR a semantic resource describing adverse drug reactions to support searching, coding, and information retrieval.

PubMed

Souvignet, Julien; Declerck, Gunnar; Asfari, Hadyl; Jaulent, Marie-Christine; Bousquet, Cédric

2016-10-01

Efficient searching and coding in databases that use terminological resources requires that they support efficient data retrieval. The Medical Dictionary for Regulatory Activities (MedDRA) is a reference terminology for several countries and organizations to code adverse drug reactions (ADRs) for pharmacovigilance. Ontologies that are available in the medical domain provide several advantages such as reasoning to improve data retrieval. The field of pharmacovigilance does not yet benefit from a fully operational ontology to formally represent the MedDRA terms. Our objective was to build a semantic resource based on formal description logic to improve MedDRA term retrieval and aid the generation of on-demand custom groupings by appropriately and efficiently selecting terms: OntoADR. The method consists of the following steps: (1) mapping between MedDRA terms and SNOMED-CT, (2) generation of semantic definitions using semi-automatic methods, (3) storage of the resource and (4) manual curation by pharmacovigilance experts. We built a semantic resource for ADRs enabling a new type of semantics-based term search. OntoADR adds new search capabilities relative to previous approaches, overcoming the usual limitations of computation using lightweight description logic, such as the intractability of unions or negation queries, bringing it closer to user needs. Our automated approach for defining MedDRA terms enabled the association of at least one defining relationship with 67% of preferred terms. The curation work performed on our sample showed an error level of 14% for this automated approach. We tested OntoADR in practice, which allowed us to build custom groupings for several medical topics of interest. The methods we describe in this article could be adapted and extended to other terminologies which do not benefit from a formal semantic representation, thus enabling better data retrieval performance. Our custom groupings of MedDRA terms were used while performing signal detection, which suggests that the graphical user interface we are currently implementing to process OntoADR could be usefully integrated into specialized pharmacovigilance software that rely on MedDRA. Copyright © 2016 Elsevier Inc. All rights reserved.

NASA Langley Research and Technology-Transfer Program in Formal Methods

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Caldwell, James L.; Carreno, Victor A.; Holloway, C. Michael; Miner, Paul S.; DiVito, Ben L.

1995-01-01

This paper presents an overview of NASA Langley research program in formal methods. The major goals of this work are to make formal methods practical for use on life critical systems, and to orchestrate the transfer of this technology to U.S. industry through use of carefully designed demonstration projects. Several direct technology transfer efforts have been initiated that apply formal methods to critical subsystems of real aerospace computer systems. The research team consists of five NASA civil servants and contractors from Odyssey Research Associates, SRI International, and VIGYAN Inc.

Approximate Micromechanics Treatise of Composite Impact

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Handler, Louis M.

2005-01-01

A formalism is described for micromechanic impact of composites. The formalism consists of numerous equations which describe all aspects of impact from impactor and composite conditions to impact contact, damage progression, and penetration or containment. The formalism is based on through-the-thickness displacement increments simulation which makes it convenient to track local damage in terms of microfailure modes and their respective characteristics. A flow chart is provided to cast the formalism (numerous equations) into a computer code for embedment in composite mechanic codes and/or finite element composite structural analysis.

Intramolecular carbolithiation of N-allyl-ynamides: an efficient entry to 1,4-dihydropyridines and pyridines - application to a formal synthesis of sarizotan.

PubMed

Gati, Wafa; Rammah, Mohamed M; Rammah, Mohamed B; Evano, Gwilherm

2012-01-01

We have developed a general synthesis of polysubstituted 1,4-dihydropyridines and pyridines based on a highly regioselective lithiation/6-endo-dig intramolecular carbolithiation from readily available N-allyl-ynamides. This reaction, which has been successfully applied to the formal synthesis of the anti-dyskinesia agent sarizotan, further extends the use of ynamides in organic synthesis and further demonstrates the synthetic efficiency of carbometallation reactions.

Universal Quantum Computing with Arbitrary Continuous-Variable Encoding.

PubMed

Lau, Hoi-Kwan; Plenio, Martin B

2016-09-02

Implementing a qubit quantum computer in continuous-variable systems conventionally requires the engineering of specific interactions according to the encoding basis states. In this work, we present a unified formalism to conduct universal quantum computation with a fixed set of operations but arbitrary encoding. By storing a qubit in the parity of two or four qumodes, all computing processes can be implemented by basis state preparations, continuous-variable exponential-swap operations, and swap tests. Our formalism inherits the advantages that the quantum information is decoupled from collective noise, and logical qubits with different encodings can be brought to interact without decoding. We also propose a possible implementation of the required operations by using interactions that are available in a variety of continuous-variable systems. Our work separates the "hardware" problem of engineering quantum-computing-universal interactions, from the "software" problem of designing encodings for specific purposes. The development of quantum computer architecture could hence be simplified.

Universal Quantum Computing with Arbitrary Continuous-Variable Encoding

NASA Astrophysics Data System (ADS)

Lau, Hoi-Kwan; Plenio, Martin B.

2016-09-01

Implementing a qubit quantum computer in continuous-variable systems conventionally requires the engineering of specific interactions according to the encoding basis states. In this work, we present a unified formalism to conduct universal quantum computation with a fixed set of operations but arbitrary encoding. By storing a qubit in the parity of two or four qumodes, all computing processes can be implemented by basis state preparations, continuous-variable exponential-swap operations, and swap tests. Our formalism inherits the advantages that the quantum information is decoupled from collective noise, and logical qubits with different encodings can be brought to interact without decoding. We also propose a possible implementation of the required operations by using interactions that are available in a variety of continuous-variable systems. Our work separates the "hardware" problem of engineering quantum-computing-universal interactions, from the "software" problem of designing encodings for specific purposes. The development of quantum computer architecture could hence be simplified.

A biologically consistent hierarchical framework for self-referencing survivalist computation

NASA Astrophysics Data System (ADS)

Cottam, Ron; Ranson, Willy; Vounckx, Roger

2000-05-01

Extensively scaled formally rational hardware and software are indirectly fallible, at the very least through temporal restrictions on the evaluation of their correctness. In addition, the apparent inability of formal rationality to successfully describe living systems as anything other than inanimate structures suggests that the development of self-referencing computational machines will require a different approach. There is currently a strong movement towards the adoption of semiotics as a descriptive medium in theoretical biology. We present a related computational semiosic construction (1, 2) consistent with evolutionary hierarchical emergence (3), which may serve as a framework for implementing anticipatory-oriented survivalist processing in real environments.

The tractable cognition thesis.

PubMed

Van Rooij, Iris

2008-09-01

The recognition that human minds/brains are finite systems with limited resources for computation has led some researchers to advance the Tractable Cognition thesis: Human cognitive capacities are constrained by computational tractability. This thesis, if true, serves cognitive psychology by constraining the space of computational-level theories of cognition. To utilize this constraint, a precise and workable definition of "computational tractability" is needed. Following computer science tradition, many cognitive scientists and psychologists define computational tractability as polynomial-time computability, leading to the P-Cognition thesis. This article explains how and why the P-Cognition thesis may be overly restrictive, risking the exclusion of veridical computational-level theories from scientific investigation. An argument is made to replace the P-Cognition thesis by the FPT-Cognition thesis as an alternative formalization of the Tractable Cognition thesis (here, FPT stands for fixed-parameter tractable). Possible objections to the Tractable Cognition thesis, and its proposed formalization, are discussed, and existing misconceptions are clarified. 2008 Cognitive Science Society, Inc.

49 CFR 236.923 - Task analysis and basic requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... classroom, simulator, computer-based, hands-on, or other formally structured training and testing, except... for Processor-Based Signal and Train Control Systems § 236.923 Task analysis and basic requirements...) Based on a formal task analysis, identify the installation, maintenance, repair, modification...

Formal Specification of Information Systems Requirements.

ERIC Educational Resources Information Center

Kampfner, Roberto R.

1985-01-01

Presents a formal model for specification of logical requirements of computer-based information systems that incorporates structural and dynamic aspects based on two separate models: the Logical Information Processing Structure and the Logical Information Processing Network. The model's role in systems development is discussed. (MBR)

Formalizing Evaluation Procedures for Marketing Faculty Research Performance.

ERIC Educational Resources Information Center

McDermott, Dennis R.; And Others

1994-01-01

Results of a national survey of marketing department heads (n=142) indicate that few marketing departments have formalized the development and communication of research performance standards to faculty. Guidelines and methods to accomplish those procedures most efficiently were proposed. (Author/JOW)

n-D shape/texture optimal synthetic description and modeling by GEOGINE

NASA Astrophysics Data System (ADS)

Fiorini, Rodolfo A.; Dacquino, Gianfranco F.

2004-12-01

GEOGINE(GEOmetrical enGINE), a state-of-the-art OMG (Ontological Model Generator) based on n-D Tensor Invariants for multidimensional shape/texture optimal synthetic description and learning, is presented. Usually elementary geometric shape robust characterization, subjected to geometric transformation, on a rigorous mathematical level is a key problem in many computer applications in different interest areas. The past four decades have seen solutions almost based on the use of n-Dimensional Moment and Fourier descriptor invariants. The present paper introduces a new approach for automatic model generation based on n -Dimensional Tensor Invariants as formal dictionary. An ontological model is the kernel used for specifying ontologies so that how close an ontology can be from the real world depends on the possibilities offered by the ontological model. By this approach even chromatic information content can be easily and reliably decoupled from target geometric information and computed into robus colour shape parameter attributes. Main GEOGINEoperational advantages over previous approaches are: 1) Automated Model Generation, 2) Invariant Minimal Complete Set for computational efficiency, 3) Arbitrary Model Precision for robust object description.

Global Sensory Qualities and Aesthetic Experience in Music

PubMed Central

Brattico, Pauli; Brattico, Elvira; Vuust, Peter

2017-01-01

A well-known tradition in the study of visual aesthetics holds that the experience of visual beauty is grounded in global computational or statistical properties of the stimulus, for example, scale-invariant Fourier spectrum or self-similarity. Some approaches rely on neural mechanisms, such as efficient computation, processing fluency, or the responsiveness of the cells in the primary visual cortex. These proposals are united by the fact that the contributing factors are hypothesized to be global (i.e., they concern the percept as a whole), formal or non-conceptual (i.e., they concern form instead of content), computational and/or statistical, and based on relatively low-level sensory properties. Here we consider that the study of aesthetic responses to music could benefit from the same approach. Thus, along with local features such as pitch, tuning, consonance/dissonance, harmony, timbre, or beat, also global sonic properties could be viewed as contributing toward creating an aesthetic musical experience. Several such properties are discussed and their neural implementation is reviewed in the light of recent advances in neuroaesthetics. PMID:28424573

Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP.

PubMed

Vitale, Valerio; Dziedzic, Jacek; Dubois, Simon M-M; Fangohr, Hans; Skylaris, Chris-Kriton

2015-07-14

Density functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFT-MD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in the understanding and assignment of experimental peaks and bands at finite temperature, particularly in the case of floppy molecules. Linear-scaling DFT methods can be used to study large and complex systems, such as peptides, DNA strands, amorphous solids, and molecules in solution. Here, we present the implementation of DFT-MD IR spectroscopy in the ONETEP linear-scaling code. In addition, two methods for partitioning the dipole moment within the ONETEP framework are presented. Dipole moment partitioning allows us to compute spectra of molecules in solution, which fully include the effects of the solvent, while at the same time removing the solvent contribution from the spectra.

An Analytic Formulation of the 21 cm Signal from the Early Phase of the Epoch of Reionization

NASA Astrophysics Data System (ADS)

Raste, Janakee; Sethi, Shiv

2018-06-01

We present an analytic formulation to model the fluctuating component of the H I signal from the epoch of reionization during the phase of partial heating. During this phase, we assume self-ionized regions, whose size distribution can be computed using excursion set formalism, to be surrounded by heated regions. We model the evolution of the heating profile around these regions (near zone) and their merger into the time-dependent background (far zone). We develop a formalism to compute the two-point correlation function for this topology, taking into account the heating autocorrelation and heating-ionization cross-correlation. We model the ionization and X-ray heating using four parameters: efficiency of ionization, ζ number of X-ray photons per stellar baryon, N heat; spectral index of X-ray photons, α and minimum frequency of X-ray photons, ν min. We compute the H I signal in the redshift range 10 < z < 20 for the ΛCDM model for a set of these parameters. We show that the H I signal for a range of scales 1–8 Mpc shows a peak strength of 100–1000 (mK)2 during the partially heated era. The redshift at which the signal makes a transition to a uniformly heated universe depends on the modeling parameters; e.g., if ν min is changed from 100 eV to 1 keV, this transition moves from z ≃ 15 to z ≃ 12. This result, along with the dependence of the H I signal on the modeling parameters, is in reasonable agreement with existing results from N-body simulations.

Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning.

PubMed

Gorban, A N; Mirkes, E M; Zinovyev, A

2016-12-01

Most of machine learning approaches have stemmed from the application of minimizing the mean squared distance principle, based on the computationally efficient quadratic optimization methods. However, when faced with high-dimensional and noisy data, the quadratic error functionals demonstrated many weaknesses including high sensitivity to contaminating factors and dimensionality curse. Therefore, a lot of recent applications in machine learning exploited properties of non-quadratic error functionals based on L 1 norm or even sub-linear potentials corresponding to quasinorms L p (0

Tailoring Quantum Dot Assemblies to Extend Exciton Coherence Times and Improve Exciton Transport

NASA Astrophysics Data System (ADS)

Seward, Kenton; Lin, Zhibin; Lusk, Mark

2012-02-01

The motion of excitons through nanostructured assemblies plays a central role in a wide range of physical phenomena including quantum computing, molecular electronics, photosynthetic processes, excitonic transistors and light emitting diodes. All of these technologies are severely handicapped, though, by quasi-particle lifetimes on the order of a nanosecond. The movement of excitons must therefore be as efficient as possible in order to move excitons meaningful distances. This is problematic for assemblies of small Si quantum dots (QDs), where excitons quickly localize and entangle with dot phonon modes. Ensuing exciton transport is then characterized by a classical random walk reduced to very short distances because of efficient recombination. We use a combination of master equation (Haken-Strobl) formalism and density functional theory to estimate the rate of decoherence in Si QD assemblies and its impact on exciton mobility. Exciton-phonon coupling and Coulomb interactions are calculated as a function of dot size, spacing and termination to minimize the rate of intra-dot phonon entanglement. This extends the time over which more efficient exciton transport, characterized by partial coherence, can be maintained.

An Efficient and Adaptive Mutual Authentication Framework for Heterogeneous Wireless Sensor Network-Based Applications

PubMed Central

Kumar, Pardeep; Ylianttila, Mika; Gurtov, Andrei; Lee, Sang-Gon; Lee, Hoon-Jae

2014-01-01

Robust security is highly coveted in real wireless sensor network (WSN) applications since wireless sensors' sense critical data from the application environment. This article presents an efficient and adaptive mutual authentication framework that suits real heterogeneous WSN-based applications (such as smart homes, industrial environments, smart grids, and healthcare monitoring). The proposed framework offers: (i) key initialization; (ii) secure network (cluster) formation (i.e., mutual authentication and dynamic key establishment); (iii) key revocation; and (iv) new node addition into the network. The correctness of the proposed scheme is formally verified. An extensive analysis shows the proposed scheme coupled with message confidentiality, mutual authentication and dynamic session key establishment, node privacy, and message freshness. Moreover, the preliminary study also reveals the proposed framework is secure against popular types of attacks, such as impersonation attacks, man-in-the-middle attacks, replay attacks, and information-leakage attacks. As a result, we believe the proposed framework achieves efficiency at reasonable computation and communication costs and it can be a safeguard to real heterogeneous WSN applications. PMID:24521942

An efficient and adaptive mutual authentication framework for heterogeneous wireless sensor network-based applications.

PubMed

Kumar, Pardeep; Ylianttila, Mika; Gurtov, Andrei; Lee, Sang-Gon; Lee, Hoon-Jae

2014-02-11

Robust security is highly coveted in real wireless sensor network (WSN) applications since wireless sensors' sense critical data from the application environment. This article presents an efficient and adaptive mutual authentication framework that suits real heterogeneous WSN-based applications (such as smart homes, industrial environments, smart grids, and healthcare monitoring). The proposed framework offers: (i) key initialization; (ii) secure network (cluster) formation (i.e., mutual authentication and dynamic key establishment); (iii) key revocation; and (iv) new node addition into the network. The correctness of the proposed scheme is formally verified. An extensive analysis shows the proposed scheme coupled with message confidentiality, mutual authentication and dynamic session key establishment, node privacy, and message freshness. Moreover, the preliminary study also reveals the proposed framework is secure against popular types of attacks, such as impersonation attacks, man-in-the-middle attacks, replay attacks, and information-leakage attacks. As a result, we believe the proposed framework achieves efficiency at reasonable computation and communication costs and it can be a safeguard to real heterogeneous WSN applications.

A Microworld Approach to the Formalization of Musical Knowledge.

ERIC Educational Resources Information Center

Honing, Henkjan

1993-01-01

Discusses the importance of applying computational modeling and artificial intelligence techniques to music cognition and computer music research. Recommends three uses of microworlds to trim computational theories to their bare minimum, allowing for better and easier comparison. (CFR)

Computational Evaluation of the Traceback Method

ERIC Educational Resources Information Center

Kol, Sheli; Nir, Bracha; Wintner, Shuly

2014-01-01

Several models of language acquisition have emerged in recent years that rely on computational algorithms for simulation and evaluation. Computational models are formal and precise, and can thus provide mathematically well-motivated insights into the process of language acquisition. Such models are amenable to robust computational evaluation,…

Efficient optical analysis of surface texture combinations for silicon solar cells

NASA Astrophysics Data System (ADS)

Tucher, Nico; Eisenlohr, Johannes; Kiefel, Peter; Gebrewold, Habtamu; Höhn, Oliver; Hauser, Hubert; Müller, Claas; Goldschmidt, Jan Christoph; Bläsi, Benedikt

2016-04-01

Surface textures can significantly improve anti-reflective and light trapping properties of silicon solar cells. Combining standard pyramidal front side textures with scattering or diffractive rear side textures has the potential to further increase the light path length inside the silicon and thereby increase the solar cell efficiency. In this work we introduce the OPTOS (Optical Properties of Textured Optical Sheets) simulation formalism and apply it to the modelling of silicon solar cells with different surface textures at front and rear side. OPTOS is a matrix-based method that allows for the computationally-efficient calculation of non-coherent light propagation within textured solar cells, featuring multiple textures that may operate in different optical regimes. After calculating redistribution matrices for each individual surface texture with the most appropriate technique, optical properties like angle dependent reflectance, transmittance or absorptance can be determined via matrix multiplications. Using OPTOS, we demonstrate for example that the integration of a diffractive grating at the rear side of solar cells with random pyramids at the front results in an absorptance gain that corresponds to a photocurrent density enhancement of 0.73 mA/cm2 for a 250 μm thick cell. The re-usability of matrices enables the investigation of different solar cell thicknesses within minutes. For thicknesses down to 50 μm the simulated gain increases up to 1.22 mA/cm2. The OPTOS formalism is furthermore not restricted with respect to the number of textured interfaces. By combining two or more textured sheets to effective interfaces, it is possible to optically model a complete photovoltaic module including EVA and potentially textured glass layers with one calculation tool.

Non-Determinism: An Abstract Concept in Computer Science Studies

ERIC Educational Resources Information Center

Armoni, Michal; Gal-Ezer, Judith

2007-01-01

Non-determinism is one of the most important, yet abstract, recurring concepts of Computer Science. It plays an important role in Computer Science areas such as formal language theory, computability theory, distributed computing, and operating systems. We conducted a series of studies on the perception of non-determinism. In the current research,…

Stakeholder Perceptions of ICT Usage across Management Institutes

ERIC Educational Resources Information Center

Goyal, Ela; Purohit, Seema; Bhagat, Manju

2013-01-01

Information and communication technology (ICT) which includes radio, television and newer digital technology such as computers and the internet, are potentially powerful tools for extending educational opportunities, formal and non-formal, to one and all. It provides opportunities to deploy innovative teaching methodologies and interesting…

Intramolecular carbolithiation of N-allyl-ynamides: an efficient entry to 1,4-dihydropyridines and pyridines – application to a formal synthesis of sarizotan

PubMed Central

Gati, Wafa; Rammah, Mohamed M; Rammah, Mohamed B

2012-01-01

Summary We have developed a general synthesis of polysubstituted 1,4-dihydropyridines and pyridines based on a highly regioselective lithiation/6-endo-dig intramolecular carbolithiation from readily available N-allyl-ynamides. This reaction, which has been successfully applied to the formal synthesis of the anti-dyskinesia agent sarizotan, further extends the use of ynamides in organic synthesis and further demonstrates the synthetic efficiency of carbometallation reactions. PMID:23365632

Tactical Synthesis Of Efficient Global Search Algorithms

NASA Technical Reports Server (NTRS)

Nedunuri, Srinivas; Smith, Douglas R.; Cook, William R.

2009-01-01

Algorithm synthesis transforms a formal specification into an efficient algorithm to solve a problem. Algorithm synthesis in Specware combines the formal specification of a problem with a high-level algorithm strategy. To derive an efficient algorithm, a developer must define operators that refine the algorithm by combining the generic operators in the algorithm with the details of the problem specification. This derivation requires skill and a deep understanding of the problem and the algorithmic strategy. In this paper we introduce two tactics to ease this process. The tactics serve a similar purpose to tactics used for determining indefinite integrals in calculus, that is suggesting possible ways to attack the problem.

The Effect of Computer Assisted and Computer Based Teaching Methods on Computer Course Success and Computer Using Attitudes of Students

ERIC Educational Resources Information Center

Tosun, Nilgün; Suçsuz, Nursen; Yigit, Birol

2006-01-01

The purpose of this research was to investigate the effects of the computer-assisted and computer-based instructional methods on students achievement at computer classes and on their attitudes towards using computers. The study, which was completed in 6 weeks, were carried out with 94 sophomores studying in formal education program of Primary…

Formal methods and digital systems validation for airborne systems

NASA Technical Reports Server (NTRS)

Rushby, John

1993-01-01

This report has been prepared to supplement a forthcoming chapter on formal methods in the FAA Digital Systems Validation Handbook. Its purpose is as follows: to outline the technical basis for formal methods in computer science; to explain the use of formal methods in the specification and verification of software and hardware requirements, designs, and implementations; to identify the benefits, weaknesses, and difficulties in applying these methods to digital systems used on board aircraft; and to suggest factors for consideration when formal methods are offered in support of certification. These latter factors assume the context for software development and assurance described in RTCA document DO-178B, 'Software Considerations in Airborne Systems and Equipment Certification,' Dec. 1992.

Computation of elementary modes: a unifying framework and the new binary approach

PubMed Central

Gagneur, Julien; Klamt, Steffen

2004-01-01

Background Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous formalism to describe and assess pathways and has proven to be valuable for many applications. However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods. Results We show that computing the set of elementary modes is equivalent to computing the set of extreme rays of a convex cone. This standard mathematical representation provides a unified framework that encompasses the most prominent algorithmic methods that compute elementary modes and allows a clear comparison between them. Taking lessons from this benchmark, we here introduce a new method, the binary approach, which computes the elementary modes as binary patterns of participating reactions from which the respective stoichiometric coefficients can be computed in a post-processing step. We implemented the binary approach in FluxAnalyzer 5.1, a software that is free for academics. The binary approach decreases the memory demand up to 96% without loss of speed giving the most efficient method available for computing elementary modes to date. Conclusions The equivalence between elementary modes and extreme ray computations offers opportunities for employing tools from polyhedral computation for metabolic pathway analysis. The new binary approach introduced herein was derived from this general theoretical framework and facilitates the computation of elementary modes in considerably larger networks. PMID:15527509

A Formalized Design Process for Bacterial Consortia That Perform Logic Computing

PubMed Central

Sun, Rui; Xi, Jingyi; Wen, Dingqiao; Feng, Jingchen; Chen, Yiwei; Qin, Xiao; Ma, Yanrong; Luo, Wenhan; Deng, Linna; Lin, Hanchi; Yu, Ruofan; Ouyang, Qi

2013-01-01

The concept of microbial consortia is of great attractiveness in synthetic biology. Despite of all its benefits, however, there are still problems remaining for large-scaled multicellular gene circuits, for example, how to reliably design and distribute the circuits in microbial consortia with limited number of well-behaved genetic modules and wiring quorum-sensing molecules. To manage such problem, here we propose a formalized design process: (i) determine the basic logic units (AND, OR and NOT gates) based on mathematical and biological considerations; (ii) establish rules to search and distribute simplest logic design; (iii) assemble assigned basic logic units in each logic operating cell; and (iv) fine-tune the circuiting interface between logic operators. We in silico analyzed gene circuits with inputs ranging from two to four, comparing our method with the pre-existing ones. Results showed that this formalized design process is more feasible concerning numbers of cells required. Furthermore, as a proof of principle, an Escherichia coli consortium that performs XOR function, a typical complex computing operation, was designed. The construction and characterization of logic operators is independent of “wiring” and provides predictive information for fine-tuning. This formalized design process provides guidance for the design of microbial consortia that perform distributed biological computation. PMID:23468999

Formal Requirements-Based Programming for Complex Systems

NASA Technical Reports Server (NTRS)

Rash, James L.; Hinchey, Michael G.; Rouff, Christopher A.; Gracanin, Denis

2005-01-01

Computer science as a field has not yet produced a general method to mechanically transform complex computer system requirements into a provably equivalent implementation. Such a method would be one major step towards dealing with complexity in computing, yet it remains the elusive holy grail of system development. Currently available tools and methods that start with a formal model of a system and mechanically produce a provably equivalent implementation are valuable but not sufficient. The gap that such tools and methods leave unfilled is that the formal models cannot be proven to be equivalent to the system requirements as originated by the customer For the classes of complex systems whose behavior can be described as a finite (but significant) set of scenarios, we offer a method for mechanically transforming requirements (expressed in restricted natural language, or appropriate graphical notations) into a provably equivalent formal model that can be used as the basis for code generation and other transformations. While other techniques are available, this method is unique in offering full mathematical tractability while using notations and techniques that are well known and well trusted. We illustrate the application of the method to an example procedure from the Hubble Robotic Servicing Mission currently under study and preliminary formulation at NASA Goddard Space Flight Center.

Technical- and environmental-efficiency analysis of irrigated cotton-cropping systems in Punjab, Pakistan using data envelopment analysis.

PubMed

Ullah, Asmat; Perret, Sylvain R

2014-08-01

Cotton cropping in Pakistan uses substantial quantities of resources and adversely affects the environment with pollutants from the inputs, particularly pesticides. A question remains regarding to what extent the reduction of such environmental impact is possible without compromising the farmers' income. This paper investigates the environmental, technical, and economic performances of selected irrigated cotton-cropping systems in Punjab to quantify the sustainability of cotton farming and reveal options for improvement. Using mostly primary data, our study quantifies the technical, cost, and environmental efficiencies of different farm sizes. A set of indicators has been computed to reflect these three domains of efficiency using the data envelopment analysis technique. The results indicate that farmers are broadly environmentally inefficient; which primarily results from poor technical inefficiency. Based on an improved input mix, the average potential environmental impact reduction for small, medium, and large farms is 9, 13, and 11 %, respectively, without compromising the economic return. Moreover, the differences in technical, cost, and environmental efficiencies between small and medium and small and large farm sizes were statistically significant. The second-stage regression analysis identifies that the entire farm size significantly affects the efficiencies, whereas exposure to extension and training has positive effects, and the sowing methods significantly affect the technical and environmental efficiencies. Paradoxically, the formal education level is determined to affect the efficiencies negatively. This paper discusses policy interventions that can improve the technical efficiency to ultimately increase the environmental efficiency and reduce the farmers' operating costs.

Using Computer Games for Instruction: The Student Experience

ERIC Educational Resources Information Center

Grimley, Michael; Green, Richard; Nilsen, Trond; Thompson, David; Tomes, Russell

2011-01-01

Computer games are fun, exciting and motivational when used as leisure pursuits. But do they have similar attributes when utilized for educational purposes? This article investigates whether learning by computer game can improve student experiences compared with a more formal lecture approach and whether computer games have potential for improving…

Preparing Future Secondary Computer Science Educators

ERIC Educational Resources Information Center

Ajwa, Iyad

2007-01-01

Although nearly every college offers a major in computer science, many computer science teachers at the secondary level have received little formal training. This paper presents details of a project that could make a significant contribution to national efforts to improve computer science education by combining teacher education and professional…

Establishing a Computer Literacy Requirement for All Students.

ERIC Educational Resources Information Center

Kieffer, Linda M.

Several factors have indicated the necessity of formally requiring computer literacy at the university level. This paper discusses the reasoning for, the development of, and content of two computer literacy courses required of all freshmen. The first course contains computer awareness and knowledge that students should have upon entering the…

Procedural Quantum Programming

NASA Astrophysics Data System (ADS)

Ömer, Bernhard

2002-09-01

While classical computing science has developed a variety of methods and programming languages around the concept of the universal computer, the typical description of quantum algorithms still uses a purely mathematical, non-constructive formalism which makes no difference between a hydrogen atom and a quantum computer. This paper investigates, how the concept of procedural programming languages, the most widely used classical formalism for describing and implementing algorithms, can be adopted to the field of quantum computing, and how non-classical features like the reversibility of unitary transformations, the non-observability of quantum states or the lack of copy and erase operations can be reflected semantically. It introduces the key concepts of procedural quantum programming (hybrid target architecture, operator hierarchy, quantum data types, memory management, etc.) and presents the experimental language QCL, which implements these principles.

Georgia Computes! An Intervention in a US State, with Formal and Informal Education in a Policy Context

ERIC Educational Resources Information Center

Guzdial, Mark; Ericson, Barbara; Mcklin, Tom; Engelman, Shelly

2014-01-01

Georgia Computes! ("GaComputes") was a six-year (2006-2012) project to improve computing education across the state of Georgia in the United States, funded by the National Science Foundation. The goal of GaComputes was to broaden participation in computing and especially to engage more members of underrepresented groups which includes…

Quantum computation in the analysis of hyperspectral data

NASA Astrophysics Data System (ADS)

Gomez, Richard B.; Ghoshal, Debabrata; Jayanna, Anil

2004-08-01

Recent research on the topic of quantum computation provides us with some quantum algorithms with higher efficiency and speedup compared to their classical counterparts. In this paper, it is our intent to provide the results of our investigation of several applications of such quantum algorithms - especially the Grover's Search algorithm - in the analysis of Hyperspectral Data. We found many parallels with Grover's method in existing data processing work that make use of classical spectral matching algorithms. Our efforts also included the study of several methods dealing with hyperspectral image analysis work where classical computation methods involving large data sets could be replaced with quantum computation methods. The crux of the problem in computation involving a hyperspectral image data cube is to convert the large amount of data in high dimensional space to real information. Currently, using the classical model, different time consuming methods and steps are necessary to analyze these data including: Animation, Minimum Noise Fraction Transform, Pixel Purity Index algorithm, N-dimensional scatter plot, Identification of Endmember spectra - are such steps. If a quantum model of computation involving hyperspectral image data can be developed and formalized - it is highly likely that information retrieval from hyperspectral image data cubes would be a much easier process and the final information content would be much more meaningful and timely. In this case, dimensionality would not be a curse, but a blessing.

Organizational Decision Making

DTIC Science & Technology

1975-08-01

the lack of formal techniques typically used by large organizations, digress on the advantages of formal over informal... optimization ; for example one might do a number of optimization calculations, each time using a different measure of effectiveness as the optimized ...final decision. The next level of computer application involves the use of computerized optimization techniques. Optimization

Applying Automated Theorem Proving to Computer Security

DTIC Science & Technology

2008-03-01

CS96]”. Violations of policy can also be specified in this model. La Padula [Pad90] discusses a domain-independent formal model which imple- ments a...Science Laboratory, SRI International, Menlo Park, CA, September 1999. Pad90. L.J. La Padula . Formal modeling in a generalized framework for ac- cess

Adaptive Importance Sampling for Control and Inference

NASA Astrophysics Data System (ADS)

Kappen, H. J.; Ruiz, H. C.

2016-03-01

Path integral (PI) control problems are a restricted class of non-linear control problems that can be solved formally as a Feynman-Kac PI and can be estimated using Monte Carlo sampling. In this contribution we review PI control theory in the finite horizon case. We subsequently focus on the problem how to compute and represent control solutions. We review the most commonly used methods in robotics and control. Within the PI theory, the question of how to compute becomes the question of importance sampling. Efficient importance samplers are state feedback controllers and the use of these requires an efficient representation. Learning and representing effective state-feedback controllers for non-linear stochastic control problems is a very challenging, and largely unsolved, problem. We show how to learn and represent such controllers using ideas from the cross entropy method. We derive a gradient descent method that allows to learn feed-back controllers using an arbitrary parametrisation. We refer to this method as the path integral cross entropy method or PICE. We illustrate this method for some simple examples. The PI control methods can be used to estimate the posterior distribution in latent state models. In neuroscience these problems arise when estimating connectivity from neural recording data using EM. We demonstrate the PI control method as an accurate alternative to particle filtering.

An Efficient and Practical Smart Card Based Anonymity Preserving User Authentication Scheme for TMIS using Elliptic Curve Cryptography.

PubMed

Amin, Ruhul; Islam, S K Hafizul; Biswas, G P; Khan, Muhammad Khurram; Kumar, Neeraj

2015-11-01

In the last few years, numerous remote user authentication and session key agreement schemes have been put forwarded for Telecare Medical Information System, where the patient and medical server exchange medical information using Internet. We have found that most of the schemes are not usable for practical applications due to known security weaknesses. It is also worth to note that unrestricted number of patients login to the single medical server across the globe. Therefore, the computation and maintenance overhead would be high and the server may fail to provide services. In this article, we have designed a medical system architecture and a standard mutual authentication scheme for single medical server, where the patient can securely exchange medical data with the doctor(s) via trusted central medical server over any insecure network. We then explored the security of the scheme with its resilience to attacks. Moreover, we formally validated the proposed scheme through the simulation using Automated Validation of Internet Security Schemes and Applications software whose outcomes confirm that the scheme is protected against active and passive attacks. The performance comparison demonstrated that the proposed scheme has lower communication cost than the existing schemes in literature. In addition, the computation cost of the proposed scheme is nearly equal to the exiting schemes. The proposed scheme not only efficient in terms of different security attacks, but it also provides an efficient login, mutual authentication, session key agreement and verification and password update phases along with password recovery.

VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data

PubMed Central

Daunizeau, Jean; Adam, Vincent; Rigoux, Lionel

2014-01-01

This work is in line with an on-going effort tending toward a computational (quantitative and refutable) understanding of human neuro-cognitive processes. Many sophisticated models for behavioural and neurobiological data have flourished during the past decade. Most of these models are partly unspecified (i.e. they have unknown parameters) and nonlinear. This makes them difficult to peer with a formal statistical data analysis framework. In turn, this compromises the reproducibility of model-based empirical studies. This work exposes a software toolbox that provides generic, efficient and robust probabilistic solutions to the three problems of model-based analysis of empirical data: (i) data simulation, (ii) parameter estimation/model selection, and (iii) experimental design optimization. PMID:24465198

Electron Correlation from the Adiabatic Connection for Multireference Wave Functions

NASA Astrophysics Data System (ADS)

Pernal, Katarzyna

2018-01-01

An adiabatic connection (AC) formula for the electron correlation energy is derived for a broad class of multireference wave functions. The AC expression recovers dynamic correlation energy and assures a balanced treatment of the correlation energy. Coupling the AC formalism with the extended random phase approximation allows one to find the correlation energy only from reference one- and two-electron reduced density matrices. If the generalized valence bond perfect pairing model is employed a simple closed-form expression for the approximate AC formula is obtained. This results in the overall M5 scaling of the computation cost making the method one of the most efficient multireference approaches accounting for dynamic electron correlation also for the strongly correlated systems.

An 'adding' algorithm for the Markov chain formalism for radiation transfer

NASA Technical Reports Server (NTRS)

Esposito, L. W.

1979-01-01

An adding algorithm is presented, that extends the Markov chain method and considers a preceding calculation as a single state of a new Markov chain. This method takes advantage of the description of the radiation transport as a stochastic process. Successive application of this procedure makes calculation possible for any optical depth without increasing the size of the linear system used. It is determined that the time required for the algorithm is comparable to that for a doubling calculation for homogeneous atmospheres. For an inhomogeneous atmosphere the new method is considerably faster than the standard adding routine. It is concluded that the algorithm is efficient, accurate, and suitable for smaller computers in calculating the diffuse intensity scattered by an inhomogeneous planetary atmosphere.

Topics in Computational Learning Theory and Graph Algorithms.

ERIC Educational Resources Information Center

Board, Raymond Acton

This thesis addresses problems from two areas of theoretical computer science. The first area is that of computational learning theory, which is the study of the phenomenon of concept learning using formal mathematical models. The goal of computational learning theory is to investigate learning in a rigorous manner through the use of techniques…

14 CFR 302.507 - Computing time for filing complaints.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Computing time for filing complaints. 302... Proceedings With Respect to Rates, Fares and Charges for Foreign Air Transportation § 302.507 Computing time for filing complaints. In computing the time for filing formal complaints pursuant to § 302.506, with...

m2-ABKS: Attribute-Based Multi-Keyword Search over Encrypted Personal Health Records in Multi-Owner Setting.

PubMed

Miao, Yinbin; Ma, Jianfeng; Liu, Ximeng; Wei, Fushan; Liu, Zhiquan; Wang, Xu An

2016-11-01

Online personal health record (PHR) is more inclined to shift data storage and search operations to cloud server so as to enjoy the elastic resources and lessen computational burden in cloud storage. As multiple patients' data is always stored in the cloud server simultaneously, it is a challenge to guarantee the confidentiality of PHR data and allow data users to search encrypted data in an efficient and privacy-preserving way. To this end, we design a secure cryptographic primitive called as attribute-based multi-keyword search over encrypted personal health records in multi-owner setting to support both fine-grained access control and multi-keyword search via Ciphertext-Policy Attribute-Based Encryption. Formal security analysis proves our scheme is selectively secure against chosen-keyword attack. As a further contribution, we conduct empirical experiments over real-world dataset to show its feasibility and practicality in a broad range of actual scenarios without incurring additional computational burden.

Overcoming free energy barriers using unconstrained molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Hénin, Jérôme; Chipot, Christophe

2004-08-01

Association of unconstrained molecular dynamics (MD) and the formalisms of thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)] have been employed to determine potentials of mean force. When implemented in a general MD code, the additional computational effort, compared to other standard, unconstrained simulations, is marginal. The force acting along a chosen reaction coordinate ξ is estimated from the individual forces exerted on the chemical system and accumulated as the simulation progresses. The estimated free energy derivative computed for small intervals of ξ is canceled by an adaptive bias to overcome the barriers of the free energy landscape. Evolution of the system along the reaction coordinate is, thus, limited by its sole self-diffusion properties. The illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, the dimerization of methane in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method.

Overcoming free energy barriers using unconstrained molecular dynamics simulations.

PubMed

Hénin, Jérôme; Chipot, Christophe

2004-08-15

Association of unconstrained molecular dynamics (MD) and the formalisms of thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)] have been employed to determine potentials of mean force. When implemented in a general MD code, the additional computational effort, compared to other standard, unconstrained simulations, is marginal. The force acting along a chosen reaction coordinate xi is estimated from the individual forces exerted on the chemical system and accumulated as the simulation progresses. The estimated free energy derivative computed for small intervals of xi is canceled by an adaptive bias to overcome the barriers of the free energy landscape. Evolution of the system along the reaction coordinate is, thus, limited by its sole self-diffusion properties. The illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, the dimerization of methane in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method. (c) 2004 American Institute of Physics.

Homeostatic reinforcement learning for integrating reward collection and physiological stability

PubMed Central

Keramati, Mehdi; Gutkin, Boris

2014-01-01

Efficient regulation of internal homeostasis and defending it against perturbations requires adaptive behavioral strategies. However, the computational principles mediating the interaction between homeostatic and associative learning processes remain undefined. Here we use a definition of primary rewards, as outcomes fulfilling physiological needs, to build a normative theory showing how learning motivated behaviors may be modulated by internal states. Within this framework, we mathematically prove that seeking rewards is equivalent to the fundamental objective of physiological stability, defining the notion of physiological rationality of behavior. We further suggest a formal basis for temporal discounting of rewards by showing that discounting motivates animals to follow the shortest path in the space of physiological variables toward the desired setpoint. We also explain how animals learn to act predictively to preclude prospective homeostatic challenges, and several other behavioral patterns. Finally, we suggest a computational role for interaction between hypothalamus and the brain reward system. DOI: http://dx.doi.org/10.7554/eLife.04811.001 PMID:25457346

The Computer as Adaptive Instructional Decision Maker.

ERIC Educational Resources Information Center

Kopstein, Felix F.; Seidel, Robert J.

The computer's potential for education, and most particularly for instruction, is contingent on the development of a class of instructional decision models (formal instructional strategies) that interact with the student through appropriate peripheral equipment (man-machine interfaces). Computer hardware and software by themselves should not be…

Towards symbiosis in knowledge representation and natural language processing for structuring clinical practice guidelines.

PubMed

Weng, Chunhua; Payne, Philip R O; Velez, Mark; Johnson, Stephen B; Bakken, Suzanne

2014-01-01

The successful adoption by clinicians of evidence-based clinical practice guidelines (CPGs) contained in clinical information systems requires efficient translation of free-text guidelines into computable formats. Natural language processing (NLP) has the potential to improve the efficiency of such translation. However, it is laborious to develop NLP to structure free-text CPGs using existing formal knowledge representations (KR). In response to this challenge, this vision paper discusses the value and feasibility of supporting symbiosis in text-based knowledge acquisition (KA) and KR. We compare two ontologies: (1) an ontology manually created by domain experts for CPG eligibility criteria and (2) an upper-level ontology derived from a semantic pattern-based approach for automatic KA from CPG eligibility criteria text. Then we discuss the strengths and limitations of interweaving KA and NLP for KR purposes and important considerations for achieving the symbiosis of KR and NLP for structuring CPGs to achieve evidence-based clinical practice.

Reconfigurable Very Long Instruction Word (VLIW) Processor

NASA Technical Reports Server (NTRS)

Velev, Miroslav N.

2015-01-01

Future NASA missions will depend on radiation-hardened, power-efficient processing systems-on-a-chip (SOCs) that consist of a range of processor cores custom tailored for space applications. Aries Design Automation, LLC, has developed a processing SOC that is optimized for software-defined radio (SDR) uses. The innovation implements the Institute of Electrical and Electronics Engineers (IEEE) RazorII voltage management technique, a microarchitectural mechanism that allows processor cores to self-monitor, self-analyze, and selfheal after timing errors, regardless of their cause (e.g., radiation; chip aging; variations in the voltage, frequency, temperature, or manufacturing process). This highly automated SOC can also execute legacy PowerPC 750 binary code instruction set architecture (ISA), which is used in the flight-control computers of many previous NASA space missions. In developing this innovation, Aries Design Automation has made significant contributions to the fields of formal verification of complex pipelined microprocessors and Boolean satisfiability (SAT) and has developed highly efficient electronic design automation tools that hold promise for future developments.

Efficient implicit LES method for the simulation of turbulent cavitating flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Egerer, Christian P., E-mail: christian.egerer@aer.mw.tum.de; Schmidt, Steffen J.; Hickel, Stefan

2016-07-01

We present a numerical method for efficient large-eddy simulation of compressible liquid flows with cavitation based on an implicit subgrid-scale model. Phase change and subgrid-scale interface structures are modeled by a homogeneous mixture model that assumes local thermodynamic equilibrium. Unlike previous approaches, emphasis is placed on operating on a small stencil (at most four cells). The truncation error of the discretization is designed to function as a physically consistent subgrid-scale model for turbulence. We formulate a sensor functional that detects shock waves or pseudo-phase boundaries within the homogeneous mixture model for localizing numerical dissipation. In smooth regions of the flowmore » field, a formally non-dissipative central discretization scheme is used in combination with a regularization term to model the effect of unresolved subgrid scales. The new method is validated by computing standard single- and two-phase test-cases. Comparison of results for a turbulent cavitating mixing layer obtained with the new method demonstrates its suitability for the target applications.« less

Refined Zigzag Theory for Homogeneous, Laminated Composite, and Sandwich Plates: A Homogeneous Limit Methodology for Zigzag Function Selection

NASA Technical Reports Server (NTRS)

Tessler, Alexander; DiSciuva, Marco; Gherlone, marco

2010-01-01

The Refined Zigzag Theory (RZT) for homogeneous, laminated composite, and sandwich plates is presented from a multi-scale formalism starting with the inplane displacement field expressed as a superposition of coarse and fine contributions. The coarse kinematic field is that of first-order shear-deformation theory, whereas the fine kinematic field has a piecewise-linear zigzag distribution through the thickness. The condition of limiting homogeneity of transverse-shear properties is proposed and yields four distinct sets of zigzag functions. By examining elastostatic solutions for highly heterogeneous sandwich plates, the best-performing zigzag functions are identified. The RZT predictive capabilities to model homogeneous and highly heterogeneous sandwich plates are critically assessed, demonstrating its superior efficiency, accuracy ; and a wide range of applicability. The present theory, which is derived from the virtual work principle, is well-suited for developing computationally efficient CO-continuous finite elements, and is thus appropriate for the analysis and design of high-performance load-bearing aerospace structures.

The 2 Es

ERIC Educational Resources Information Center

Kroog, Heidi; Hess, Kristin King; Ruiz-Primo, Maria Araceli

2016-01-01

What are the characteristics of formal formative assessments that are both effective in improving student learning and an efficient use of a teacher's time and efforts? That's the question that the authors explore in this article drawing on a five-year research study. First, formal formative assessment is defined as being planned in advance,…

A Case Study of the Introduction of Computer Science in NZ Schools

ERIC Educational Resources Information Center

Bell, Tim; Andreae, Peter; Robins, Anthony

2014-01-01

For many years computing in New Zealand schools was focused on teaching students how to use computers, and there was little opportunity for students to learn about programming and computer science as formal subjects. In this article we review a series of initiatives that occurred from 2007 to 2009 that led to programming and computer science being…

Formal Solutions for Polarized Radiative Transfer. II. High-order Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janett, Gioele; Steiner, Oskar; Belluzzi, Luca, E-mail: gioele.janett@irsol.ch

When integrating the radiative transfer equation for polarized light, the necessity of high-order numerical methods is well known. In fact, well-performing high-order formal solvers enable higher accuracy and the use of coarser spatial grids. Aiming to provide a clear comparison between formal solvers, this work presents different high-order numerical schemes and applies the systematic analysis proposed by Janett et al., emphasizing their advantages and drawbacks in terms of order of accuracy, stability, and computational cost.

Smarr formula for Lovelock black holes: A Lagrangian approach

NASA Astrophysics Data System (ADS)

Liberati, Stefano; Pacilio, Costantino

2016-04-01

The mass formula for black holes can be formally expressed in terms of a Noether charge surface integral plus a suitable volume integral, for any gravitational theory. The integrals can be constructed as an application of Wald's formalism. We apply this formalism to compute the mass and the Smarr formula for static Lovelock black holes. Finally, we propose a new prescription for Wald's entropy in the case of Lovelock black holes, which takes into account topological contributions to the entropy functional.

Development of a fully implicit particle-in-cell scheme for gyrokinetic electromagnetic turbulence simulation in XGC1

NASA Astrophysics Data System (ADS)

Ku, Seung-Hoe; Hager, R.; Chang, C. S.; Chacon, L.; Chen, G.; EPSI Team

2016-10-01

The cancelation problem has been a long-standing issue for long wavelengths modes in electromagnetic gyrokinetic PIC simulations in toroidal geometry. As an attempt of resolving this issue, we implemented a fully implicit time integration scheme in the full-f, gyrokinetic PIC code XGC1. The new scheme - based on the implicit Vlasov-Darwin PIC algorithm by G. Chen and L. Chacon - can potentially resolve cancelation problem. The time advance for the field and the particle equations is space-time-centered, with particle sub-cycling. The resulting system of equations is solved by a Picard iteration solver with fixed-point accelerator. The algorithm is implemented in the parallel velocity formalism instead of the canonical parallel momentum formalism. XGC1 specializes in simulating the tokamak edge plasma with magnetic separatrix geometry. A fully implicit scheme could be a way to accurate and efficient gyrokinetic simulations. We will test if this numerical scheme overcomes the cancelation problem, and reproduces the dispersion relation of Alfven waves and tearing modes in cylindrical geometry. Funded by US DOE FES and ASCR, and computing resources provided by OLCF through ALCC.

The Capabilities of Chaos and Complexity

PubMed Central

Abel, David L.

2009-01-01

To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization? PMID:19333445

Extended abstract: Managing disjunction for practical temporal reasoning

NASA Technical Reports Server (NTRS)

Boddy, Mark; Schrag, Bob; Carciofini, Jim

1992-01-01

One of the problems that must be dealt with in either a formal or implemented temporal reasoning system is the ambiguity arising from uncertain information. Lack of precise information about when events happen leads to uncertainty regarding the effects of those events. Incomplete information and nonmonotonic inference lead to situations where there is more than one set of possible inferences, even when there is no temporal uncertainty at all. In an implemented system, this ambiguity is a computational problem as well as a semantic one. In this paper, we discuss some of the sources of this ambiguity, which we will treat as explicit disjunction, in the sense that ambiguous information can be interpreted as defining a set of possible inferences. We describe the application of three techniques for managing disjunction in an implementation of Dean's Time Map Manager. Briefly, the disjunction is either: removed by limiting the expressive power of the system, or approximated by a weaker form of representation that subsumes the disjunction. We use a combination of these methods to implement an expressive and efficient temporal reasoning engine that performs sound inference in accordance with a well-defined formal semantics.

User Participation and Participatory Design: Topics in Computing Education.

ERIC Educational Resources Information Center

Kautz, Karlheinz

1996-01-01

Discusses user participation and participatory design in the context of formal education for computing professionals. Topics include the current curriculum debate; mathematical- and engineering-based education; traditional system-development training; and an example of a course program that includes computers and society, and prototyping. (53…

Quantum Analog Computing

NASA Technical Reports Server (NTRS)

Zak, M.

1998-01-01

Quantum analog computing is based upon similarity between mathematical formalism of quantum mechanics and phenomena to be computed. It exploits a dynamical convergence of several competing phenomena to an attractor which can represent an externum of a function, an image, a solution to a system of ODE, or a stochastic process.

Formal Methods Specification and Verification Guidebook for Software and Computer Systems. Volume 1; Planning and Technology Insertion

NASA Technical Reports Server (NTRS)

1995-01-01

The Formal Methods Specification and Verification Guidebook for Software and Computer Systems describes a set of techniques called Formal Methods (FM), and outlines their use in the specification and verification of computer systems and software. Development of increasingly complex systems has created a need for improved specification and verification techniques. NASA's Safety and Mission Quality Office has supported the investigation of techniques such as FM, which are now an accepted method for enhancing the quality of aerospace applications. The guidebook provides information for managers and practitioners who are interested in integrating FM into an existing systems development process. Information includes technical and administrative considerations that must be addressed when establishing the use of FM on a specific project. The guidebook is intended to aid decision makers in the successful application of FM to the development of high-quality systems at reasonable cost. This is the first volume of a planned two-volume set. The current volume focuses on administrative and planning considerations for the successful application of FM.

Proceedings 3rd NASA/IEEE Workshop on Formal Approaches to Agent-Based Systems (FAABS-III)

NASA Technical Reports Server (NTRS)

Hinchey, Michael (Editor); Rash, James (Editor); Truszkowski, Walt (Editor); Rouff, Christopher (Editor)

2004-01-01

These preceedings contain 18 papers and 4 poster presentation, covering topics such as: multi-agent systems, agent-based control, formalism, norms, as well as physical and biological models of agent-based systems. Some applications presented in the proceedings include systems analysis, software engineering, computer networks and robot control.

Formal and Informal CALL Preparation and Teacher Attitude toward Technology

ERIC Educational Resources Information Center

Kessler, Greg

2007-01-01

Recent research suggests that there is a general lack of a computer-assisted language learning (CALL) presence in teacher preparation programs. There is also evidence that teachers obtain a majority of their CALL knowledge from informal sources and personal experience rather than through formalized preparation. Further, graduates of these programs…

Developing Formal Object-oriented Requirements Specifications: A Model, Tool and Technique.

ERIC Educational Resources Information Center

Jackson, Robert B.; And Others

1995-01-01

Presents a formal object-oriented specification model (OSS) for computer software system development that is supported by a tool that automatically generates a prototype from an object-oriented analysis model (OSA) instance, lets the user examine the prototype, and permits the user to refine the OSA model instance to generate a requirements…

Combining neural networks and signed particles to simulate quantum systems more efficiently

NASA Astrophysics Data System (ADS)

Sellier, Jean Michel

2018-04-01

Recently a new formulation of quantum mechanics has been suggested which describes systems by means of ensembles of classical particles provided with a sign. This novel approach mainly consists of two steps: the computation of the Wigner kernel, a multi-dimensional function describing the effects of the potential over the system, and the field-less evolution of the particles which eventually create new signed particles in the process. Although this method has proved to be extremely advantageous in terms of computational resources - as a matter of fact it is able to simulate in a time-dependent fashion many-body systems on relatively small machines - the Wigner kernel can represent the bottleneck of simulations of certain systems. Moreover, storing the kernel can be another issue as the amount of memory needed is cursed by the dimensionality of the system. In this work, we introduce a new technique which drastically reduces the computation time and memory requirement to simulate time-dependent quantum systems which is based on the use of an appropriately tailored neural network combined with the signed particle formalism. In particular, the suggested neural network is able to compute efficiently and reliably the Wigner kernel without any training as its entire set of weights and biases is specified by analytical formulas. As a consequence, the amount of memory for quantum simulations radically drops since the kernel does not need to be stored anymore as it is now computed by the neural network itself, only on the cells of the (discretized) phase-space which are occupied by particles. As its is clearly shown in the final part of this paper, not only this novel approach drastically reduces the computational time, it also remains accurate. The author believes this work opens the way towards effective design of quantum devices, with incredible practical implications.

Design Strategy for a Formally Verified Reliable Computing Platform

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Caldwell, James L.; DiVito, Ben L.

1991-01-01

This paper presents a high-level design for a reliable computing platform for real-time control applications. The design tradeoffs and analyses related to the development of a formally verified reliable computing platform are discussed. The design strategy advocated in this paper requires the use of techniques that can be completely characterized mathematically as opposed to more powerful or more flexible algorithms whose performance properties can only be analyzed by simulation and testing. The need for accurate reliability models that can be related to the behavior models is also stressed. Tradeoffs between reliability and voting complexity are explored. In particular, the transient recovery properties of the system are found to be fundamental to both the reliability analysis as well as the "correctness" models.

Senior Surfing: Computer Use, Aging, and Formal Training

ERIC Educational Resources Information Center

Warren-Peace, Paula; Parrish, Elaine; Peace, C. Brian; Xu, Jianzhong

2008-01-01

In this article, we describe data from two case studies of seniors (one younger senior and one older senior) in learning to use computers. The study combined interviews, observations, and documents to take a close look at their experiences with computers, as well as the influences of aging and computer training on their experiences. The study…

Quantum computation with indefinite causal structures

NASA Astrophysics Data System (ADS)

Araújo, Mateus; Guérin, Philippe Allard; Baumeler, ńmin

2017-11-01

One way to study the physical plausibility of closed timelike curves (CTCs) is to examine their computational power. This has been done for Deutschian CTCs (D-CTCs) and postselection CTCs (P-CTCs), with the result that they allow for the efficient solution of problems in PSPACE and PP, respectively. Since these are extremely powerful complexity classes, which are not expected to be solvable in reality, this can be taken as evidence that these models for CTCs are pathological. This problem is closely related to the nonlinearity of this models, which also allows, for example, cloning quantum states, in the case of D-CTCs, or distinguishing nonorthogonal quantum states, in the case of P-CTCs. In contrast, the process matrix formalism allows one to model indefinite causal structures in a linear way, getting rid of these effects and raising the possibility that its computational power is rather tame. In this paper, we show that process matrices correspond to a linear particular case of P-CTCs, and therefore that its computational power is upperbounded by that of PP. We show, furthermore, a family of processes that can violate causal inequalities but nevertheless can be simulated by a causally ordered quantum circuit with only a constant overhead, showing that indefinite causality is not necessarily hard to simulate.

Photovoltaic reciprocity and quasi-Fermi level splitting in nanostructure-based solar cells (Conference Presentation)

NASA Astrophysics Data System (ADS)

Aeberhard, Urs

2017-04-01

The photovoltaic reciprocity theory relates the electroluminescence spectrum of a solar cell under applied bias to the external photovoltaic quantum efficiency of the device as measured at short circuit conditions [1]. So far, the theory has been verified for a wide range of devices and material systems and forms the basis of a growing number of luminesecence imaging techniques used in the characterization of photovoltaic materials, cells and modules [2-5]. However, there are also some examples where the theory fails, such as in the case of amorphous silicon. In our contribution, we critically assess the assumptions made in the derivation of the theory and compare its predictions with rigorous formal relations as well as numerical computations in the framework of a comprehensive quantum-kinetic theory of photovoltaics [6] as applied to ultra-thin absorber architectures [7]. One of the main applications of the photovoltaic reciprocity relation is the determination of quasi-Fermi level splittings (QFLS) in solar cells from the measurement of luminescence. In nanostructure-based photovoltaic architectures, the determination of QFLS is challenging, but instrumental to assess the performance potential of the concepts. Here, we use our quasi-Fermi level-free theory to investigate existence and size of QFLS in quantum well and quantum dot solar cells. [1] Uwe Rau. Reciprocity relation between photovoltaic quantum efficiency and electrolumines- cent emission of solar cells. Phys. Rev. B, 76(8):085303, 2007. [2] Thomas Kirchartz and Uwe Rau. Electroluminescence analysis of high efficiency cu(in,ga)se2 solar cells. J. Appl. Phys., 102(10), 2007. [3] Thomas Kirchartz, Uwe Rau, Martin Hermle, Andreas W. Bett, Anke Helbig, and Jrgen H. Werner. Internal voltages in GaInP-GaInAs-Ge multijunction solar cells determined by electro- luminescence measurements. Appl. Phys. Lett., 92(12), 2008. [4] Thomas Kirchartz, Anke Helbig, Wilfried Reetz, Michael Reuter, Jürgen H. Werner, and Uwe Rau. Reciprocity between electroluminescence and quantum efficiency used for the characterization of silicon solar cells. Prog. Photovolt: Res. Appl., 17(6):394-402, 2009. [5] U. Hoyer, M. Wagner, Th. Swonke, J. Bachmann, R. Auer, A. Osvet, and C. J. Brabec. Electroluminescence imaging of organic photovoltaic modules. Appl. Phys. Lett., 97(23), 2010. [6] U. Aeberhard. Theory and simulation of quantum photovoltaic devices based on the non-equilibrium Greens function formalism. J. Comput. Electron., 10:394-413, 2011. [7] U. Aeberhard. Simulation of ultrathin solar cells beyond the limits of the semiclassical bulk picture. IEEE J. Photovolt., 6(3):654-660, 2016.

The Fourth Revolution--Computers and Learning.

ERIC Educational Resources Information Center

Bork, Alfred

The personal computer is sparking a major historical change in the way people learn, a change that could lead to the disappearance of formal education as we know it. The computer can help resolve many of the difficulties now crippling education by enabling expert teachers and curriculum developers to prepare interactive and individualized…

Introduction to the theory of machines and languages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weidhaas, P. P.

1976-04-01

This text is intended to be an elementary ''guided tour'' through some basic concepts of modern computer science. Various models of computing machines and formal languages are studied in detail. Discussions center around questions such as, ''What is the scope of problems that can or cannot be solved by computers.''

Learning with Ubiquitous Computing

ERIC Educational Resources Information Center

Rosenheck, Louisa

2008-01-01

If ubiquitous computing becomes a reality and is widely adopted, it will inevitably have an impact on education. This article reviews the background of ubiquitous computing and current research projects done involving educational "ubicomp." Finally it explores how ubicomp may and may not change education in both formal and informal settings and…

Computer Proficiency for Online Learning: Factorial Invariance of Scores among Teachers

ERIC Educational Resources Information Center

Martin, Amy L.; Reeves, Todd D.; Smith, Thomas J.; Walker, David A.

2016-01-01

Online learning is variously employed in K-12 education, including for teacher professional development. However, the use of computer-based technologies for learning purposes assumes learner computer proficiency, making this construct an important domain of procedural knowledge in formal and informal online learning contexts. Addressing this…

Towards Co-Engineering Communicating Autonomous Cyber-Physical Systems

NASA Technical Reports Server (NTRS)

Bujorianu, Marius C.; Bujorianu, Manuela L.

2009-01-01

In this paper, we sketch a framework for interdisciplinary modeling of space systems, by proposing a holistic view. We consider different system dimensions and their interaction. Specifically, we study the interactions between computation, physics, communication, uncertainty and autonomy. The most comprehensive computational paradigm that supports a holistic perspective on autonomous space systems is given by cyber-physical systems. For these, the state of art consists of collaborating multi-engineering efforts that prompt for an adequate formal foundation. To achieve this, we propose a leveraging of the traditional content of formal modeling by a co-engineering process.

Parent Involvement in Education in Terms of Their Socio-Economic Status

ERIC Educational Resources Information Center

Kuru Cetin, Saadet; Taskin, Pelin

2016-01-01

Problem Statement: Increasing the quality of education and educating well-qualified students is one of the most important objectives of formal education. Informal resources are as important as formal resources in improving this efficiency and productivity. In this respect, it can be said that family is the most important informal structure…

Assessing, Recognising and Certifying Informal and Non-Formal Learning (ARCNIL): Evolution and Challenges

ERIC Educational Resources Information Center

Svetlik, Ivan

2009-01-01

Certifying non-formal and informal knowledge may be a consequence of separating education and training from other social and economic activities. Specialisation and formalisation of education and training both aim to increase learning efficiency. In the emerging knowledge society, this has attracted particular attention among researchers and…

Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling.

PubMed

Castagné, Raphaële; Boulangé, Claire Laurence; Karaman, Ibrahim; Campanella, Gianluca; Santos Ferreira, Diana L; Kaluarachchi, Manuja R; Lehne, Benjamin; Moayyeri, Alireza; Lewis, Matthew R; Spagou, Konstantina; Dona, Anthony C; Evangelos, Vangelis; Tracy, Russell; Greenland, Philip; Lindon, John C; Herrington, David; Ebbels, Timothy M D; Elliott, Paul; Tzoulaki, Ioanna; Chadeau-Hyam, Marc

2017-10-06

1 H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum 1 H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies.

Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling

PubMed Central

2017-01-01

1H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum 1H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies. PMID:28823158

Computer literacy among first year medical students in a developing country: a cross sectional study.

PubMed

Ranasinghe, Priyanga; Wickramasinghe, Sashimali A; Pieris, Wa Rasanga; Karunathilake, Indika; Constantine, Godwin R

2012-09-14

The use of computer assisted learning (CAL) has enhanced undergraduate medical education. CAL improves performance at examinations, develops problem solving skills and increases student satisfaction. The study evaluates computer literacy among first year medical students in Sri Lanka. The study was conducted at Faculty of Medicine, University of Colombo, Sri Lanka between August-September 2008. First year medical students (n = 190) were invited for the study. Data on computer literacy and associated factors were collected by an expert-validated pre-tested self-administered questionnaire. Computer literacy was evaluated by testing knowledge on 6 domains; common software packages, operating systems, database management and the usage of internet and E-mail. A linear regression was conducted using total score for computer literacy as the continuous dependant variable and other independent covariates. Sample size-181 (Response rate-95.3%), 49.7% were Males. Majority of the students (77.3%) owned a computer (Males-74.4%, Females-80.2%). Students have gained their present computer knowledge by; a formal training programme (64.1%), self learning (63.0%) or by peer learning (49.2%). The students used computers for predominately; word processing (95.6%), entertainment (95.0%), web browsing (80.1%) and preparing presentations (76.8%). Majority of the students (75.7%) expressed their willingness for a formal computer training programme at the faculty.Mean score for the computer literacy questionnaire was 48.4 ± 20.3, with no significant gender difference (Males-47.8 ± 21.1, Females-48.9 ± 19.6). There were 47.9% students that had a score less than 50% for the computer literacy questionnaire. Students from Colombo district, Western Province and Student owning a computer had a significantly higher mean score in comparison to other students (p < 0.001). In the linear regression analysis, formal computer training was the strongest predictor of computer literacy (β = 13.034), followed by using internet facility, being from Western province, using computers for Web browsing and computer programming, computer ownership and doing IT (Information Technology) as a subject in GCE (A/L) examination. Sri Lankan medical undergraduates had a low-intermediate level of computer literacy. There is a need to improve computer literacy, by increasing computer training in schools, or by introducing computer training in the initial stages of the undergraduate programme. These two options require improvement in infrastructure and other resources.

Evolution of thermally pulsing asymptotic giant branch stars - II. Dust production at varying metallicity

NASA Astrophysics Data System (ADS)

Nanni, Ambra; Bressan, Alessandro; Marigo, Paola; Girardi, Léo

2013-09-01

We present the dust ejecta of the new stellar models for the thermally pulsing asymptotic giant branch (TP-AGB) phase computed with the COLIBRI code. We use a formalism of dust growth coupled with a stationary wind for both M- and C-stars. In the original version of this formalism, the most efficient destruction process of silicate dust in M-giants is chemisputtering by H2 molecules. For these stars, we find that dust grains can only form at relatively large radial distances (r ˜ 5R*), where they cannot be efficiently accelerated, in agreement with other investigations. In the light of recent laboratory results, we also consider the alternative case that the condensation temperature of silicates is determined only by the competition between growth and free evaporation processes (i.e. no chemisputtering). With this latter approach we obtain dust condensation temperatures that are significantly higher (up to Tcond ˜ 1400 K) than those found when chemisputtering is included (Tcond ˜ 900 K), and in better agreement with condensation experiments. As a consequence, silicate grains can remain stable in inner regions of the circumstellar envelopes (r ˜ 2 R*), where they can rapidly grow and can be efficiently accelerated. With this modification, our models nicely reproduce the observed trend between terminal velocities and mass-loss rates of Galactic M-giants. For C-stars the formalism is based on the homogeneous growth scheme where the key role is played by the carbon over oxygen excess. The models reproduce fairly well the terminal velocities of Galactic stars and there is no need to invoke changes in the standard assumptions. At decreasing metallicity the carbon excess becomes more pronounced and the efficiency of dust formation increases. This trend could be in tension with recent observational evidence in favour of a decreasing efficiency, at decreasing metallicity. If confirmed by more observational data, it would indicate that either the amount of the carbon excess, determined by the complex interplay between mass-loss, third dredge-up and hot-bottom burning, or the homogeneous growth scheme should be revised. Finally, we analyse the differences in the total dust production of M-stars that arise from the use of the two approaches (i.e. with or without chemisputtering). We find that, in spite of the differences in the expected dust stratification, for a given set of TP-AGB models, the ejecta are only weakly sensitive to the specific assumption. This work also shows that the properties of TP-AGB circumstellar envelopes are important diagnostic tools that may be profitably added to the traditional calibrators for setting further constraints on this complex phase of stellar evolution.

Sign use and cognition in automated scientific discovery: are computers only special kinds of signs?

NASA Astrophysics Data System (ADS)

Giza, Piotr

2018-04-01

James Fetzer criticizes the computational paradigm, prevailing in cognitive science by questioning, what he takes to be, its most elementary ingredient: that cognition is computation across representations. He argues that if cognition is taken to be a purposive, meaningful, algorithmic problem solving activity, then computers are incapable of cognition. Instead, they appear to be signs of a special kind, that can facilitate computation. He proposes the conception of minds as semiotic systems as an alternative paradigm for understanding mental phenomena, one that seems to overcome the difficulties of computationalism. Now, I argue, that with computer systems dealing with scientific discovery, the matter is not so simple as that. The alleged superiority of humans using signs to stand for something other over computers being merely "physical symbol systems" or "automatic formal systems" is only easy to establish in everyday life, but becomes far from obvious when scientific discovery is at stake. In science, as opposed to everyday life, the meaning of symbols is, apart from very low-level experimental investigations, defined implicitly by the way the symbols are used in explanatory theories or experimental laws relevant to the field, and in consequence, human and machine discoverers are much more on a par. Moreover, the great practical success of the genetic programming method and recent attempts to apply it to automatic generation of cognitive theories seem to show, that computer systems are capable of very efficient problem solving activity in science, which is neither purposive nor meaningful, nor algorithmic. This, I think, undermines Fetzer's argument that computer systems are incapable of cognition because computation across representations is bound to be a purposive, meaningful, algorithmic problem solving activity.

Ultrafast and scalable cone-beam CT reconstruction using MapReduce in a cloud computing environment.

PubMed

Meng, Bowen; Pratx, Guillem; Xing, Lei

2011-12-01

Four-dimensional CT (4DCT) and cone beam CT (CBCT) are widely used in radiation therapy for accurate tumor target definition and localization. However, high-resolution and dynamic image reconstruction is computationally demanding because of the large amount of data processed. Efficient use of these imaging techniques in the clinic requires high-performance computing. The purpose of this work is to develop a novel ultrafast, scalable and reliable image reconstruction technique for 4D CBCT∕CT using a parallel computing framework called MapReduce. We show the utility of MapReduce for solving large-scale medical physics problems in a cloud computing environment. In this work, we accelerated the Feldcamp-Davis-Kress (FDK) algorithm by porting it to Hadoop, an open-source MapReduce implementation. Gated phases from a 4DCT scans were reconstructed independently. Following the MapReduce formalism, Map functions were used to filter and backproject subsets of projections, and Reduce function to aggregate those partial backprojection into the whole volume. MapReduce automatically parallelized the reconstruction process on a large cluster of computer nodes. As a validation, reconstruction of a digital phantom and an acquired CatPhan 600 phantom was performed on a commercial cloud computing environment using the proposed 4D CBCT∕CT reconstruction algorithm. Speedup of reconstruction time is found to be roughly linear with the number of nodes employed. For instance, greater than 10 times speedup was achieved using 200 nodes for all cases, compared to the same code executed on a single machine. Without modifying the code, faster reconstruction is readily achievable by allocating more nodes in the cloud computing environment. Root mean square error between the images obtained using MapReduce and a single-threaded reference implementation was on the order of 10(-7). Our study also proved that cloud computing with MapReduce is fault tolerant: the reconstruction completed successfully with identical results even when half of the nodes were manually terminated in the middle of the process. An ultrafast, reliable and scalable 4D CBCT∕CT reconstruction method was developed using the MapReduce framework. Unlike other parallel computing approaches, the parallelization and speedup required little modification of the original reconstruction code. MapReduce provides an efficient and fault tolerant means of solving large-scale computing problems in a cloud computing environment.

Ultrafast and scalable cone-beam CT reconstruction using MapReduce in a cloud computing environment

PubMed Central

Meng, Bowen; Pratx, Guillem; Xing, Lei

2011-01-01

Purpose: Four-dimensional CT (4DCT) and cone beam CT (CBCT) are widely used in radiation therapy for accurate tumor target definition and localization. However, high-resolution and dynamic image reconstruction is computationally demanding because of the large amount of data processed. Efficient use of these imaging techniques in the clinic requires high-performance computing. The purpose of this work is to develop a novel ultrafast, scalable and reliable image reconstruction technique for 4D CBCT/CT using a parallel computing framework called MapReduce. We show the utility of MapReduce for solving large-scale medical physics problems in a cloud computing environment. Methods: In this work, we accelerated the Feldcamp–Davis–Kress (FDK) algorithm by porting it to Hadoop, an open-source MapReduce implementation. Gated phases from a 4DCT scans were reconstructed independently. Following the MapReduce formalism, Map functions were used to filter and backproject subsets of projections, and Reduce function to aggregate those partial backprojection into the whole volume. MapReduce automatically parallelized the reconstruction process on a large cluster of computer nodes. As a validation, reconstruction of a digital phantom and an acquired CatPhan 600 phantom was performed on a commercial cloud computing environment using the proposed 4D CBCT/CT reconstruction algorithm. Results: Speedup of reconstruction time is found to be roughly linear with the number of nodes employed. For instance, greater than 10 times speedup was achieved using 200 nodes for all cases, compared to the same code executed on a single machine. Without modifying the code, faster reconstruction is readily achievable by allocating more nodes in the cloud computing environment. Root mean square error between the images obtained using MapReduce and a single-threaded reference implementation was on the order of 10−7. Our study also proved that cloud computing with MapReduce is fault tolerant: the reconstruction completed successfully with identical results even when half of the nodes were manually terminated in the middle of the process. Conclusions: An ultrafast, reliable and scalable 4D CBCT/CT reconstruction method was developed using the MapReduce framework. Unlike other parallel computing approaches, the parallelization and speedup required little modification of the original reconstruction code. MapReduce provides an efficient and fault tolerant means of solving large-scale computing problems in a cloud computing environment. PMID:22149842

Teaching Fundamental Skills in Microsoft Excel to First-Year Students in Quantitative Analysis

ERIC Educational Resources Information Center

Rubin, Samuel J.; Abrams, Binyomin

2015-01-01

Despite their technological savvy, most students entering university lack the necessary computer skills to succeed in a quantitative analysis course, in which they are often expected to input, analyze, and plot results of experiments without any previous formal education in Microsoft Excel or similar programs. This lack of formal education results…

Privatization of solid waste collection services: Lessons from Gaborone.

PubMed

Bolaane, Benjamin; Isaac, Emmanuel

2015-06-01

Formal privatization of solid waste collection activities has often been flagged as a suitable intervention for some of the challenges of solid waste management experienced by developing countries. Proponents of outsourcing collection to the private sector argue that in contrast to the public sector, it is more effective and efficient in delivering services. This essay is a comparative case study of efficiency and effectiveness attributes between the public and the formal private sector, in relation to the collection of commercial waste in Gaborone. The paper is based on analysis of secondary data and key informant interviews. It was found that while, the private sector performed comparatively well in most of the chosen indicators of efficiency and effectiveness, the public sector also had areas where it had a competitive advantage. For instance, the private sector used the collection crew more efficiently, while the public sector was found to have a more reliable workforce. The study recommends that, while formal private sector participation in waste collection has some positive effects in terms of quality of service rendered, in most developing countries, it has to be enhanced by building sufficient capacity within the public sector on information about services contracted out and evaluation of performance criteria within the contracting process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dissipative quantum computing with open quantum walks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sinayskiy, Ilya; Petruccione, Francesco

An open quantum walk approach to the implementation of a dissipative quantum computing scheme is presented. The formalism is demonstrated for the example of an open quantum walk implementation of a 3 qubit quantum circuit consisting of 10 gates.

Relevancy in Problem Solving: A Computational Framework

ERIC Educational Resources Information Center

Kwisthout, Johan

2012-01-01

When computer scientists discuss the computational complexity of, for example, finding the shortest path from building A to building B in some town or city, their starting point typically is a formal description of the problem at hand, e.g., a graph with weights on every edge where buildings correspond to vertices, routes between buildings to…

Chromotomography for a rotating-prism instrument using backprojection, then filtering.

PubMed

Deming, Ross W

2006-08-01

A simple closed-form solution is derived for reconstructing a 3D spatial-chromatic image cube from a set of chromatically dispersed 2D image frames. The algorithm is tailored for a particular instrument in which the dispersion element is a matching set of mechanically rotated direct vision prisms positioned between a lens and a focal plane array. By using a linear operator formalism to derive the Tikhonov-regularized pseudoinverse operator, it is found that the unique minimum-norm solution is obtained by applying the adjoint operator, followed by 1D filtering with respect to the chromatic variable. Thus the filtering and backprojection (adjoint) steps are applied in reverse order relative to an existing method. Computational efficiency is provided by use of the fast Fourier transform in the filtering step.

Effects of molecular packing in organic crystals on singlet fission with ab initio many body perturbation theory

NASA Astrophysics Data System (ADS)

Haber, Jonah; Refaely-Abramson, Sivan; da Jornada, Felipe H.; Louie, Steven G.; Neaton, Jeffrey B.

Multi-exciton generation processes, in which multiple charge carriers are generated from a single photon, are mechanisms of significant interest for achieving efficiencies beyond the Shockley-Queisser limit of conventional p-n junction solar cells. One well-studied multiexciton process is singlet fission, whereby a singlet decays into two spin-correlated triplet excitons. Here, we use a newly developed computational approach to calculate singlet-fission coupling terms and rates with an ab initio Green's function formalism based on many-body perturbation theory (MBPT) within the GW approximation and the Bethe-Salpeter equation approach. We compare results for crystalline pentacene and TIPS-pentacene and explore the effect of molecular packing on the singlet fission mechanism. This work is supported by the Department of Energy.

The Role of the Board of Education in the Process of Resource Allocation for Public Schools.

ERIC Educational Resources Information Center

Chichura, Elaine Marie

Public schools as formal organizations have broad-based goals, limited resources, and a formal hierarchy with which to manage the goal achievement process. The board of education combines this organization's economic and political dimensions to provide a thorough, efficient education for all children in the state. This paper investigates the…

Formal Solutions for Polarized Radiative Transfer. III. Stiffness and Instability

NASA Astrophysics Data System (ADS)

Janett, Gioele; Paganini, Alberto

2018-04-01

Efficient numerical approximation of the polarized radiative transfer equation is challenging because this system of ordinary differential equations exhibits stiff behavior, which potentially results in numerical instability. This negatively impacts the accuracy of formal solvers, and small step-sizes are often necessary to retrieve physical solutions. This work presents stability analyses of formal solvers for the radiative transfer equation of polarized light, identifies instability issues, and suggests practical remedies. In particular, the assumptions and the limitations of the stability analysis of Runge–Kutta methods play a crucial role. On this basis, a suitable and pragmatic formal solver is outlined and tested. An insightful comparison to the scalar radiative transfer equation is also presented.

Development of highly accurate approximate scheme for computing the charge transfer integral

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pershin, Anton; Szalay, Péter G.

The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, itmore » was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the “exact” scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the “exact” calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.« less

Parallelization and implementation of approximate root isolation for nonlinear system by Monte Carlo

NASA Astrophysics Data System (ADS)

Khosravi, Ebrahim

1998-12-01

This dissertation solves a fundamental problem of isolating the real roots of nonlinear systems of equations by Monte-Carlo that were published by Bush Jones. This algorithm requires only function values and can be applied readily to complicated systems of transcendental functions. The implementation of this sequential algorithm provides scientists with the means to utilize function analysis in mathematics or other fields of science. The algorithm, however, is so computationally intensive that the system is limited to a very small set of variables, and this will make it unfeasible for large systems of equations. Also a computational technique was needed for investigating a metrology of preventing the algorithm structure from converging to the same root along different paths of computation. The research provides techniques for improving the efficiency and correctness of the algorithm. The sequential algorithm for this technique was corrected and a parallel algorithm is presented. This parallel method has been formally analyzed and is compared with other known methods of root isolation. The effectiveness, efficiency, enhanced overall performance of the parallel processing of the program in comparison to sequential processing is discussed. The message passing model was used for this parallel processing, and it is presented and implemented on Intel/860 MIMD architecture. The parallel processing proposed in this research has been implemented in an ongoing high energy physics experiment: this algorithm has been used to track neutrinoes in a super K detector. This experiment is located in Japan, and data can be processed on-line or off-line locally or remotely.

Intrinsic retrieval efficiency for quantum memories: A three-dimensional theory of light interaction with an atomic ensemble

NASA Astrophysics Data System (ADS)

Gujarati, Tanvi P.; Wu, Yukai; Duan, Luming

2018-03-01

Duan-Lukin-Cirac-Zoller quantum repeater protocol, which was proposed to realize long distance quantum communication, requires usage of quantum memories. Atomic ensembles interacting with optical beams based on off-resonant Raman scattering serve as convenient on-demand quantum memories. Here, a complete free space, three-dimensional theory of the associated read and write process for this quantum memory is worked out with the aim of understanding intrinsic retrieval efficiency. We develop a formalism to calculate the transverse mode structure for the signal and the idler photons and use the formalism to study the intrinsic retrieval efficiency under various configurations. The effects of atomic density fluctuations and atomic motion are incorporated by numerically simulating this system for a range of realistic experimental parameters. We obtain results that describe the variation in the intrinsic retrieval efficiency as a function of the memory storage time for skewed beam configuration at a finite temperature, which provides valuable information for optimization of the retrieval efficiency in experiments.

Graph Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanfilippo, Antonio P.

2005-12-27

Graph theory is a branch of discrete combinatorial mathematics that studies the properties of graphs. The theory was pioneered by the Swiss mathematician Leonhard Euler in the 18th century, commenced its formal development during the second half of the 19th century, and has witnessed substantial growth during the last seventy years, with applications in areas as diverse as engineering, computer science, physics, sociology, chemistry and biology. Graph theory has also had a strong impact in computational linguistics by providing the foundations for the theory of features structures that has emerged as one of the most widely used frameworks for themore » representation of grammar formalisms.« less

Automatic Estimation of Verified Floating-Point Round-Off Errors via Static Analysis

NASA Technical Reports Server (NTRS)

Moscato, Mariano; Titolo, Laura; Dutle, Aaron; Munoz, Cesar A.

2017-01-01

This paper introduces a static analysis technique for computing formally verified round-off error bounds of floating-point functional expressions. The technique is based on a denotational semantics that computes a symbolic estimation of floating-point round-o errors along with a proof certificate that ensures its correctness. The symbolic estimation can be evaluated on concrete inputs using rigorous enclosure methods to produce formally verified numerical error bounds. The proposed technique is implemented in the prototype research tool PRECiSA (Program Round-o Error Certifier via Static Analysis) and used in the verification of floating-point programs of interest to NASA.

On the Accuracy and Parallelism of GPGPU-Powered Incremental Clustering Algorithms.

PubMed

Chen, Chunlei; He, Li; Zhang, Huixiang; Zheng, Hao; Wang, Lei

2017-01-01

Incremental clustering algorithms play a vital role in various applications such as massive data analysis and real-time data processing. Typical application scenarios of incremental clustering raise high demand on computing power of the hardware platform. Parallel computing is a common solution to meet this demand. Moreover, General Purpose Graphic Processing Unit (GPGPU) is a promising parallel computing device. Nevertheless, the incremental clustering algorithm is facing a dilemma between clustering accuracy and parallelism when they are powered by GPGPU. We formally analyzed the cause of this dilemma. First, we formalized concepts relevant to incremental clustering like evolving granularity. Second, we formally proved two theorems. The first theorem proves the relation between clustering accuracy and evolving granularity. Additionally, this theorem analyzes the upper and lower bounds of different-to-same mis-affiliation. Fewer occurrences of such mis-affiliation mean higher accuracy. The second theorem reveals the relation between parallelism and evolving granularity. Smaller work-depth means superior parallelism. Through the proofs, we conclude that accuracy of an incremental clustering algorithm is negatively related to evolving granularity while parallelism is positively related to the granularity. Thus the contradictory relations cause the dilemma. Finally, we validated the relations through a demo algorithm. Experiment results verified theoretical conclusions.

High-efficiency high-energy Ka source for the critically-required maximum illumination of x-ray optics on Z using Z-petawatt-driven laser-breakout-afterburner accelerated ultrarelativistic electrons LDRD .

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sefkow, Adam B.; Bennett, Guy R.

2010-09-01

Under the auspices of the Science of Extreme Environments LDRD program, a <2 year theoretical- and computational-physics study was performed (LDRD Project 130805) by Guy R Bennett (formally in Center-01600) and Adam B. Sefkow (Center-01600): To investigate novel target designs by which a short-pulse, PW-class beam could create a brighter K{alpha} x-ray source than by simple, direct-laser-irradiation of a flat foil; Direct-Foil-Irradiation (DFI). The computational studies - which are still ongoing at this writing - were performed primarily on the RedStorm supercomputer at Sandia National Laboratories Albuquerque site. The motivation for a higher efficiency K{alpha} emitter was very clear: asmore » the backlighter flux for any x-ray imaging technique on the Z accelerator increases, the signal-to-noise and signal-to-background ratios improve. This ultimately allows the imaging system to reach its full quantitative potential as a diagnostic. Depending on the particular application/experiment this would imply, for example, that the system would have reached its full design spatial resolution and thus the capability to see features that might otherwise be indiscernible with a traditional DFI-like x-ray source. This LDRD began FY09 and ended FY10.« less

Ab Initio Optimized Effective Potentials for Real Molecules in Optical Cavities: Photon Contributions to the Molecular Ground State

PubMed Central

2018-01-01

We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density-functional theory (QEDFT).1−5 Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical cavities and described in full real space. While the first example is a two-dimensional system and allows to benchmark the employed approximations, the latter two examples demonstrate that the correlated electron-photon interaction appreciably distorts the ground-state electronic structure of a real molecule. By using this scheme, we not only construct typical electronic observables, such as the electronic ground-state density, but also illustrate how photon observables, such as the photon number, and mixed electron-photon observables, for example, electron–photon correlation functions, become accessible in a density-functional theory (DFT) framework. This work constitutes the first three-dimensional ab initio calculation within the new QEDFT formalism and thus opens up a new computational route for the ab initio study of correlated electron–photon systems in quantum cavities. PMID:29594185

Computational foundations of the visual number sense.

PubMed

Stoianov, Ivilin Peev; Zorzi, Marco

2017-01-01

We provide an emergentist perspective on the computational mechanism underlying numerosity perception, its development, and the role of inhibition, based on our deep neural network model. We argue that the influence of continuous visual properties does not challenge the notion of number sense, but reveals limit conditions for the computation that yields invariance in numerosity perception. Alternative accounts should be formalized in a computational model.

Empowering People through Technology. Proceedings of the International Conference of the Association for the Development of Computer-Based Instructional Systems (34th, Norfolk, Virginia, November 8-11, 1992).

ERIC Educational Resources Information Center

Association for the Development of Computer-based Instructional Systems.

These proceedings present 74 selected abstracts and 47 selected formal papers under 14 special interest group headings. Topics addressed by the papers include constructing multimedia; interactive video; computers in secondary school mathematics; access in computer-based instruction; implementing computer-based technology; advisor development;…

Bose-Einstein condensates form in heuristics learned by ciliates deciding to signal 'social' commitments.

PubMed

Clark, Kevin B

2010-03-01

Fringe quantum biology theories often adopt the concept of Bose-Einstein condensation when explaining how consciousness, emotion, perception, learning, and reasoning emerge from operations of intact animal nervous systems and other computational media. However, controversial empirical evidence and mathematical formalism concerning decoherence rates of bioprocesses keep these frameworks from satisfactorily accounting for the physical nature of cognitive-like events. This study, inspired by the discovery that preferential attachment rules computed by complex technological networks obey Bose-Einstein statistics, is the first rigorous attempt to examine whether analogues of Bose-Einstein condensation precipitate learned decision making in live biological systems as bioenergetics optimization predicts. By exploiting the ciliate Spirostomum ambiguum's capacity to learn and store behavioral strategies advertising mating availability into heuristics of topologically invariant computational networks, three distinct phases of strategy use were found to map onto statistical distributions described by Bose-Einstein, Fermi-Dirac, and classical Maxwell-Boltzmann behavior. Ciliates that sensitized or habituated signaling patterns to emit brief periods of either deceptive 'harder-to-get' or altruistic 'easier-to-get' serial escape reactions began testing condensed on initially perceived fittest 'courting' solutions. When these ciliates switched from their first strategy choices, Bose-Einstein condensation of strategy use abruptly dissipated into a Maxwell-Boltzmann computational phase no longer dominated by a single fittest strategy. Recursive trial-and-error strategy searches annealed strategy use back into a condensed phase consistent with performance optimization. 'Social' decisions performed by ciliates showing no nonassociative learning were largely governed by Fermi-Dirac statistics, resulting in degenerate distributions of strategy choices. These findings corroborate previous work demonstrating ciliates with improving expertise search grouped 'courting' assurances at quantum efficiencies and verify efficient processing by primitive 'social' intelligences involves network forms of Bose-Einstein condensation coupled to preceding thermodynamic-sensitive computational phases. 2009 Elsevier Ireland Ltd. All rights reserved.

Quantum Monte Carlo: Faster, More Reliable, And More Accurate

NASA Astrophysics Data System (ADS)

Anderson, Amos Gerald

2010-06-01

The Schrodinger Equation has been available for about 83 years, but today, we still strain to apply it accurately to molecules of interest. The difficulty is not theoretical in nature, but practical, since we're held back by lack of sufficient computing power. Consequently, effort is applied to find acceptable approximations to facilitate real time solutions. In the meantime, computer technology has begun rapidly advancing and changing the way we think about efficient algorithms. For those who can reorganize their formulas to take advantage of these changes and thereby lift some approximations, incredible new opportunities await. Over the last decade, we've seen the emergence of a new kind of computer processor, the graphics card. Designed to accelerate computer games by optimizing quantity instead of quality in processor, they have become of sufficient quality to be useful to some scientists. In this thesis, we explore the first known use of a graphics card to computational chemistry by rewriting our Quantum Monte Carlo software into the requisite "data parallel" formalism. We find that notwithstanding precision considerations, we are able to speed up our software by about a factor of 6. The success of a Quantum Monte Carlo calculation depends on more than just processing power. It also requires the scientist to carefully design the trial wavefunction used to guide simulated electrons. We have studied the use of Generalized Valence Bond wavefunctions to simply, and yet effectively, captured the essential static correlation in atoms and molecules. Furthermore, we have developed significantly improved two particle correlation functions, designed with both flexibility and simplicity considerations, representing an effective and reliable way to add the necessary dynamic correlation. Lastly, we present our method for stabilizing the statistical nature of the calculation, by manipulating configuration weights, thus facilitating efficient and robust calculations. Our combination of Generalized Valence Bond wavefunctions, improved correlation functions, and stabilized weighting techniques for calculations run on graphics cards, represents a new way for using Quantum Monte Carlo to study arbitrarily sized molecules.

The emergence of mind and brain: an evolutionary, computational, and philosophical approach.

PubMed

Mainzer, Klaus

2008-01-01

Modern philosophy of mind cannot be understood without recent developments in computer science, artificial intelligence (AI), robotics, neuroscience, biology, linguistics, and psychology. Classical philosophy of formal languages as well as symbolic AI assume that all kinds of knowledge must explicitly be represented by formal or programming languages. This assumption is limited by recent insights into the biology of evolution and developmental psychology of the human organism. Most of our knowledge is implicit and unconscious. It is not formally represented, but embodied knowledge, which is learnt by doing and understood by bodily interacting with changing environments. That is true not only for low-level skills, but even for high-level domains of categorization, language, and abstract thinking. The embodied mind is considered an emergent capacity of the brain as a self-organizing complex system. Actually, self-organization has been a successful strategy of evolution to handle the increasing complexity of the world. Genetic programs are not sufficient and cannot prepare the organism for all kinds of complex situations in the future. Self-organization and emergence are fundamental concepts in the theory of complex dynamical systems. They are also applied in organic computing as a recent research field of computer science. Therefore, cognitive science, AI, and robotics try to model the embodied mind in an artificial evolution. The paper analyzes these approaches in the interdisciplinary framework of complex dynamical systems and discusses their philosophical impact.

Formality of the Chinese collective leadership.

PubMed

Li, Haiying; Graesser, Arthur C

2016-09-01

We investigated the linguistic patterns in the discourse of four generations of the collective leadership of the Communist Party of China (CPC) from 1921 to 2012. The texts of Mao Zedong, Deng Xiaoping, Jiang Zemin, and Hu Jintao were analyzed using computational linguistic techniques (a Chinese formality score) to explore the persuasive linguistic features of the leaders in the contexts of power phase, the nation's education level, power duration, and age. The study was guided by the elaboration likelihood model of persuasion, which includes a central route (represented by formal discourse) versus a peripheral route (represented by informal discourse) to persuasion. The results revealed that these leaders adopted the formal, central route more when they were in power than before they came into power. The nation's education level was a significant factor in the leaders' adoption of the persuasion strategy. The leaders' formality also decreased with their increasing age and in-power times. However, the predictability of these factors for formality had subtle differences among the different types of leaders. These results enhance our understanding of the Chinese collective leadership and the role of formality in politically persuasive messages.

A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms.

PubMed

Balbi, Pietro; Massobrio, Paolo; Hellgren Kotaleski, Jeanette

2017-09-01

Modelling ionic channels represents a fundamental step towards developing biologically detailed neuron models. Until recently, the voltage-gated ion channels have been mainly modelled according to the formalism introduced by the seminal works of Hodgkin and Huxley (HH). However, following the continuing achievements in the biophysical and molecular comprehension of these pore-forming transmembrane proteins, the HH formalism turned out to carry limitations and inconsistencies in reproducing the ion-channels electrophysiological behaviour. At the same time, Markov-type kinetic models have been increasingly proven to successfully replicate both the electrophysiological and biophysical features of different ion channels. However, in order to model even the finest non-conducting molecular conformational change, they are often equipped with a considerable number of states and related transitions, which make them computationally heavy and less suitable for implementation in conductance-based neurons and large networks of those. In this purely modelling study we develop a Markov-type kinetic model for all human voltage-gated sodium channels (VGSCs). The model framework is detailed, unifying (i.e., it accounts for all ion-channel isoforms) and computationally efficient (i.e. with a minimal set of states and transitions). The electrophysiological data to be modelled are gathered from previously published studies on whole-cell patch-clamp experiments in mammalian cell lines heterologously expressing the human VGSC subtypes (from NaV1.1 to NaV1.9). By adopting a minimum sequence of states, and using the same state diagram for all the distinct isoforms, the model ensures the lightest computational load when used in neuron models and neural networks of increasing complexity. The transitions between the states are described by original ordinary differential equations, which represent the rate of the state transitions as a function of voltage (i.e., membrane potential). The kinetic model, developed in the NEURON simulation environment, appears to be the simplest and most parsimonious way for a detailed phenomenological description of the human VGSCs electrophysiological behaviour.

Design, Specification, and Synthesis of Aircraft Electric Power Systems Control Logic

NASA Astrophysics Data System (ADS)

Xu, Huan

Cyber-physical systems integrate computation, networking, and physical processes. Substantial research challenges exist in the design and verification of such large-scale, distributed sensing, actuation, and control systems. Rapidly improving technology and recent advances in control theory, networked systems, and computer science give us the opportunity to drastically improve our approach to integrated flow of information and cooperative behavior. Current systems rely on text-based specifications and manual design. Using new technology advances, we can create easier, more efficient, and cheaper ways of developing these control systems. This thesis will focus on design considerations for system topologies, ways to formally and automatically specify requirements, and methods to synthesize reactive control protocols, all within the context of an aircraft electric power system as a representative application area. This thesis consists of three complementary parts: synthesis, specification, and design. The first section focuses on the synthesis of central and distributed reactive controllers for an aircraft elec- tric power system. This approach incorporates methodologies from computer science and control. The resulting controllers are correct by construction with respect to system requirements, which are formulated using the specification language of linear temporal logic (LTL). The second section addresses how to formally specify requirements and introduces a domain-specific language for electric power systems. A software tool automatically converts high-level requirements into LTL and synthesizes a controller. The final sections focus on design space exploration. A design methodology is proposed that uses mixed-integer linear programming to obtain candidate topologies, which are then used to synthesize controllers. The discrete-time control logic is then verified in real-time by two methods: hardware and simulation. Finally, the problem of partial observability and dynamic state estimation is explored. Given a set placement of sensors on an electric power system, measurements from these sensors can be used in conjunction with control logic to infer the state of the system.

A Computer-Assisted Instruction Program for Exercises on Finding Axioms. Technical Report Number 186.

ERIC Educational Resources Information Center

Goldberg, Adele; Suppes, Patrick

An interactive computer-assisted system for teaching elementary logic is described, which was designed to handle formalizations of first-order theories suitable for presentation in a computer-assisted instruction environment. The system provides tools with which the user can develop and then study a nonlogical axiomatic theory along whatever lines…

A Computational Turn: Fiction and the Forms of Invention, 1965-1980

ERIC Educational Resources Information Center

Sims, Matthew

2017-01-01

This dissertation examines the relationship between American fiction and computing. More specifically, it argues that each domain explored similar formal possibilities during a period I refer to as Early Postmodernism (1965-1980). In the case of computing, the 60s and 70s represent a turning point in which modern systems and approaches were…

SU-E-T-477: An Efficient Dose Correction Algorithm Accounting for Tissue Heterogeneities in LDR Brachytherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mashouf, S; Lai, P; Karotki, A

2014-06-01

Purpose: Seed brachytherapy is currently used for adjuvant radiotherapy of early stage prostate and breast cancer patients. The current standard for calculation of dose surrounding the brachytherapy seeds is based on American Association of Physicist in Medicine Task Group No. 43 (TG-43 formalism) which generates the dose in homogeneous water medium. Recently, AAPM Task Group No. 186 emphasized the importance of accounting for tissue heterogeneities. This can be done using Monte Carlo (MC) methods, but it requires knowing the source structure and tissue atomic composition accurately. In this work we describe an efficient analytical dose inhomogeneity correction algorithm implemented usingmore » MIM Symphony treatment planning platform to calculate dose distributions in heterogeneous media. Methods: An Inhomogeneity Correction Factor (ICF) is introduced as the ratio of absorbed dose in tissue to that in water medium. ICF is a function of tissue properties and independent of source structure. The ICF is extracted using CT images and the absorbed dose in tissue can then be calculated by multiplying the dose as calculated by the TG-43 formalism times ICF. To evaluate the methodology, we compared our results with Monte Carlo simulations as well as experiments in phantoms with known density and atomic compositions. Results: The dose distributions obtained through applying ICF to TG-43 protocol agreed very well with those of Monte Carlo simulations as well as experiments in all phantoms. In all cases, the mean relative error was reduced by at least 50% when ICF correction factor was applied to the TG-43 protocol. Conclusion: We have developed a new analytical dose calculation method which enables personalized dose calculations in heterogeneous media. The advantages over stochastic methods are computational efficiency and the ease of integration into clinical setting as detailed source structure and tissue segmentation are not needed. University of Toronto, Natural Sciences and Engineering Research Council of Canada.« less

Space Radiation Transport Code Development: 3DHZETRN

NASA Technical Reports Server (NTRS)

Wilson, John W.; Slaba, Tony C.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.

2015-01-01

The space radiation transport code, HZETRN, has been used extensively for research, vehicle design optimization, risk analysis, and related applications. One of the simplifying features of the HZETRN transport formalism is the straight-ahead approximation, wherein all particles are assumed to travel along a common axis. This reduces the governing equation to one spatial dimension allowing enormous simplification and highly efficient computational procedures to be implemented. Despite the physical simplifications, the HZETRN code is widely used for space applications and has been found to agree well with fully 3D Monte Carlo simulations in many circumstances. Recent work has focused on the development of 3D transport corrections for neutrons and light ions (Z < 2) for which the straight-ahead approximation is known to be less accurate. Within the development of 3D corrections, well-defined convergence criteria have been considered, allowing approximation errors at each stage in model development to be quantified. The present level of development assumes the neutron cross sections have an isotropic component treated within N explicit angular directions and a forward component represented by the straight-ahead approximation. The N = 1 solution refers to the straight-ahead treatment, while N = 2 represents the bi-directional model in current use for engineering design. The figure below shows neutrons, protons, and alphas for various values of N at locations in an aluminum sphere exposed to a solar particle event (SPE) spectrum. The neutron fluence converges quickly in simple geometry with N > 14 directions. The improved code, 3DHZETRN, transports neutrons, light ions, and heavy ions under space-like boundary conditions through general geometry while maintaining a high degree of computational efficiency. A brief overview of the 3D transport formalism for neutrons and light ions is given, and extensive benchmarking results with the Monte Carlo codes Geant4, FLUKA, and PHITS are provided for a variety of boundary conditions and geometries. Improvements provided by the 3D corrections are made clear in the comparisons. Developments needed to connect 3DHZETRN to vehicle design and optimization studies will be discussed. Future theoretical development will relax the forward plus isotropic interaction assumption to more general angular dependence.

GPU-completeness: theory and implications

NASA Astrophysics Data System (ADS)

Lin, I.-Jong

2011-01-01

This paper formalizes a major insight into a class of algorithms that relate parallelism and performance. The purpose of this paper is to define a class of algorithms that trades off parallelism for quality of result (e.g. visual quality, compression rate), and we propose a similar method for algorithmic classification based on NP-Completeness techniques, applied toward parallel acceleration. We will define this class of algorithm as "GPU-Complete" and will postulate the necessary properties of the algorithms for admission into this class. We will also formally relate his algorithmic space and imaging algorithms space. This concept is based upon our experience in the print production area where GPUs (Graphic Processing Units) have shown a substantial cost/performance advantage within the context of HPdelivered enterprise services and commercial printing infrastructure. While CPUs and GPUs are converging in their underlying hardware and functional blocks, their system behaviors are clearly distinct in many ways: memory system design, programming paradigms, and massively parallel SIMD architecture. There are applications that are clearly suited to each architecture: for CPU: language compilation, word processing, operating systems, and other applications that are highly sequential in nature; for GPU: video rendering, particle simulation, pixel color conversion, and other problems clearly amenable to massive parallelization. While GPUs establishing themselves as a second, distinct computing architecture from CPUs, their end-to-end system cost/performance advantage in certain parts of computation inform the structure of algorithms and their efficient parallel implementations. While GPUs are merely one type of architecture for parallelization, we show that their introduction into the design space of printing systems demonstrate the trade-offs against competing multi-core, FPGA, and ASIC architectures. While each architecture has its own optimal application, we believe that the selection of architecture can be defined in terms of properties of GPU-Completeness. For a welldefined subset of algorithms, GPU-Completeness is intended to connect the parallelism, algorithms and efficient architectures into a unified framework to show that multiple layers of parallel implementation are guided by the same underlying trade-off.

Computer literacy among first year medical students in a developing country: A cross sectional study

PubMed Central

2012-01-01

Background The use of computer assisted learning (CAL) has enhanced undergraduate medical education. CAL improves performance at examinations, develops problem solving skills and increases student satisfaction. The study evaluates computer literacy among first year medical students in Sri Lanka. Methods The study was conducted at Faculty of Medicine, University of Colombo, Sri Lanka between August-September 2008. First year medical students (n = 190) were invited for the study. Data on computer literacy and associated factors were collected by an expert-validated pre-tested self-administered questionnaire. Computer literacy was evaluated by testing knowledge on 6 domains; common software packages, operating systems, database management and the usage of internet and E-mail. A linear regression was conducted using total score for computer literacy as the continuous dependant variable and other independent covariates. Results Sample size-181 (Response rate-95.3%), 49.7% were Males. Majority of the students (77.3%) owned a computer (Males-74.4%, Females-80.2%). Students have gained their present computer knowledge by; a formal training programme (64.1%), self learning (63.0%) or by peer learning (49.2%). The students used computers for predominately; word processing (95.6%), entertainment (95.0%), web browsing (80.1%) and preparing presentations (76.8%). Majority of the students (75.7%) expressed their willingness for a formal computer training programme at the faculty. Mean score for the computer literacy questionnaire was 48.4 ± 20.3, with no significant gender difference (Males-47.8 ± 21.1, Females-48.9 ± 19.6). There were 47.9% students that had a score less than 50% for the computer literacy questionnaire. Students from Colombo district, Western Province and Student owning a computer had a significantly higher mean score in comparison to other students (p < 0.001). In the linear regression analysis, formal computer training was the strongest predictor of computer literacy (β = 13.034), followed by using internet facility, being from Western province, using computers for Web browsing and computer programming, computer ownership and doing IT (Information Technology) as a subject in GCE (A/L) examination. Conclusion Sri Lankan medical undergraduates had a low-intermediate level of computer literacy. There is a need to improve computer literacy, by increasing computer training in schools, or by introducing computer training in the initial stages of the undergraduate programme. These two options require improvement in infrastructure and other resources. PMID:22980096

Rule acquisition in formal decision contexts based on formal, object-oriented and property-oriented concept lattices.

PubMed

Ren, Yue; Li, Jinhai; Aswani Kumar, Cherukuri; Liu, Wenqi

2014-01-01

Rule acquisition is one of the main purposes in the analysis of formal decision contexts. Up to now, there have been several types of rules in formal decision contexts such as decision rules, decision implications, and granular rules, which can be viewed as ∧-rules since all of them have the following form: "if conditions 1,2,…, and m hold, then decisions hold." In order to enrich the existing rule acquisition theory in formal decision contexts, this study puts forward two new types of rules which are called ∨-rules and ∨-∧ mixed rules based on formal, object-oriented, and property-oriented concept lattices. Moreover, a comparison of ∨-rules, ∨-∧ mixed rules, and ∧-rules is made from the perspectives of inclusion and inference relationships. Finally, some real examples and numerical experiments are conducted to compare the proposed rule acquisition algorithms with the existing one in terms of the running efficiency.

Rule Acquisition in Formal Decision Contexts Based on Formal, Object-Oriented and Property-Oriented Concept Lattices

PubMed Central

Ren, Yue; Aswani Kumar, Cherukuri; Liu, Wenqi

2014-01-01

Rule acquisition is one of the main purposes in the analysis of formal decision contexts. Up to now, there have been several types of rules in formal decision contexts such as decision rules, decision implications, and granular rules, which can be viewed as ∧-rules since all of them have the following form: “if conditions 1,2,…, and m hold, then decisions hold.” In order to enrich the existing rule acquisition theory in formal decision contexts, this study puts forward two new types of rules which are called ∨-rules and ∨-∧ mixed rules based on formal, object-oriented, and property-oriented concept lattices. Moreover, a comparison of ∨-rules, ∨-∧ mixed rules, and ∧-rules is made from the perspectives of inclusion and inference relationships. Finally, some real examples and numerical experiments are conducted to compare the proposed rule acquisition algorithms with the existing one in terms of the running efficiency. PMID:25165744

Report on the formal specification and partial verification of the VIPER microprocessor

NASA Technical Reports Server (NTRS)

Brock, Bishop; Hunt, Warren A., Jr.

1991-01-01

The formal specification and partial verification of the VIPER microprocessor is reviewed. The VIPER microprocessor was designed by RSRE, Malvern, England, for safety critical computing applications (e.g., aircraft, reactor control, medical instruments, armaments). The VIPER was carefully specified and partially verified in an attempt to provide a microprocessor with completely predictable operating characteristics. The specification of VIPER is divided into several levels of abstraction, from a gate-level description up to an instruction execution model. Although the consistency between certain levels was demonstrated with mechanically-assisted mathematical proof, the formal verification of VIPER was never completed.

An Efficient Soft Set-Based Approach for Conflict Analysis

PubMed Central

Sutoyo, Edi; Mungad, Mungad; Hamid, Suraya; Herawan, Tutut

2016-01-01

Conflict analysis has been used as an important tool in economic, business, governmental and political dispute, games, management negotiations, military operations and etc. There are many mathematical formal models have been proposed to handle conflict situations and one of the most popular is rough set theory. With the ability to handle vagueness from the conflict data set, rough set theory has been successfully used. However, computational time is still an issue when determining the certainty, coverage, and strength of conflict situations. In this paper, we present an alternative approach to handle conflict situations, based on some ideas using soft set theory. The novelty of the proposed approach is that, unlike in rough set theory that uses decision rules, it is based on the concept of co-occurrence of parameters in soft set theory. We illustrate the proposed approach by means of a tutorial example of voting analysis in conflict situations. Furthermore, we elaborate the proposed approach on real world dataset of political conflict in Indonesian Parliament. We show that, the proposed approach achieves lower computational time as compared to rough set theory of up to 3.9%. PMID:26928627

Large margin nearest neighbor classifiers.

PubMed

Domeniconi, Carlotta; Gunopulos, Dimitrios; Peng, Jing

2005-07-01

The nearest neighbor technique is a simple and appealing approach to addressing classification problems. It relies on the assumption of locally constant class conditional probabilities. This assumption becomes invalid in high dimensions with a finite number of examples due to the curse of dimensionality. Severe bias can be introduced under these conditions when using the nearest neighbor rule. The employment of a locally adaptive metric becomes crucial in order to keep class conditional probabilities close to uniform, thereby minimizing the bias of estimates. We propose a technique that computes a locally flexible metric by means of support vector machines (SVMs). The decision function constructed by SVMs is used to determine the most discriminant direction in a neighborhood around the query. Such a direction provides a local feature weighting scheme. We formally show that our method increases the margin in the weighted space where classification takes place. Moreover, our method has the important advantage of online computational efficiency over competing locally adaptive techniques for nearest neighbor classification. We demonstrate the efficacy of our method using both real and simulated data.

A method for exploring implicit concept relatedness in biomedical knowledge network.

PubMed

Bai, Tian; Gong, Leiguang; Wang, Ye; Wang, Yan; Kulikowski, Casimir A; Huang, Lan

2016-07-19

Biomedical information and knowledge, structural and non-structural, stored in different repositories can be semantically connected to form a hybrid knowledge network. How to compute relatedness between concepts and discover valuable but implicit information or knowledge from it effectively and efficiently is of paramount importance for precision medicine, and a major challenge facing the biomedical research community. In this study, a hybrid biomedical knowledge network is constructed by linking concepts across multiple biomedical ontologies as well as non-structural biomedical knowledge sources. To discover implicit relatedness between concepts in ontologies for which potentially valuable relationships (implicit knowledge) may exist, we developed a Multi-Ontology Relatedness Model (MORM) within the knowledge network, for which a relatedness network (RN) is defined and computed across multiple ontologies using a formal inference mechanism of set-theoretic operations. Semantic constraints are designed and implemented to prune the search space of the relatedness network. Experiments to test examples of several biomedical applications have been carried out, and the evaluation of the results showed an encouraging potential of the proposed approach to biomedical knowledge discovery.

An Efficient Soft Set-Based Approach for Conflict Analysis.

PubMed

Sutoyo, Edi; Mungad, Mungad; Hamid, Suraya; Herawan, Tutut

2016-01-01

Conflict analysis has been used as an important tool in economic, business, governmental and political dispute, games, management negotiations, military operations and etc. There are many mathematical formal models have been proposed to handle conflict situations and one of the most popular is rough set theory. With the ability to handle vagueness from the conflict data set, rough set theory has been successfully used. However, computational time is still an issue when determining the certainty, coverage, and strength of conflict situations. In this paper, we present an alternative approach to handle conflict situations, based on some ideas using soft set theory. The novelty of the proposed approach is that, unlike in rough set theory that uses decision rules, it is based on the concept of co-occurrence of parameters in soft set theory. We illustrate the proposed approach by means of a tutorial example of voting analysis in conflict situations. Furthermore, we elaborate the proposed approach on real world dataset of political conflict in Indonesian Parliament. We show that, the proposed approach achieves lower computational time as compared to rough set theory of up to 3.9%.

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model

PubMed Central

Jensen, Greg; Muñoz, Fabian; Alkan, Yelda; Ferrera, Vincent P.; Terrace, Herbert S.

2015-01-01

Transitive inference (the ability to infer that B > D given that B > C and C > D) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort, inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, and the betasort algorithm, as well as Q-learning, an established reward-prediction error (RPE) model. Of these, only Q-learning failed to respond above chance during critical test trials. Betasort’s success (when compared to RPE models) and its computational efficiency (when compared to full Markov decision process implementations) suggests that the study of reinforcement learning in organisms will be best served by a feature-driven approach to comparing formal models. PMID:26407227

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model.

PubMed

Jensen, Greg; Muñoz, Fabian; Alkan, Yelda; Ferrera, Vincent P; Terrace, Herbert S

2015-01-01

Transitive inference (the ability to infer that B > D given that B > C and C > D) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort, inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, and the betasort algorithm, as well as Q-learning, an established reward-prediction error (RPE) model. Of these, only Q-learning failed to respond above chance during critical test trials. Betasort's success (when compared to RPE models) and its computational efficiency (when compared to full Markov decision process implementations) suggests that the study of reinforcement learning in organisms will be best served by a feature-driven approach to comparing formal models.

General formalism of local thermodynamics with an example: Quantum Otto engine with a spin-1/2 coupled to an arbitrary spin.

PubMed

Altintas, Ferdi; Müstecaplıoğlu, Özgür E

2015-08-01

We investigate a quantum heat engine with a working substance of two particles, one with a spin-1/2 and the other with an arbitrary spin (spin s), coupled by Heisenberg exchange interaction, and subject to an external magnetic field. The engine operates in a quantum Otto cycle. Work harvested in the cycle and its efficiency are calculated using quantum thermodynamical definitions. It is found that the engine has higher efficiencies at higher spins and can harvest work at higher exchange interaction strengths. The role of exchange coupling and spin s on the work output and the thermal efficiency is studied in detail. In addition, the engine operation is analyzed from the perspective of local work and efficiency. We develop a general formalism to explore local thermodynamics applicable to any coupled bipartite system. Our general framework allows for examination of local thermodynamics even when global parameters of the system are varied in thermodynamic cycles. The generalized definitions of local and cooperative work are introduced by using mean field Hamiltonians. The general conditions for which the global work is not equal to the sum of the local works are given in terms of the covariance of the subsystems. Our coupled spin quantum Otto engine is used as an example of the general formalism.

General formalism of local thermodynamics with an example: Quantum Otto engine with a spin-1 /2 coupled to an arbitrary spin

NASA Astrophysics Data System (ADS)

Altintas, Ferdi; Müstecaplıoǧlu, Ã.-zgür E.

2015-08-01

We investigate a quantum heat engine with a working substance of two particles, one with a spin-1 /2 and the other with an arbitrary spin (spin s ), coupled by Heisenberg exchange interaction, and subject to an external magnetic field. The engine operates in a quantum Otto cycle. Work harvested in the cycle and its efficiency are calculated using quantum thermodynamical definitions. It is found that the engine has higher efficiencies at higher spins and can harvest work at higher exchange interaction strengths. The role of exchange coupling and spin s on the work output and the thermal efficiency is studied in detail. In addition, the engine operation is analyzed from the perspective of local work and efficiency. We develop a general formalism to explore local thermodynamics applicable to any coupled bipartite system. Our general framework allows for examination of local thermodynamics even when global parameters of the system are varied in thermodynamic cycles. The generalized definitions of local and cooperative work are introduced by using mean field Hamiltonians. The general conditions for which the global work is not equal to the sum of the local works are given in terms of the covariance of the subsystems. Our coupled spin quantum Otto engine is used as an example of the general formalism.

Energy Efficiency Collaboratives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Michael; Bryson, Joe

2015-09-01

Collaboratives for energy efficiency have a long and successful history and are currently used, in some form, in more than half of the states. Historically, many state utility commissions have used some form of collaborative group process to resolve complex issues that emerge during a rate proceeding. Rather than debate the issues through the formality of a commission proceeding, disagreeing parties are sent to discuss issues in a less-formal setting and bring back resolutions to the commission. Energy efficiency collaboratives take this concept and apply it specifically to energy efficiency programs—often in anticipation of future issues as opposed to reactingmore » to a present disagreement. Energy efficiency collaboratives can operate long term and can address the full suite of issues associated with designing, implementing, and improving energy efficiency programs. Collaboratives can be useful to gather stakeholder input on changing program budgets and program changes in response to performance or market shifts, as well as to provide continuity while regulators come and go, identify additional energy efficiency opportunities and innovations, assess the role of energy efficiency in new regulatory contexts, and draw on lessons learned and best practices from a diverse group. Details about specific collaboratives in the United States are in the appendix to this guide. Collectively, they demonstrate the value of collaborative stakeholder processes in producing successful energy efficiency programs.« less

Software Design for Real-Time Systems on Parallel Computers: Formal Specifications.

DTIC Science & Technology

1996-04-01

This research investigated the important issues related to the analysis and design of real - time systems targeted to parallel architectures. In...particular, the software specification models for real - time systems on parallel architectures were evaluated. A survey of current formal methods for...uniprocessor real - time systems specifications was conducted to determine their extensibility in specifying real - time systems on parallel architectures. In

META-GLARE: A meta-system for defining your own computer interpretable guideline system-Architecture and acquisition.

PubMed

Bottrighi, Alessio; Terenziani, Paolo

2016-09-01

Several different computer-assisted management systems of computer interpretable guidelines (CIGs) have been developed by the Artificial Intelligence in Medicine community. Each CIG system is characterized by a specific formalism to represent CIGs, and usually provides a manager to acquire, consult and execute them. Though there are several commonalities between most formalisms in the literature, each formalism has its own peculiarities. The goal of our work is to provide a flexible support to the extension or definition of CIGs formalisms, and of their acquisition and execution engines. Instead of defining "yet another CIG formalism and its manager", we propose META-GLARE (META Guideline Acquisition, Representation, and Execution), a "meta"-system to define new CIG systems. In this paper, META-GLARE, a meta-system to define new CIG systems, is presented. We try to capture the commonalities among current CIG approaches, by providing (i) a general manager for the acquisition, consultation and execution of hierarchical graphs (representing the control flow of actions in CIGs), parameterized over the types of nodes and of arcs constituting it, and (ii) a library of different elementary components of guidelines nodes (actions) and arcs, in which each type definition involves the specification of how objects of this type can be acquired, consulted and executed. We provide generality and flexibility, by allowing free aggregations of such elementary components to define new primitive node and arc types. We have drawn several experiments, in which we have used META-GLARE to build a CIG system (Experiment 1 in Section 8), or to extend it (Experiments 2 and 3). Such experiments show that META-GLARE provides a useful and easy-to-use support to such tasks. For instance, re-building the Guideline Acquisition, Representation, and Execution (GLARE) system using META-GLARE required less than one day (Experiment 1). META-GLARE is a meta-system for CIGs supporting fast prototyping. Since META-GLARE provides acquisition and execution engines that are parametric over the specific CIG formalism, it supports easy update and construction of CIG systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Two-phase thermodynamic model for computing entropies of liquids reanalyzed

NASA Astrophysics Data System (ADS)

Sun, Tao; Xian, Jiawei; Zhang, Huai; Zhang, Zhigang; Zhang, Yigang

2017-11-01

The two-phase thermodynamic (2PT) model [S.-T. Lin et al., J. Chem. Phys. 119, 11792-11805 (2003)] provides a promising paradigm to efficiently determine the ionic entropies of liquids from molecular dynamics. In this model, the vibrational density of states (VDoS) of a liquid is decomposed into a diffusive gas-like component and a vibrational solid-like component. By treating the diffusive component as hard sphere (HS) gas and the vibrational component as harmonic oscillators, the ionic entropy of the liquid is determined. Here we examine three issues crucial for practical implementations of the 2PT model: (i) the mismatch between the VDoS of the liquid system and that of the HS gas; (ii) the excess entropy of the HS gas; (iii) the partition of the gas-like and solid-like components. Some of these issues have not been addressed before, yet they profoundly change the entropy predicted from the model. Based on these findings, a revised 2PT formalism is proposed and successfully tested in systems with Lennard-Jones potentials as well as many-atom potentials of liquid metals. Aside from being capable of performing quick entropy estimations for a wide range of systems, the formalism also supports fine-tuning to accurately determine entropies at specific thermal states.

Big questions, big science: meeting the challenges of global ecology.

PubMed

Schimel, David; Keller, Michael

2015-04-01

Ecologists are increasingly tackling questions that require significant infrastucture, large experiments, networks of observations, and complex data and computation. Key hypotheses in ecology increasingly require more investment, and larger data sets to be tested than can be collected by a single investigator's or s group of investigator's labs, sustained for longer than a typical grant. Large-scale projects are expensive, so their scientific return on the investment has to justify the opportunity cost-the science foregone because resources were expended on a large project rather than supporting a number of individual projects. In addition, their management must be accountable and efficient in the use of significant resources, requiring the use of formal systems engineering and project management to mitigate risk of failure. Mapping the scientific method into formal project management requires both scientists able to work in the context, and a project implementation team sensitive to the unique requirements of ecology. Sponsoring agencies, under pressure from external and internal forces, experience many pressures that push them towards counterproductive project management but a scientific community aware and experienced in large project science can mitigate these tendencies. For big ecology to result in great science, ecologists must become informed, aware and engaged in the advocacy and governance of large ecological projects.

Modeling Of Object- And Scene-Prototypes With Hierarchically Structured Classes

NASA Astrophysics Data System (ADS)

Ren, Z.; Jensch, P.; Ameling, W.

1989-03-01

The success of knowledge-based image analysis methodology and implementation tools depends largely on an appropriately and efficiently built model wherein the domain-specific context information about and the inherent structure of the observed image scene have been encoded. For identifying an object in an application environment a computer vision system needs to know firstly the description of the object to be found in an image or in an image sequence, secondly the corresponding relationships between object descriptions within the image sequence. This paper presents models of image objects scenes by means of hierarchically structured classes. Using the topovisual formalism of graph and higraph, we are currently studying principally the relational aspect and data abstraction of the modeling in order to visualize the structural nature resident in image objects and scenes, and to formalize. their descriptions. The goal is to expose the structure of image scene and the correspondence of image objects in the low level image interpretation. process. The object-based system design approach has been applied to build the model base. We utilize the object-oriented programming language C + + for designing, testing and implementing the abstracted entity classes and the operation structures which have been modeled topovisually. The reference images used for modeling prototypes of objects and scenes are from industrial environments as'well as medical applications.

Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Xujun; Li, Jiyuan; Jiang, Xikai

An efficient parallel Stokes’s solver is developed towards the complete inclusion of hydrodynamic interactions of Brownian particles in any geometry. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green’s function formalism. We present a scalable parallel computational approach, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the General geometry Ewald-like method. Our approach employs a highly-efficient iterative finite element Stokes’ solver for the accurate treatment of long-range hydrodynamic interactions within arbitrary confined geometries. A combination of mid-point time integration of the Brownian stochastic differential equation, the parallelmore » Stokes’ solver, and a Chebyshev polynomial approximation for the fluctuation-dissipation theorem result in an O(N) parallel algorithm. We also illustrate the new algorithm in the context of the dynamics of confined polymer solutions in equilibrium and non-equilibrium conditions. Our method is extended to treat suspended finite size particles of arbitrary shape in any geometry using an Immersed Boundary approach.« less

Efficient evaluation of nonlocal operators in density functional theory

NASA Astrophysics Data System (ADS)

Chen, Ying-Chih; Chen, Jing-Zhe; Michaud-Rioux, Vincent; Shi, Qing; Guo, Hong

2018-02-01

We present a method which combines plane waves (PW) and numerical atomic orbitals (NAO) to efficiently evaluate nonlocal operators in density functional theory with periodic boundary conditions. Nonlocal operators are first expanded using PW and then transformed to NAO so that the problem of distance-truncation is avoided. The general formalism is implemented using the hybrid functional HSE06 where the nonlocal operator is the exact exchange. Comparison of electronic structures of a wide range of semiconductors to a pure PW scheme validates the accuracy of our method. Due to the locality of NAO, thus sparsity of matrix representations of the operators, the computational complexity of the method is asymptotically quadratic in the number of electrons. Finally, we apply the technique to investigate the electronic structure of the interface between a single-layer black phosphorous and the high-κ dielectric material c -HfO2 . We predict that the band offset between the two materials is 1.29 eV and 2.18 eV for valence and conduction band edges, respectively, and such offsets are suitable for 2D field-effect transistor applications.

Formal and heuristic system decomposition methods in multidisciplinary synthesis. Ph.D. Thesis, 1991

NASA Technical Reports Server (NTRS)

Bloebaum, Christina L.

1991-01-01

The multidisciplinary interactions which exist in large scale engineering design problems provide a unique set of difficulties. These difficulties are associated primarily with unwieldy numbers of design variables and constraints, and with the interdependencies of the discipline analysis modules. Such obstacles require design techniques which account for the inherent disciplinary couplings in the analyses and optimizations. The objective of this work was to develop an efficient holistic design synthesis methodology that takes advantage of the synergistic nature of integrated design. A general decomposition approach for optimization of large engineering systems is presented. The method is particularly applicable for multidisciplinary design problems which are characterized by closely coupled interactions among discipline analyses. The advantage of subsystem modularity allows for implementation of specialized methods for analysis and optimization, computational efficiency, and the ability to incorporate human intervention and decision making in the form of an expert systems capability. The resulting approach is not a method applicable to only a specific situation, but rather, a methodology which can be used for a large class of engineering design problems in which the system is non-hierarchic in nature.

On delay adjustment for dynamic load balancing in distributed virtual environments.

PubMed

Deng, Yunhua; Lau, Rynson W H

2012-04-01

Distributed virtual environments (DVEs) are becoming very popular in recent years, due to the rapid growing of applications, such as massive multiplayer online games (MMOGs). As the number of concurrent users increases, scalability becomes one of the major challenges in designing an interactive DVE system. One solution to address this scalability problem is to adopt a multi-server architecture. While some methods focus on the quality of partitioning the load among the servers, others focus on the efficiency of the partitioning process itself. However, all these methods neglect the effect of network delay among the servers on the accuracy of the load balancing solutions. As we show in this paper, the change in the load of the servers due to network delay would affect the performance of the load balancing algorithm. In this work, we conduct a formal analysis of this problem and discuss two efficient delay adjustment schemes to address the problem. Our experimental results show that our proposed schemes can significantly improve the performance of the load balancing algorithm with neglectable computation overhead.

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

PubMed Central

Chevalier, Michael W.; El-Samad, Hana

2014-01-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled. PMID:25481130

A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics

NASA Astrophysics Data System (ADS)

Byun, Hye Suk; El-Naggar, Mohamed Y.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2017-10-01

Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

NASA Astrophysics Data System (ADS)

Chevalier, Michael W.; El-Samad, Hana

2014-12-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.

Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries

DOE PAGES

Zhao, Xujun; Li, Jiyuan; Jiang, Xikai; ...

2017-06-29

An efficient parallel Stokes’s solver is developed towards the complete inclusion of hydrodynamic interactions of Brownian particles in any geometry. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green’s function formalism. We present a scalable parallel computational approach, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the General geometry Ewald-like method. Our approach employs a highly-efficient iterative finite element Stokes’ solver for the accurate treatment of long-range hydrodynamic interactions within arbitrary confined geometries. A combination of mid-point time integration of the Brownian stochastic differential equation, the parallelmore » Stokes’ solver, and a Chebyshev polynomial approximation for the fluctuation-dissipation theorem result in an O(N) parallel algorithm. We also illustrate the new algorithm in the context of the dynamics of confined polymer solutions in equilibrium and non-equilibrium conditions. Our method is extended to treat suspended finite size particles of arbitrary shape in any geometry using an Immersed Boundary approach.« less

An Efficient numerical method to calculate the conductivity tensor for disordered topological matter

NASA Astrophysics Data System (ADS)

Garcia, Jose H.; Covaci, Lucian; Rappoport, Tatiana G.

2015-03-01

We propose a new efficient numerical approach to calculate the conductivity tensor in solids. We use a real-space implementation of the Kubo formalism where both diagonal and off-diagonal conductivities are treated in the same footing. We adopt a formulation of the Kubo theory that is known as Bastin formula and expand the Green's functions involved in terms of Chebyshev polynomials using the kernel polynomial method. Within this method, all the computational effort is on the calculation of the expansion coefficients. It also has the advantage of obtaining both conductivities in a single calculation step and for various values of temperature and chemical potential, capturing the topology of the band-structure. Our numerical technique is very general and is suitable for the calculation of transport properties of disordered systems. We analyze how the method's accuracy varies with the number of moments used in the expansion and illustrate our approach by calculating the transverse conductivity of different topological systems. T.G.R, J.H.G and L.C. acknowledge Brazilian agencies CNPq, FAPERJ and INCT de Nanoestruturas de Carbono, Flemish Science Foundation for financial support.

An efficient method of reducing glass dispersion tolerance sensitivity

NASA Astrophysics Data System (ADS)

Sparrold, Scott W.; Shepard, R. Hamilton

2014-12-01

Constraining the Seidel aberrations of optical surfaces is a common technique for relaxing tolerance sensitivities in the optimization process. We offer an observation that a lens's Abbe number tolerance is directly related to the magnitude by which its longitudinal and transverse color are permitted to vary in production. Based on this observation, we propose a computationally efficient and easy-to-use merit function constraint for relaxing dispersion tolerance sensitivity. Using the relationship between an element's chromatic aberration and dispersion sensitivity, we derive a fundamental limit for lens scale and power that is capable of achieving high production yield for a given performance specification, which provides insight on the point at which lens splitting or melt fitting becomes necessary. The theory is validated by comparing its predictions to a formal tolerance analysis of a Cooke Triplet, and then applied to the design of a 1.5x visible linescan lens to illustrate optimization for reduced dispersion sensitivity. A selection of lenses in high volume production is then used to corroborate the proposed method of dispersion tolerance allocation.

A Secure and Robust User Authenticated Key Agreement Scheme for Hierarchical Multi-medical Server Environment in TMIS.

PubMed

Das, Ashok Kumar; Odelu, Vanga; Goswami, Adrijit

2015-09-01

The telecare medicine information system (TMIS) helps the patients to gain the health monitoring facility at home and access medical services over the Internet of mobile networks. Recently, Amin and Biswas presented a smart card based user authentication and key agreement security protocol usable for TMIS system using the cryptographic one-way hash function and biohashing function, and claimed that their scheme is secure against all possible attacks. Though their scheme is efficient due to usage of one-way hash function, we show that their scheme has several security pitfalls and design flaws, such as (1) it fails to protect privileged-insider attack, (2) it fails to protect strong replay attack, (3) it fails to protect strong man-in-the-middle attack, (4) it has design flaw in user registration phase, (5) it has design flaw in login phase, (6) it has design flaw in password change phase, (7) it lacks of supporting biometric update phase, and (8) it has flaws in formal security analysis. In order to withstand these security pitfalls and design flaws, we aim to propose a secure and robust user authenticated key agreement scheme for the hierarchical multi-server environment suitable in TMIS using the cryptographic one-way hash function and fuzzy extractor. Through the rigorous security analysis including the formal security analysis using the widely-accepted Burrows-Abadi-Needham (BAN) logic, the formal security analysis under the random oracle model and the informal security analysis, we show that our scheme is secure against possible known attacks. Furthermore, we simulate our scheme using the most-widely accepted and used Automated Validation of Internet Security Protocols and Applications (AVISPA) tool. The simulation results show that our scheme is also secure. Our scheme is more efficient in computation and communication as compared to Amin-Biswas's scheme and other related schemes. In addition, our scheme supports extra functionality features as compared to other related schemes. As a result, our scheme is very appropriate for practical applications in TMIS.

Analytic and Computational Perspectives of Multi-Scale Theory for Homogeneous, Laminated Composite, and Sandwich Beams and Plates

NASA Technical Reports Server (NTRS)

Tessler, Alexander; Gherlone, Marco; Versino, Daniele; DiSciuva, Marco

2012-01-01

This paper reviews the theoretical foundation and computational mechanics aspects of the recently developed shear-deformation theory, called the Refined Zigzag Theory (RZT). The theory is based on a multi-scale formalism in which an equivalent single-layer plate theory is refined with a robust set of zigzag local layer displacements that are free of the usual deficiencies found in common plate theories with zigzag kinematics. In the RZT, first-order shear-deformation plate theory is used as the equivalent single-layer plate theory, which represents the overall response characteristics. Local piecewise-linear zigzag displacements are used to provide corrections to these overall response characteristics that are associated with the plate heterogeneity and the relative stiffnesses of the layers. The theory does not rely on shear correction factors and is equally accurate for homogeneous, laminated composite, and sandwich beams and plates. Regardless of the number of material layers, the theory maintains only seven kinematic unknowns that describe the membrane, bending, and transverse shear plate-deformation modes. Derived from the virtual work principle, RZT is well-suited for developing computationally efficient, C(sup 0)-continuous finite elements; formulations of several RZT-based elements are highlighted. The theory and its finite element approximations thus provide a unified and reliable computational platform for the analysis and design of high-performance load-bearing aerospace structures.

Gaussianization for fast and accurate inference from cosmological data

NASA Astrophysics Data System (ADS)

Schuhmann, Robert L.; Joachimi, Benjamin; Peiris, Hiranya V.

2016-06-01

We present a method to transform multivariate unimodal non-Gaussian posterior probability densities into approximately Gaussian ones via non-linear mappings, such as Box-Cox transformations and generalizations thereof. This permits an analytical reconstruction of the posterior from a point sample, like a Markov chain, and simplifies the subsequent joint analysis with other experiments. This way, a multivariate posterior density can be reported efficiently, by compressing the information contained in Markov Chain Monte Carlo samples. Further, the model evidence integral (I.e. the marginal likelihood) can be computed analytically. This method is analogous to the search for normal parameters in the cosmic microwave background, but is more general. The search for the optimally Gaussianizing transformation is performed computationally through a maximum-likelihood formalism; its quality can be judged by how well the credible regions of the posterior are reproduced. We demonstrate that our method outperforms kernel density estimates in this objective. Further, we select marginal posterior samples from Planck data with several distinct strongly non-Gaussian features, and verify the reproduction of the marginal contours. To demonstrate evidence computation, we Gaussianize the joint distribution of data from weak lensing and baryon acoustic oscillations, for different cosmological models, and find a preference for flat Λcold dark matter. Comparing to values computed with the Savage-Dickey density ratio, and Population Monte Carlo, we find good agreement of our method within the spread of the other two.

Analytic and Computational Perspectives of Multi-Scale Theory for Homogeneous, Laminated Composite, and Sandwich Beams and Plates

NASA Technical Reports Server (NTRS)

Tessler, Alexander; Gherlone, Marco; Versino, Daniele; Di Sciuva, Marco

2012-01-01

This paper reviews the theoretical foundation and computational mechanics aspects of the recently developed shear-deformation theory, called the Refined Zigzag Theory (RZT). The theory is based on a multi-scale formalism in which an equivalent single-layer plate theory is refined with a robust set of zigzag local layer displacements that are free of the usual deficiencies found in common plate theories with zigzag kinematics. In the RZT, first-order shear-deformation plate theory is used as the equivalent single-layer plate theory, which represents the overall response characteristics. Local piecewise-linear zigzag displacements are used to provide corrections to these overall response characteristics that are associated with the plate heterogeneity and the relative stiffnesses of the layers. The theory does not rely on shear correction factors and is equally accurate for homogeneous, laminated composite, and sandwich beams and plates. Regardless of the number of material layers, the theory maintains only seven kinematic unknowns that describe the membrane, bending, and transverse shear plate-deformation modes. Derived from the virtual work principle, RZT is well-suited for developing computationally efficient, C0-continuous finite elements; formulations of several RZT-based elements are highlighted. The theory and its finite elements provide a unified and reliable computational platform for the analysis and design of high-performance load-bearing aerospace structures.

Mechanisms of Developmental Change in Infant Categorization

ERIC Educational Resources Information Center

Westermann, Gert; Mareschal, Denis

2012-01-01

Computational models are tools for testing mechanistic theories of learning and development. Formal models allow us to instantiate theories of cognitive development in computer simulations. Model behavior can then be compared to real performance. Connectionist models, loosely based on neural information processing, have been successful in…

Trust models in ubiquitous computing.

PubMed

Krukow, Karl; Nielsen, Mogens; Sassone, Vladimiro

2008-10-28

We recapture some of the arguments for trust-based technologies in ubiquitous computing, followed by a brief survey of some of the models of trust that have been introduced in this respect. Based on this, we argue for the need of more formal and foundational trust models.

A Formally-Verified Decision Procedure for Univariate Polynomial Computation Based on Sturm's Theorem

NASA Technical Reports Server (NTRS)

Narkawicz, Anthony J.; Munoz, Cesar A.

2014-01-01

Sturm's Theorem is a well-known result in real algebraic geometry that provides a function that computes the number of roots of a univariate polynomial in a semiopen interval. This paper presents a formalization of this theorem in the PVS theorem prover, as well as a decision procedure that checks whether a polynomial is always positive, nonnegative, nonzero, negative, or nonpositive on any input interval. The soundness and completeness of the decision procedure is proven in PVS. The procedure and its correctness properties enable the implementation of a PVS strategy for automatically proving existential and universal univariate polynomial inequalities. Since the decision procedure is formally verified in PVS, the soundness of the strategy depends solely on the internal logic of PVS rather than on an external oracle. The procedure itself uses a combination of Sturm's Theorem, an interval bisection procedure, and the fact that a polynomial with exactly one root in a bounded interval is always nonnegative on that interval if and only if it is nonnegative at both endpoints.

A Formal Model of Partitioning for Integrated Modular Avionics

NASA Technical Reports Server (NTRS)

DiVito, Ben L.

1998-01-01

The aviation industry is gradually moving toward the use of integrated modular avionics (IMA) for civilian transport aircraft. An important concern for IMA is ensuring that applications are safely partitioned so they cannot interfere with one another. We have investigated the problem of ensuring safe partitioning and logical non-interference among separate applications running on a shared Avionics Computer Resource (ACR). This research was performed in the context of ongoing standardization efforts, in particular, the work of RTCA committee SC-182, and the recently completed ARINC 653 application executive (APEX) interface standard. We have developed a formal model of partitioning suitable for evaluating the design of an ACR. The model draws from the mathematical modeling techniques developed by the computer security community. This report presents a formulation of partitioning requirements expressed first using conventional mathematical notation, then formalized using the language of SRI'S Prototype Verification System (PVS). The approach is demonstrated on three candidate designs, each an abstraction of features found in real systems.

Software Safety Risk in Legacy Safety-Critical Computer Systems

NASA Technical Reports Server (NTRS)

Hill, Janice; Baggs, Rhoda

2007-01-01

Safety-critical computer systems must be engineered to meet system and software safety requirements. For legacy safety-critical computer systems, software safety requirements may not have been formally specified during development. When process-oriented software safety requirements are levied on a legacy system after the fact, where software development artifacts don't exist or are incomplete, the question becomes 'how can this be done?' The risks associated with only meeting certain software safety requirements in a legacy safety-critical computer system must be addressed should such systems be selected as candidates for reuse. This paper proposes a method for ascertaining formally, a software safety risk assessment, that provides measurements for software safety for legacy systems which may or may not have a suite of software engineering documentation that is now normally required. It relies upon the NASA Software Safety Standard, risk assessment methods based upon the Taxonomy-Based Questionnaire, and the application of reverse engineering CASE tools to produce original design documents for legacy systems.

Marr's levels and the minimalist program.

PubMed

Johnson, Mark

2017-02-01

A simple change to a cognitive system at Marr's computational level may entail complex changes at the other levels of description of the system. The implementational level complexity of a change, rather than its computational level complexity, may be more closely related to the plausibility of a discrete evolutionary event causing that change. Thus the formal complexity of a change at the computational level may not be a good guide to the plausibility of an evolutionary event introducing that change. For example, while the Minimalist Program's Merge is a simple formal operation (Berwick & Chomsky, 2016), the computational mechanisms required to implement the language it generates (e.g., to parse the language) may be considerably more complex. This has implications for the theory of grammar: theories of grammar which involve several kinds of syntactic operations may be no less evolutionarily plausible than a theory of grammar that involves only one. A deeper understanding of human language at the algorithmic and implementational levels could strengthen Minimalist Program's account of the evolution of language.

SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory

NASA Astrophysics Data System (ADS)

Guo, Yang; Sivalingam, Kantharuban; Valeev, Edward F.; Neese, Frank

2016-03-01

Multi-reference (MR) electronic structure methods, such as MR configuration interaction or MR perturbation theory, can provide reliable energies and properties for many molecular phenomena like bond breaking, excited states, transition states or magnetic properties of transition metal complexes and clusters. However, owing to their inherent complexity, most MR methods are still too computationally expensive for large systems. Therefore the development of more computationally attractive MR approaches is necessary to enable routine application for large-scale chemical systems. Among the state-of-the-art MR methods, second-order N-electron valence state perturbation theory (NEVPT2) is an efficient, size-consistent, and intruder-state-free method. However, there are still two important bottlenecks in practical applications of NEVPT2 to large systems: (a) the high computational cost of NEVPT2 for large molecules, even with moderate active spaces and (b) the prohibitive cost for treating large active spaces. In this work, we address problem (a) by developing a linear scaling "partially contracted" NEVPT2 method. This development uses the idea of domain-based local pair natural orbitals (DLPNOs) to form a highly efficient algorithm. As shown previously in the framework of single-reference methods, the DLPNO concept leads to an enormous reduction in computational effort while at the same time providing high accuracy (approaching 99.9% of the correlation energy), robustness, and black-box character. In the DLPNO approach, the virtual space is spanned by pair natural orbitals that are expanded in terms of projected atomic orbitals in large orbital domains, while the inactive space is spanned by localized orbitals. The active orbitals are left untouched. Our implementation features a highly efficient "electron pair prescreening" that skips the negligible inactive pairs. The surviving pairs are treated using the partially contracted NEVPT2 formalism. A detailed comparison between the partial and strong contraction schemes is made, with conclusions that discourage the strong contraction scheme as a basis for local correlation methods due to its non-invariance with respect to rotations in the inactive and external subspaces. A minimal set of conservatively chosen truncation thresholds controls the accuracy of the method. With the default thresholds, about 99.9% of the canonical partially contracted NEVPT2 correlation energy is recovered while the crossover of the computational cost with the already very efficient canonical method occurs reasonably early; in linear chain type compounds at a chain length of around 80 atoms. Calculations are reported for systems with more than 300 atoms and 5400 basis functions.

Engaging Scientists in NASA Education and Public Outreach: K - 12 Formal Education

NASA Astrophysics Data System (ADS)

Bartolone, Lindsay; Smith, D. A.; Eisenhamer, B.; Lawton, B. L.; Universe Professional Development Collaborative, Multiwavelength; NASA Data Collaborative, Use of; SEPOF K-12 Formal Education Working Group; E/PO Community, SMD

2014-01-01

The NASA Science Education and Public Outreach Forums support the NASA Science Mission Directorate (SMD) and its education and public outreach (E/PO) community through a coordinated effort to enhance the coherence and efficiency of SMD-funded E/PO programs. The Forums foster collaboration between scientists with content expertise and educators with pedagogy expertise. We present opportunities for the astronomy community to participate in collaborations supporting the NASA SMD efforts in the K - 12 Formal Education community. Members of the K - 12 Formal Education community include classroom educators, homeschool educators, students, and curriculum developers. The Forums’ efforts for the K - 12 Formal Education community include a literature review, appraisal of educators’ needs, coordination of audience-based NASA resources and opportunities, professional development, and support with the Next Generation Science Standards. Learn how to join in our collaborative efforts to support the K - 12 Formal Education community based upon mutual needs and interests.

Computer Experiments in Transformational Grammar; French I. Department of Computer and Communication Sciences Natural Language Studies No. 3.

ERIC Educational Resources Information Center

Morin, Yves Ch.

Described in this paper is the implementation of Querido's French grammar ("Grammaire I, Description transformationelle d'un sous-ensemble du Francais," 1969) on the computer system for transformational grammar at the University of Michigan (Friedman 1969). The purpose was to demonstrate the ease of transcribing a relative formal grammar into the…

Evaluating a Computational Model of Social Causality and Responsibility

DTIC Science & Technology

2006-01-01

Evaluating a Computational Model of Social Causality and Responsibility Wenji Mao University of Southern California Institute for Creative...empirically evaluate a computa- tional model of social causality and responsibility against human social judgments. Results from our experimental...developed a general computational model of social cau- sality and responsibility [10, 11] that formalizes the factors people use in reasoning about

A formal approach to the analysis of clinical computer-interpretable guideline modeling languages.

PubMed

Grando, M Adela; Glasspool, David; Fox, John

2012-01-01

To develop proof strategies to formally study the expressiveness of workflow-based languages, and to investigate their applicability to clinical computer-interpretable guideline (CIG) modeling languages. We propose two strategies for studying the expressiveness of workflow-based languages based on a standard set of workflow patterns expressed as Petri nets (PNs) and notions of congruence and bisimilarity from process calculus. Proof that a PN-based pattern P can be expressed in a language L can be carried out semi-automatically. Proof that a language L cannot provide the behavior specified by a PNP requires proof by exhaustion based on analysis of cases and cannot be performed automatically. The proof strategies are generic but we exemplify their use with a particular CIG modeling language, PROforma. To illustrate the method we evaluate the expressiveness of PROforma against three standard workflow patterns and compare our results with a previous similar but informal comparison. We show that the two proof strategies are effective in evaluating a CIG modeling language against standard workflow patterns. We find that using the proposed formal techniques we obtain different results to a comparable previously published but less formal study. We discuss the utility of these analyses as the basis for principled extensions to CIG modeling languages. Additionally we explain how the same proof strategies can be reused to prove the satisfaction of patterns expressed in the declarative language CIGDec. The proof strategies we propose are useful tools for analysing the expressiveness of CIG modeling languages. This study provides good evidence of the benefits of applying formal methods of proof over semi-formal ones. Copyright © 2011 Elsevier B.V. All rights reserved.

iGen: An automated generator of simplified models with provable error bounds.

NASA Astrophysics Data System (ADS)

Tang, D.; Dobbie, S.

2009-04-01

Climate models employ various simplifying assumptions and parameterisations in order to increase execution speed. However, in order to draw conclusions about the Earths climate from the results of a climate simulation it is necessary to have information about the error that these assumptions and parameterisations introduce. A novel computer program, called iGen, is being developed which automatically generates fast, simplified models by analysing the source code of a slower, high resolution model. The resulting simplified models have provable bounds on error compared to the high resolution model and execute at speeds that are typically orders of magnitude faster. iGen's input is a definition of the prognostic variables of the simplified model, a set of bounds on acceptable error and the source code of a model that captures the behaviour of interest. In the case of an atmospheric model, for example, this would be a global cloud resolving model with very high resolution. Although such a model would execute far too slowly to be used directly in a climate model, iGen never executes it. Instead, it converts the code of the resolving model into a mathematical expression which is then symbolically manipulated and approximated to form a simplified expression. This expression is then converted back into a computer program and output as a simplified model. iGen also derives and reports formal bounds on the error of the simplified model compared to the resolving model. These error bounds are always maintained below the user-specified acceptable error. Results will be presented illustrating the success of iGen's analysis of a number of example models. These extremely encouraging results have lead on to work which is currently underway to analyse a cloud resolving model and so produce an efficient parameterisation of moist convection with formally bounded error.

COSMOS: Python library for massively parallel workflows

PubMed Central

Gafni, Erik; Luquette, Lovelace J.; Lancaster, Alex K.; Hawkins, Jared B.; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P.; Tonellato, Peter J.

2014-01-01

Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Availability and implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. Contact: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24982428

Spectral properties from Matsubara Green's function approach: Application to molecules

NASA Astrophysics Data System (ADS)

Schüler, M.; Pavlyukh, Y.

2018-03-01

We present results for many-body perturbation theory for the one-body Green's function at finite temperatures using the Matsubara formalism. Our method relies on the accurate representation of the single-particle states in standard Gaussian basis sets, allowing to efficiently compute, among other observables, quasiparticle energies and Dyson orbitals of atoms and molecules. In particular, we challenge the second-order treatment of the Coulomb interaction by benchmarking its accuracy for a well-established test set of small molecules, which includes also systems where the usual Hartree-Fock treatment encounters difficulties. We discuss different schemes how to extract quasiparticle properties and assess their range of applicability. With an accurate solution and compact representation, our method is an ideal starting point to study electron dynamics in time-resolved experiments by the propagation of the Kadanoff-Baym equations.

Controllability of Surface Water Networks

NASA Astrophysics Data System (ADS)

Riasi, M. Sadegh; Yeghiazarian, Lilit

2017-12-01

To sustainably manage water resources, we must understand how to control complex networked systems. In this paper, we study surface water networks from the perspective of structural controllability, a concept that integrates classical control theory with graph-theoretic formalism. We present structural controllability theory and compute four metrics: full and target controllability, control centrality and control profile (FTCP) that collectively determine the structural boundaries of the system's control space. We use these metrics to answer the following questions: How does the structure of a surface water network affect its controllability? How to efficiently control a preselected subset of the network? Which nodes have the highest control power? What types of topological structures dominate controllability? Finally, we demonstrate the structural controllability theory in the analysis of a wide range of surface water networks, such as tributary, deltaic, and braided river systems.

COSMOS: Python library for massively parallel workflows.

PubMed

Gafni, Erik; Luquette, Lovelace J; Lancaster, Alex K; Hawkins, Jared B; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P; Tonellato, Peter J

2014-10-15

Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Applying the Network Simulation Method for testing chaos in a resistively and capacitively shunted Josephson junction model

NASA Astrophysics Data System (ADS)

Bellver, Fernando Gimeno; Garratón, Manuel Caravaca; Soto Meca, Antonio; López, Juan Antonio Vera; Guirao, Juan L. G.; Fernández-Martínez, Manuel

In this paper, we explore the chaotic behavior of resistively and capacitively shunted Josephson junctions via the so-called Network Simulation Method. Such a numerical approach establishes a formal equivalence among physical transport processes and electrical networks, and hence, it can be applied to efficiently deal with a wide range of differential systems. The generality underlying that electrical equivalence allows to apply the circuit theory to several scientific and technological problems. In this work, the Fast Fourier Transform has been applied for chaos detection purposes and the calculations have been carried out in PSpice, an electrical circuit software. Overall, it holds that such a numerical approach leads to quickly computationally solve Josephson differential models. An empirical application regarding the study of the Josephson model completes the paper.

Extended phase graphs with anisotropic diffusion

NASA Astrophysics Data System (ADS)

Weigel, M.; Schwenk, S.; Kiselev, V. G.; Scheffler, K.; Hennig, J.

2010-08-01

The extended phase graph (EPG) calculus gives an elegant pictorial description of magnetization response in multi-pulse MR sequences. The use of the EPG calculus enables a high computational efficiency for the quantitation of echo intensities even for complex sequences with multiple refocusing pulses with arbitrary flip angles. In this work, the EPG concept dealing with RF pulses with arbitrary flip angles and phases is extended to account for anisotropic diffusion in the presence of arbitrary varying gradients. The diffusion effect can be expressed by specific diffusion weightings of individual magnetization pathways. This can be represented as an action of a linear operator on the magnetization state. The algorithm allows easy integration of diffusion anisotropy effects. The formalism is validated on known examples from literature and used to calculate the effective diffusion weighting in multi-echo sequences with arbitrary refocusing flip angles.

Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation.

PubMed

Kühn, Michael; Weigend, Florian

2015-01-21

We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy)3 (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its "spin-forbidden" triplet-singlet transition.

Elementary solutions of coupled model equations in the kinetic theory of gases

NASA Technical Reports Server (NTRS)

Kriese, J. T.; Siewert, C. E.; Chang, T. S.

1974-01-01

The method of elementary solutions is employed to solve two coupled integrodifferential equations sufficient for determining temperature-density effects in a linearized BGK model in the kinetic theory of gases. Full-range completeness and orthogonality theorems are proved for the developed normal modes and the infinite-medium Green's function is constructed as an illustration of the full-range formalism. The appropriate homogeneous matrix Riemann problem is discussed, and half-range completeness and orthogonality theorems are proved for a certain subset of the normal modes. The required existence and uniqueness theorems relevant to the H matrix, basic to the half-range analysis, are proved, and an accurate and efficient computational method is discussed. The half-space temperature-slip problem is solved analytically, and a highly accurate value of the temperature-slip coefficient is reported.

Computer Software for Intelligent Systems.

ERIC Educational Resources Information Center

Lenat, Douglas B.

1984-01-01

Discusses the development and nature of computer software for intelligent systems, indicating that the key to intelligent problem-solving lies in reducing the random search for solutions. Formal reasoning methods, expert systems, and sources of power in problem-solving are among the areas considered. Specific examples of such software are…

Modeling formalisms in Systems Biology

PubMed Central

2011-01-01

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

Evaluation of light extraction efficiency for the light-emitting diodes based on the transfer matrix formalism and ray-tracing method

NASA Astrophysics Data System (ADS)

Pingbo, An; Li, Wang; Hongxi, Lu; Zhiguo, Yu; Lei, Liu; Xin, Xi; Lixia, Zhao; Junxi, Wang; Jinmin, Li

2016-06-01

The internal quantum efficiency (IQE) of the light-emitting diodes can be calculated by the ratio of the external quantum efficiency (EQE) and the light extraction efficiency (LEE). The EQE can be measured experimentally, but the LEE is difficult to calculate due to the complicated LED structures. In this work, a model was established to calculate the LEE by combining the transfer matrix formalism and an in-plane ray tracing method. With the calculated LEE, the IQE was determined and made a good agreement with that obtained by the ABC model and temperature-dependent photoluminescence method. The proposed method makes the determination of the IQE more practical and conventional. Project supported by the National Natural Science Foundation of China (Nos.11574306, 61334009), the China International Science and Technology Cooperation Program (No. 2014DFG62280), and the National High Technology Program of China (No. 2015AA03A101).

Publication Bias in Methodological Computational Research.

PubMed

Boulesteix, Anne-Laure; Stierle, Veronika; Hapfelmeier, Alexander

2015-01-01

The problem of publication bias has long been discussed in research fields such as medicine. There is a consensus that publication bias is a reality and that solutions should be found to reduce it. In methodological computational research, including cancer informatics, publication bias may also be at work. The publication of negative research findings is certainly also a relevant issue, but has attracted very little attention to date. The present paper aims at providing a new formal framework to describe the notion of publication bias in the context of methodological computational research, facilitate and stimulate discussions on this topic, and increase awareness in the scientific community. We report an exemplary pilot study that aims at gaining experiences with the collection and analysis of information on unpublished research efforts with respect to publication bias, and we outline the encountered problems. Based on these experiences, we try to formalize the notion of publication bias.

Formal Representations of Eligibility Criteria: A Literature Review

PubMed Central

Weng, Chunhua; Tu, Samson W.; Sim, Ida; Richesson, Rachel

2010-01-01

Standards-based, computable knowledge representations for eligibility criteria are increasingly needed to provide computer-based decision support for automated research participant screening, clinical evidence application, and clinical research knowledge management. We surveyed the literature and identified five aspects of eligibility criteria knowledge representations that contribute to the various research and clinical applications: the intended use of computable eligibility criteria, the classification of eligibility criteria, the expression language for representing eligibility rules, the encoding of eligibility concepts, and the modeling of patient data. We consider three of them (expression language, codification of eligibility concepts, and patient data modeling), to be essential constructs of a formal knowledge representation for eligibility criteria. The requirements for each of the three knowledge constructs vary for different use cases, which therefore should inform the development and choice of the constructs toward cost-effective knowledge representation efforts. We discuss the implications of our findings for standardization efforts toward sharable knowledge representation of eligibility criteria. PMID:20034594

Modeling the fusion of cylindrical bioink particles in post bioprinting structure formation

NASA Astrophysics Data System (ADS)

McCune, Matt; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

2015-03-01

Cellular Particle Dynamics (CPD) is an effective computational method to describe the shape evolution and biomechanical relaxation processes in multicellular systems. Thus, CPD is a useful tool to predict the outcome of post-printing structure formation in bioprinting. The predictive power of CPD has been demonstrated for multicellular systems composed of spherical bioink units. Experiments and computer simulations were related through an independently developed theoretical formalism based on continuum mechanics. Here we generalize the CPD formalism to (i) include cylindrical bioink particles often used in specific bioprinting applications, (ii) describe the more realistic experimental situation in which both the length and the volume of the cylindrical bioink units decrease during post-printing structure formation, and (iii) directly connect CPD simulations to the corresponding experiments without the need of the intermediate continuum theory inherently based on simplifying assumptions. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

Non-standard analysis and embedded software

NASA Technical Reports Server (NTRS)

Platek, Richard

1995-01-01

One model for computing in the future is ubiquitous, embedded computational devices analogous to embedded electrical motors. Many of these computers will control physical objects and processes. Such hidden computerized environments introduce new safety and correctness concerns whose treatment go beyond present Formal Methods. In particular, one has to begin to speak about Real Space software in analogy with Real Time software. By this we mean, computerized systems which have to meet requirements expressed in the real geometry of space. How to translate such requirements into ordinary software specifications and how to carry out proofs is a major challenge. In this talk we propose a research program based on the use of no-standard analysis. Much detail remains to be carried out. The purpose of the talk is to inform the Formal Methods community that Non-Standard Analysis provides a possible avenue to attack which we believe will be fruitful.

Products of composite operators in the exact renormalization group formalism

NASA Astrophysics Data System (ADS)

Pagani, C.; Sonoda, H.

2018-02-01

We discuss a general method of constructing the products of composite operators using the exact renormalization group formalism. Considering mainly the Wilson action at a generic fixed point of the renormalization group, we give an argument for the validity of short-distance expansions of operator products. We show how to compute the expansion coefficients by solving differential equations, and test our method with some simple examples.

Discrete mathematics, formal methods, the Z schema and the software life cycle

NASA Technical Reports Server (NTRS)

Bown, Rodney L.

1991-01-01

The proper role and scope for the use of discrete mathematics and formal methods in support of engineering the security and integrity of components within deployed computer systems are discussed. It is proposed that the Z schema can be used as the specification language to capture the precise definition of system and component interfaces. This can be accomplished with an object oriented development paradigm.

On the Accuracy and Parallelism of GPGPU-Powered Incremental Clustering Algorithms

PubMed Central

He, Li; Zheng, Hao; Wang, Lei

2017-01-01

Incremental clustering algorithms play a vital role in various applications such as massive data analysis and real-time data processing. Typical application scenarios of incremental clustering raise high demand on computing power of the hardware platform. Parallel computing is a common solution to meet this demand. Moreover, General Purpose Graphic Processing Unit (GPGPU) is a promising parallel computing device. Nevertheless, the incremental clustering algorithm is facing a dilemma between clustering accuracy and parallelism when they are powered by GPGPU. We formally analyzed the cause of this dilemma. First, we formalized concepts relevant to incremental clustering like evolving granularity. Second, we formally proved two theorems. The first theorem proves the relation between clustering accuracy and evolving granularity. Additionally, this theorem analyzes the upper and lower bounds of different-to-same mis-affiliation. Fewer occurrences of such mis-affiliation mean higher accuracy. The second theorem reveals the relation between parallelism and evolving granularity. Smaller work-depth means superior parallelism. Through the proofs, we conclude that accuracy of an incremental clustering algorithm is negatively related to evolving granularity while parallelism is positively related to the granularity. Thus the contradictory relations cause the dilemma. Finally, we validated the relations through a demo algorithm. Experiment results verified theoretical conclusions. PMID:29123546

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, A.; Tsiounis, Y.; Frankel, Y.

Recently, there has been an interest in making electronic cash protocols more practical for electronic commerce by developing e-cash which is divisible (e.g., a coin which can be spent incrementally but total purchases are limited to the monetary value of the coin). In Crypto`95, T. Okamoto presented the first practical divisible, untraceable, off-line e-cash scheme, which requires only O(log N) computations for each of the withdrawal, payment and deposit procedures, where N = (total coin value)/(smallest divisible unit). However, Okamoto`s set-up procedure is quite inefficient (on the order of 4,000 multi-exponentiations and depending on the size of the RSA modulus).more » The authors formalize the notion of range-bounded commitment, originally used in Okamoto`s account establishment protocol, and present a very efficient instantiation which allows one to construct the first truly efficient divisible e-cash system. The scheme only requires the equivalent of one (1) exponentiation for set-up, less than 2 exponentiations for withdrawal and around 20 for payment, while the size of the coin remains about 300 Bytes. Hence, the withdrawal protocol is 3 orders of magnitude faster than Okamoto`s, while the rest of the system remains equally efficient, allowing for implementation in smart-cards. Similar to Okamoto`s, the scheme is based on proofs whose cryptographic security assumptions are theoretically clarified.« less

E-SAP: Efficient-Strong Authentication Protocol for Healthcare Applications Using Wireless Medical Sensor Networks

PubMed Central

Kumar, Pardeep; Lee, Sang-Gon; Lee, Hoon-Jae

2012-01-01

A wireless medical sensor network (WMSN) can sense humans’ physiological signs without sacrificing patient comfort and transmit patient vital signs to health professionals’ hand-held devices. The patient physiological data are highly sensitive and WMSNs are extremely vulnerable to many attacks. Therefore, it must be ensured that patients’ medical signs are not exposed to unauthorized users. Consequently, strong user authentication is the main concern for the success and large scale deployment of WMSNs. In this regard, this paper presents an efficient, strong authentication protocol, named E-SAP, for healthcare application using WMSNs. The proposed E-SAP includes: (1) a two-factor (i.e., password and smartcard) professional authentication; (2) mutual authentication between the professional and the medical sensor; (3) symmetric encryption/decryption for providing message confidentiality; (4) establishment of a secure session key at the end of authentication; and (5) professionals can change their password. Further, the proposed protocol requires three message exchanges between the professional, medical sensor node and gateway node, and achieves efficiency (i.e., low computation and communication cost). Through the formal analysis, security analysis and performance analysis, we demonstrate that E-SAP is more secure against many practical attacks, and allows a tradeoff between the security and the performance cost for healthcare application using WMSNs. PMID:22438729

A Model for Protostellar Cluster Luminosities and the Impact on the CO–H2 Conversion Factor

NASA Astrophysics Data System (ADS)

Gaches, Brandt A. L.; Offner, Stella S. R.

2018-02-01

We construct a semianalytic model to study the effect of far-ultraviolet (FUV) radiation on gas chemistry from embedded protostars. We use the protostellar luminosity function (PLF) formalism of Offner & McKee to calculate the total, FUV, and ionizing cluster luminosity for various protostellar accretion histories and cluster sizes. We2 compare the model predictions with surveys of Gould Belt star-forming regions and find that the tapered turbulent core model matches best the mean luminosities and the spread in the data. We combine the cluster model with the photodissociation region astrochemistry code, 3D-PDR, to compute the impact of the FUV luminosity from embedded protostars on the CO-to-H2 conversion factor, X CO, as a function of cluster size, gas mass, and star formation efficiency. We find that X CO has a weak dependence on the FUV radiation from embedded sources for large clusters owing to high cloud optical depths. In smaller and more efficient clusters the embedded FUV increases X CO to levels consistent with the average Milky Way values. The internal physical and chemical structures of the cloud are significantly altered, and X CO depends strongly on the protostellar cluster mass for small efficient clouds.

E-SAP: efficient-strong authentication protocol for healthcare applications using wireless medical sensor networks.

PubMed

Kumar, Pardeep; Lee, Sang-Gon; Lee, Hoon-Jae

2012-01-01

A wireless medical sensor network (WMSN) can sense humans' physiological signs without sacrificing patient comfort and transmit patient vital signs to health professionals' hand-held devices. The patient physiological data are highly sensitive and WMSNs are extremely vulnerable to many attacks. Therefore, it must be ensured that patients' medical signs are not exposed to unauthorized users. Consequently, strong user authentication is the main concern for the success and large scale deployment of WMSNs. In this regard, this paper presents an efficient, strong authentication protocol, named E-SAP, for healthcare application using WMSNs. The proposed E-SAP includes: (1) a two-factor (i.e., password and smartcard) professional authentication; (2) mutual authentication between the professional and the medical sensor; (3) symmetric encryption/decryption for providing message confidentiality; (4) establishment of a secure session key at the end of authentication; and (5) professionals can change their password. Further, the proposed protocol requires three message exchanges between the professional, medical sensor node and gateway node, and achieves efficiency (i.e., low computation and communication cost). Through the formal analysis, security analysis and performance analysis, we demonstrate that E-SAP is more secure against many practical attacks, and allows a tradeoff between the security and the performance cost for healthcare application using WMSNs.

Formal Methods Specification and Analysis Guidebook for the Verification of Software and Computer Systems. Volume 2; A Practitioner's Companion

NASA Technical Reports Server (NTRS)

1995-01-01

This guidebook, the second of a two-volume series, is intended to facilitate the transfer of formal methods to the avionics and aerospace community. The 1st volume concentrates on administrative and planning issues [NASA-95a], and the second volume focuses on the technical issues involved in applying formal methods to avionics and aerospace software systems. Hereafter, the term "guidebook" refers exclusively to the second volume of the series. The title of this second volume, A Practitioner's Companion, conveys its intent. The guidebook is written primarily for the nonexpert and requires little or no prior experience with formal methods techniques and tools. However, it does attempt to distill some of the more subtle ingredients in the productive application of formal methods. To the extent that it succeeds, those conversant with formal methods will also nd the guidebook useful. The discussion is illustrated through the development of a realistic example, relevant fragments of which appear in each chapter. The guidebook focuses primarily on the use of formal methods for analysis of requirements and high-level design, the stages at which formal methods have been most productively applied. Although much of the discussion applies to low-level design and implementation, the guidebook does not discuss issues involved in the later life cycle application of formal methods.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadayappan, Ponnuswamy

Exascale computing systems will provide a thousand-fold increase in parallelism and a proportional increase in failure rate relative to today's machines. Systems software for exascale machines must provide the infrastructure to support existing applications while simultaneously enabling efficient execution of new programming models that naturally express dynamic, adaptive, irregular computation; coupled simulations; and massive data analysis in a highly unreliable hardware environment with billions of threads of execution. We propose a new approach to the data and work distribution model provided by system software based on the unifying formalism of an abstract file system. The proposed hierarchical data model providesmore » simple, familiar visibility and access to data structures through the file system hierarchy, while providing fault tolerance through selective redundancy. The hierarchical task model features work queues whose form and organization are represented as file system objects. Data and work are both first class entities. By exposing the relationships between data and work to the runtime system, information is available to optimize execution time and provide fault tolerance. The data distribution scheme provides replication (where desirable and possible) for fault tolerance and efficiency, and it is hierarchical to make it possible to take advantage of locality. The user, tools, and applications, including legacy applications, can interface with the data, work queues, and one another through the abstract file model. This runtime environment will provide multiple interfaces to support traditional Message Passing Interface applications, languages developed under DARPA's High Productivity Computing Systems program, as well as other, experimental programming models. We will validate our runtime system with pilot codes on existing platforms and will use simulation to validate for exascale-class platforms. In this final report, we summarize research results from the work done at the Ohio State University towards the larger goals of the project listed above.« less

Improving the efficiency of single and multiple teleportation protocols based on the direct use of partially entangled states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fortes, Raphael; Rigolin, Gustavo, E-mail: rigolin@ifi.unicamp.br

We push the limits of the direct use of partially pure entangled states to perform quantum teleportation by presenting several protocols in many different scenarios that achieve the optimal efficiency possible. We review and put in a single formalism the three major strategies known to date that allow one to use partially entangled states for direct quantum teleportation (no distillation strategies permitted) and compare their efficiencies in real world implementations. We show how one can improve the efficiency of many direct teleportation protocols by combining these techniques. We then develop new teleportation protocols employing multipartite partially entangled states. The threemore » techniques are also used here in order to achieve the highest efficiency possible. Finally, we prove the upper bound for the optimal success rate for protocols based on partially entangled Bell states and show that some of the protocols here developed achieve such a bound. -- Highlights: •Optimal direct teleportation protocols using directly partially entangled states. •We put in a single formalism all strategies of direct teleportation. •We extend these techniques for multipartite partially entangle states. •We give upper bounds for the optimal efficiency of these protocols.« less

Formal Methods, Design, and Collaborative Learning in the First Computer Science Course.

ERIC Educational Resources Information Center

Troeger, Douglas R.

1995-01-01

A new introductory computer science course at City College of New York builds on a foundation of logic to teach programming based on a "design idea," a strong departure from conventional programming courses. Reduced attrition and increased student and teacher enthusiasm have resulted. (MSE)

Implicational Markedness and Frequency in Constraint-Based Computational Models of Phonological Learning

ERIC Educational Resources Information Center

Jarosz, Gaja

2010-01-01

This study examines the interacting roles of implicational markedness and frequency from the joint perspectives of formal linguistic theory, phonological acquisition and computational modeling. The hypothesis that child grammars are rankings of universal constraints, as in Optimality Theory (Prince & Smolensky, 1993/2004), that learning involves a…

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Neuro-Oncology Branch (NOB), Center for Cancer Research (CCR), National Cancer Institute (NCI) of the National Institutes of Health (NIH) is seeking outstanding postdoctoral candidates interested in studying metabolic and cell signaling pathways in the context of brain cancers through construction of computational models amenable to formal computational analysis and

31 CFR 29.105 - Computation of time.

Code of Federal Regulations, 2011 CFR

2011-07-01

... annuity computation purposes— (i) The service of a participant under the Police and Firefighters Plan who... pay (LWOP) that is creditable service. (1) Under the Police and Firefighters Plan, credit is allowed...'s credit under a formal leave system; and (ii) The service of a participant under the Teachers Plan...

31 CFR 29.105 - Computation of time.

Code of Federal Regulations, 2013 CFR

2013-07-01

... annuity computation purposes— (i) The service of a participant under the Police and Firefighters Plan who... pay (LWOP) that is creditable service. (1) Under the Police and Firefighters Plan, credit is allowed...'s credit under a formal leave system; and (ii) The service of a participant under the Teachers Plan...

31 CFR 29.105 - Computation of time.

Code of Federal Regulations, 2012 CFR

2012-07-01

... annuity computation purposes— (i) The service of a participant under the Police and Firefighters Plan who... pay (LWOP) that is creditable service. (1) Under the Police and Firefighters Plan, credit is allowed...'s credit under a formal leave system; and (ii) The service of a participant under the Teachers Plan...

31 CFR 29.105 - Computation of time.

Code of Federal Regulations, 2014 CFR

2014-07-01

... annuity computation purposes— (i) The service of a participant under the Police and Firefighters Plan who... pay (LWOP) that is creditable service. (1) Under the Police and Firefighters Plan, credit is allowed...'s credit under a formal leave system; and (ii) The service of a participant under the Teachers Plan...

7 CFR 1.427 - Filing; identification of parties of record; service; and computation of time.

Code of Federal Regulations, 2010 CFR

2010-01-01

... ADMINISTRATIVE REGULATIONS Rules of Practice Governing Adjudication of Sourcing Area Applications and Formal Review of Sourcing Areas Pursuant to the Forest Resources Conservation and Shortage Relief Act of 1990... officer or employee. (e) Computations of time. Saturdays, Sundays and Federal holidays shall be included...

Formal and Information Learning in a Computer Clubhouse Environment

ERIC Educational Resources Information Center

McDougall, Anne; Lowe, Jenny; Hopkins, Josie

2004-01-01

This paper outlines the establishment and running of an after-school Computer Clubhouse, describing aspects of the leadership, mentoring and learning activities undertaken there. Research data has been collected from examination of documents associated with the Clubhouse, interviews with its founders, Director, session leaders and mentors, and…

Components of Understanding in Proportional Reasoning: A Fuzzy Set Representation of Developmental Progressions.

ERIC Educational Resources Information Center

Moore, Colleen F.; And Others

1991-01-01

Examined the development of proportional reasoning by means of a temperature mixture task. Results show the importance of distinguishing between intuitive knowledge and formal computational knowledge of proportional concepts. Provides a new perspective on the relation of intuitive and computational knowledge during development. (GLR)

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…

A 'Benign Addiction'? Research on ICT and Pre-School Children.

ERIC Educational Resources Information Center

Plowman, Lydia; Stephen, C.

2003-01-01

Reviews the international research evidence on the ways in which information and communication technologies (ICT) are used in both formal and informal pre-school settings. Addresses the debate over the value and desirability of young children using computers and computational toys; relationship to the media environment; literacies involved; and…

Computation of Capacitors in Complex Arrangements

ERIC Educational Resources Information Center

Rizhov, Alexander

2011-01-01

There is a remarkable difference between formal knowledge and true understanding of the subject. While the former helps students earn top grades, the latter is crucial to the solution of real-world problems. An excellent example is the computation of capacitance, with which some students have difficulty. Also, most textbooks limit problem analysis…

Computers in Knowledge-Based Fields.

ERIC Educational Resources Information Center

Myers, Charles A.

Last in a series of research projects on the implications of technological change and automation, this study is concerned with the use of computers in formal education and educational administration; in library systems and subsystems; in legal, legislative, and related services; in medical and hospital services; and in national and centralized…

Overview of a Linguistic Theory of Design. AI Memo 383A.

ERIC Educational Resources Information Center

Miller, Mark L.; Goldstein, Ira P.

The SPADE theory, which uses linguistic formalisms to model the planning and debugging processes of computer programming, was simultaneously developed and tested in three separate contexts--computer uses in education, automatic programming (a traditional artificial intelligence arena), and protocol analysis (the domain of information processing…

Describing the What and Why of Students' Difficulties in Boolean Logic

ERIC Educational Resources Information Center

Herman, Geoffrey L.; Loui, Michael C.; Kaczmarczyk, Lisa; Zilles, Craig

2012-01-01

The ability to reason with formal logic is a foundational skill for computer scientists and computer engineers that scaffolds the abilities to design, debug, and optimize. By interviewing students about their understanding of propositional logic and their ability to translate from English specifications to Boolean expressions, we characterized…

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals.

PubMed

Zuehlsdorff, T J; Hine, N D M; Payne, M C; Haynes, P D

2015-11-28

We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

Efficient Algorithms for Segmentation of Item-Set Time Series

NASA Astrophysics Data System (ADS)

Chundi, Parvathi; Rosenkrantz, Daniel J.

We propose a special type of time series, which we call an item-set time series, to facilitate the temporal analysis of software version histories, email logs, stock market data, etc. In an item-set time series, each observed data value is a set of discrete items. We formalize the concept of an item-set time series and present efficient algorithms for segmenting a given item-set time series. Segmentation of a time series partitions the time series into a sequence of segments where each segment is constructed by combining consecutive time points of the time series. Each segment is associated with an item set that is computed from the item sets of the time points in that segment, using a function which we call a measure function. We then define a concept called the segment difference, which measures the difference between the item set of a segment and the item sets of the time points in that segment. The segment difference values are required to construct an optimal segmentation of the time series. We describe novel and efficient algorithms to compute segment difference values for each of the measure functions described in the paper. We outline a dynamic programming based scheme to construct an optimal segmentation of the given item-set time series. We use the item-set time series segmentation techniques to analyze the temporal content of three different data sets—Enron email, stock market data, and a synthetic data set. The experimental results show that an optimal segmentation of item-set time series data captures much more temporal content than a segmentation constructed based on the number of time points in each segment, without examining the item set data at the time points, and can be used to analyze different types of temporal data.

Underworld: What we set out to do, How far did we get, What did we Learn ? (Invited)

NASA Astrophysics Data System (ADS)

Moresi, L. N.

2013-12-01

Underworld was conceived as a tool for modelling 3D lithospheric deformation coupled with the underlying / surrounding mantle flow. The challenges involved were to find a method capable of representing the complicated, non-linear, history dependent rheology of the near surface as well as being able to model mantle convection, and, simultaneously, to be able to solve the numerical system efficiently. Underworld is a hybrid particle / mesh code reminiscent of the particle-in-cell techniques from the early 1960s. The Underworld team (*) was not the first to use this approach, nor the last, but the team does have considerable experience and much has been learned along the way. The use of a finite element method as the underlying "cell" in which the Lagrangian particles are embedded considerably reduces errors associated with mapping material properties to the cells. The particles are treated as moving quadrature points in computing the stiffness matrix integrals. The decoupling of deformation markers from computation points allows the use of structured meshes, efficient parallel decompositions, and simple-to-code geometric multigrid solution methods. For a 3D code such efficiencies are very important. The elegance of the method is that it can be completely described in a couple of sentences. However, there are some limitations: it is not obvious how to retain this elegance for unstructured or adaptive meshes, arbitrary element types are not sufficiently well integrated by the simple quadrature approach, and swarms of particles representing volumes are usually an inefficient representation of surfaces. This will be discussed ! (*) Although not formally constituted, my co-conspirators in this exercise are listed as the Underworld team and I will reveal their true identities on the day.

Proceedings of the Sixth NASA Langley Formal Methods (LFM) Workshop

NASA Technical Reports Server (NTRS)

Rozier, Kristin Yvonne (Editor)

2008-01-01

Today's verification techniques are hard-pressed to scale with the ever-increasing complexity of safety critical systems. Within the field of aeronautics alone, we find the need for verification of algorithms for separation assurance, air traffic control, auto-pilot, Unmanned Aerial Vehicles (UAVs), adaptive avionics, automated decision authority, and much more. Recent advances in formal methods have made verifying more of these problems realistic. Thus we need to continually re-assess what we can solve now and identify the next barriers to overcome. Only through an exchange of ideas between theoreticians and practitioners from academia to industry can we extend formal methods for the verification of ever more challenging problem domains. This volume contains the extended abstracts of the talks presented at LFM 2008: The Sixth NASA Langley Formal Methods Workshop held on April 30 - May 2, 2008 in Newport News, Virginia, USA. The topics of interest that were listed in the call for abstracts were: advances in formal verification techniques; formal models of distributed computing; planning and scheduling; automated air traffic management; fault tolerance; hybrid systems/hybrid automata; embedded systems; safety critical applications; safety cases; accident/safety analysis.

MatLab Programming for Engineers Having No Formal Programming Knowledge

NASA Technical Reports Server (NTRS)

Shaykhian, Linda H.; Shaykhian, Gholam Ali

2007-01-01

MatLab is one of the most widely used very high level programming languages for Scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. Also, stated are the current limitations of the MatLab, which possibly can be taken care of by Mathworks Inc. in a future version to make MatLab more versatile.

Research on Synthesis of Concurrent Computing Systems.

DTIC Science & Technology

1982-09-01

20 1.5.1 An Informal Description of the Techniques ....... ..................... 20 1.5 2 Formal Definitions of Aggregation and Virtualisation ...sparsely interconnected networks . We have also developed techniques to create Kung’s systolic array parallel structure from a specification of matrix...resufts of the computation of that element. For example, if A,j is computed using a single enumeration, then virtualisation would produce a three

On introduction of artificial intelligence elements to heat power engineering

NASA Astrophysics Data System (ADS)

Dregalin, A. F.; Nazyrova, R. R.

1993-10-01

The basic problems of 'the thermodynamic intelligence' of personal computers have been outlined. The thermodynamic intellect of personal computers as a concept has been introduced to heat processes occurring in engines of flying vehicles. In particular, the thermodynamic intellect of computers is determined by the possibility of deriving formal relationships between thermodynamic functions. In chemical thermodynamics, a concept of a characteristic function has been introduced.

QuTiP 2: A Python framework for the dynamics of open quantum systems

NASA Astrophysics Data System (ADS)

Johansson, J. R.; Nation, P. D.; Nori, Franco

2013-04-01

We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version. Catalog identifier: AEMB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 33625 No. of bytes in distributed program, including test data, etc.: 410064 Distribution format: tar.gz Programming language: Python. Computer: i386, x86-64. Operating system: Linux, Mac OSX. RAM: 2+ Gigabytes Classification: 7. External routines: NumPy, SciPy, Matplotlib, Cython Catalog identifier of previous version: AEMB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1760 Does the new version supercede the previous version?: Yes Nature of problem: Dynamics of open quantum systems Solution method: Numerical solutions to Lindblad, Floquet-Markov, and Bloch-Redfield master equations, as well as the Monte Carlo wave function method. Reasons for new version: Compared to the preceding version we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Restrictions: Problems must meet the criteria for using the master equation in Lindblad, Floquet-Markov, or Bloch-Redfield form. Running time: A few seconds up to several tens of hours, depending on size of the underlying Hilbert space.

Formal Synthesis of (±)-Aplykurodinone-1 through a Hetero-Pauson-Khand Cycloaddition Approach.

PubMed

Tao, Cheng; Zhang, Jing; Chen, Xiaoming; Wang, Huifei; Li, Yun; Cheng, Bin; Zhai, Hongbin

2017-03-03

The tricyclic intermediate 2 has been synthesized in eight steps from known compound 6 in 20% overall yield. As such, this constitutes a highly efficient formal synthesis of (±)-aplykurodinone-1. This synthesis features a unique, one-pot, intramolecular hetero-Pauson-Khand reaction (h-PKR)/desilylation sequence to expeditiously construct the tricyclic framework, providing valuable insights for expanding the scope and boundaries of h-PKR.

Phonological Iconicity Electrifies: An ERP Study on Affective Sound-to-Meaning Correspondences in German

PubMed Central

Ullrich, Susann; Kotz, Sonja A.; Schmidtke, David S.; Aryani, Arash; Conrad, Markus

2016-01-01

While linguistic theory posits an arbitrary relation between signifiers and the signified (de Saussure, 1916), our analysis of a large-scale German database containing affective ratings of words revealed that certain phoneme clusters occur more often in words denoting concepts with negative and arousing meaning. Here, we investigate how such phoneme clusters that potentially serve as sublexical markers of affect can influence language processing. We registered the EEG signal during a lexical decision task with a novel manipulation of the words' putative sublexical affective potential: the means of valence and arousal values for single phoneme clusters, each computed as a function of respective values of words from the database these phoneme clusters occur in. Our experimental manipulations also investigate potential contributions of formal salience to the sublexical affective potential: Typically, negative high-arousing phonological segments—based on our calculations—tend to be less frequent and more structurally complex than neutral ones. We thus constructed two experimental sets, one involving this natural confound, while controlling for it in the other. A negative high-arousing sublexical affective potential in the strictly controlled stimulus set yielded an early posterior negativity (EPN), in similar ways as an independent manipulation of lexical affective content did. When other potentially salient formal features at the sublexical level were not controlled for, the effect of the sublexical affective potential was strengthened and prolonged (250–650 ms), presumably because formal salience helps making specific phoneme clusters efficient sublexical markers of negative high-arousing affective meaning. These neurophysiological data support the assumption that the organization of a language's vocabulary involves systematic sound-to-meaning correspondences at the phonemic level that influence the way we process language. PMID:27588008

Mori-Zwanzig theory for dissipative forces in coarse-grained dynamics in the Markov limit

NASA Astrophysics Data System (ADS)

Izvekov, Sergei

2017-01-01

We derive alternative Markov approximations for the projected (stochastic) force and memory function in the coarse-grained (CG) generalized Langevin equation, which describes the time evolution of the center-of-mass coordinates of clusters of particles in the microscopic ensemble. This is done with the aid of the Mori-Zwanzig projection operator method based on the recently introduced projection operator [S. Izvekov, J. Chem. Phys. 138, 134106 (2013), 10.1063/1.4795091]. The derivation exploits the "generalized additive fluctuating force" representation to which the projected force reduces in the adopted projection operator formalism. For the projected force, we present a first-order time expansion which correctly extends the static fluctuating force ansatz with the terms necessary to maintain the required orthogonality of the projected dynamics in the Markov limit to the space of CG phase variables. The approximant of the memory function correctly accounts for the momentum dependence in the lowest (second) order and indicates that such a dependence may be important in the CG dynamics approaching the Markov limit. In the case of CG dynamics with a weak dependence of the memory effects on the particle momenta, the expression for the memory function presented in this work is applicable to non-Markov systems. The approximations are formulated in a propagator-free form allowing their efficient evaluation from the microscopic data sampled by standard molecular dynamics simulations. A numerical application is presented for a molecular liquid (nitromethane). With our formalism we do not observe the "plateau-value problem" if the friction tensors for dissipative particle dynamics (DPD) are computed using the Green-Kubo relation. Our formalism provides a consistent bottom-up route for hierarchical parametrization of DPD models from atomistic simulations.

Super-sample covariance approximations and partial sky coverage

NASA Astrophysics Data System (ADS)

Lacasa, Fabien; Lima, Marcos; Aguena, Michel

2018-04-01

Super-sample covariance (SSC) is the dominant source of statistical error on large scale structure (LSS) observables for both current and future galaxy surveys. In this work, we concentrate on the SSC of cluster counts, also known as sample variance, which is particularly useful for the self-calibration of the cluster observable-mass relation; our approach can similarly be applied to other observables, such as galaxy clustering and lensing shear. We first examined the accuracy of two analytical approximations proposed in the literature for the flat sky limit, finding that they are accurate at the 15% and 30-35% level, respectively, for covariances of counts in the same redshift bin. We then developed a harmonic expansion formalism that allows for the prediction of SSC in an arbitrary survey mask geometry, such as large sky areas of current and future surveys. We show analytically and numerically that this formalism recovers the full sky and flat sky limits present in the literature. We then present an efficient numerical implementation of the formalism, which allows fast and easy runs of covariance predictions when the survey mask is modified. We applied our method to a mask that is broadly similar to the Dark Energy Survey footprint, finding a non-negligible negative cross-z covariance, i.e. redshift bins are anti-correlated. We also examined the case of data removal from holes due to, for example bright stars, quality cuts, or systematic removals, and find that this does not have noticeable effects on the structure of the SSC matrix, only rescaling its amplitude by the effective survey area. These advances enable analytical covariances of LSS observables to be computed for current and future galaxy surveys, which cover large areas of the sky where the flat sky approximation fails.

Analysis of Phase-Type Stochastic Petri Nets With Discrete and Continuous Timing

NASA Technical Reports Server (NTRS)

Jones, Robert L.; Goode, Plesent W. (Technical Monitor)

2000-01-01

The Petri net formalism is useful in studying many discrete-state, discrete-event systems exhibiting concurrency, synchronization, and other complex behavior. As a bipartite graph, the net can conveniently capture salient aspects of the system. As a mathematical tool, the net can specify an analyzable state space. Indeed, one can reason about certain qualitative properties (from state occupancies) and how they arise (the sequence of events leading there). By introducing deterministic or random delays, the model is forced to sojourn in states some amount of time, giving rise to an underlying stochastic process, one that can be specified in a compact way and capable of providing quantitative, probabilistic measures. We formalize a new non-Markovian extension to the Petri net that captures both discrete and continuous timing in the same model. The approach affords efficient, stationary analysis in most cases and efficient transient analysis under certain restrictions. Moreover, this new formalism has the added benefit in modeling fidelity stemming from the simultaneous capture of discrete- and continuous-time events (as opposed to capturing only one and approximating the other). We show how the underlying stochastic process, which is non-Markovian, can be resolved into simpler Markovian problems that enjoy efficient solutions. Solution algorithms are provided that can be easily programmed.

An enhanced biometric authentication scheme for telecare medicine information systems with nonce using chaotic hash function.

PubMed

Das, Ashok Kumar; Goswami, Adrijit

2014-06-01

Recently, Awasthi and Srivastava proposed a novel biometric remote user authentication scheme for the telecare medicine information system (TMIS) with nonce. Their scheme is very efficient as it is based on efficient chaotic one-way hash function and bitwise XOR operations. In this paper, we first analyze Awasthi-Srivastava's scheme and then show that their scheme has several drawbacks: (1) incorrect password change phase, (2) fails to preserve user anonymity property, (3) fails to establish a secret session key beween a legal user and the server, (4) fails to protect strong replay attack, and (5) lacks rigorous formal security analysis. We then a propose a novel and secure biometric-based remote user authentication scheme in order to withstand the security flaw found in Awasthi-Srivastava's scheme and enhance the features required for an idle user authentication scheme. Through the rigorous informal and formal security analysis, we show that our scheme is secure against possible known attacks. In addition, we simulate our scheme for the formal security verification using the widely-accepted AVISPA (Automated Validation of Internet Security Protocols and Applications) tool and show that our scheme is secure against passive and active attacks, including the replay and man-in-the-middle attacks. Our scheme is also efficient as compared to Awasthi-Srivastava's scheme.

Formal Specification and Analysis of Cloud Computing Management

DTIC Science & Technology

2012-01-24

te r Cloud Computing in a Nutshell We begin this introduction to Cloud Computing with a famous quote by Larry Ellison: “The interesting thing about...the wording of some of our ads.” — Larry Ellison, Oracle CEO [106] In view of this statement, we summarize the essential aspects of Cloud Computing...1] M. Abadi, M. Burrows , M. Manasse, and T. Wobber. Moderately hard, memory-bound functions. ACM Transactions on Internet Technology, 5(2):299–327

A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking

PubMed Central

Gilbert, David

2016-01-01

Insights gained from multilevel computational models of biological systems can be translated into real-life applications only if the model correctness has been verified first. One of the most frequently employed in silico techniques for computational model verification is model checking. Traditional model checking approaches only consider the evolution of numeric values, such as concentrations, over time and are appropriate for computational models of small scale systems (e.g. intracellular networks). However for gaining a systems level understanding of how biological organisms function it is essential to consider more complex large scale biological systems (e.g. organs). Verifying computational models of such systems requires capturing both how numeric values and properties of (emergent) spatial structures (e.g. area of multicellular population) change over time and across multiple levels of organization, which are not considered by existing model checking approaches. To address this limitation we have developed a novel approximate probabilistic multiscale spatio-temporal meta model checking methodology for verifying multilevel computational models relative to specifications describing the desired/expected system behaviour. The methodology is generic and supports computational models encoded using various high-level modelling formalisms because it is defined relative to time series data and not the models used to generate it. In addition, the methodology can be automatically adapted to case study specific types of spatial structures and properties using the spatio-temporal meta model checking concept. To automate the computational model verification process we have implemented the model checking approach in the software tool Mule (http://mule.modelchecking.org). Its applicability is illustrated against four systems biology computational models previously published in the literature encoding the rat cardiovascular system dynamics, the uterine contractions of labour, the Xenopus laevis cell cycle and the acute inflammation of the gut and lung. Our methodology and software will enable computational biologists to efficiently develop reliable multilevel computational models of biological systems. PMID:27187178

A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking.

PubMed

Pârvu, Ovidiu; Gilbert, David

2016-01-01

Insights gained from multilevel computational models of biological systems can be translated into real-life applications only if the model correctness has been verified first. One of the most frequently employed in silico techniques for computational model verification is model checking. Traditional model checking approaches only consider the evolution of numeric values, such as concentrations, over time and are appropriate for computational models of small scale systems (e.g. intracellular networks). However for gaining a systems level understanding of how biological organisms function it is essential to consider more complex large scale biological systems (e.g. organs). Verifying computational models of such systems requires capturing both how numeric values and properties of (emergent) spatial structures (e.g. area of multicellular population) change over time and across multiple levels of organization, which are not considered by existing model checking approaches. To address this limitation we have developed a novel approximate probabilistic multiscale spatio-temporal meta model checking methodology for verifying multilevel computational models relative to specifications describing the desired/expected system behaviour. The methodology is generic and supports computational models encoded using various high-level modelling formalisms because it is defined relative to time series data and not the models used to generate it. In addition, the methodology can be automatically adapted to case study specific types of spatial structures and properties using the spatio-temporal meta model checking concept. To automate the computational model verification process we have implemented the model checking approach in the software tool Mule (http://mule.modelchecking.org). Its applicability is illustrated against four systems biology computational models previously published in the literature encoding the rat cardiovascular system dynamics, the uterine contractions of labour, the Xenopus laevis cell cycle and the acute inflammation of the gut and lung. Our methodology and software will enable computational biologists to efficiently develop reliable multilevel computational models of biological systems.

Quantifying aggregated uncertainty in Plasmodium falciparum malaria prevalence and populations at risk via efficient space-time geostatistical joint simulation.

PubMed

Gething, Peter W; Patil, Anand P; Hay, Simon I

2010-04-01

Risk maps estimating the spatial distribution of infectious diseases are required to guide public health policy from local to global scales. The advent of model-based geostatistics (MBG) has allowed these maps to be generated in a formal statistical framework, providing robust metrics of map uncertainty that enhances their utility for decision-makers. In many settings, decision-makers require spatially aggregated measures over large regions such as the mean prevalence within a country or administrative region, or national populations living under different levels of risk. Existing MBG mapping approaches provide suitable metrics of local uncertainty--the fidelity of predictions at each mapped pixel--but have not been adapted for measuring uncertainty over large areas, due largely to a series of fundamental computational constraints. Here the authors present a new efficient approximating algorithm that can generate for the first time the necessary joint simulation of prevalence values across the very large prediction spaces needed for global scale mapping. This new approach is implemented in conjunction with an established model for P. falciparum allowing robust estimates of mean prevalence at any specified level of spatial aggregation. The model is used to provide estimates of national populations at risk under three policy-relevant prevalence thresholds, along with accompanying model-based measures of uncertainty. By overcoming previously unchallenged computational barriers, this study illustrates how MBG approaches, already at the forefront of infectious disease mapping, can be extended to provide large-scale aggregate measures appropriate for decision-makers.

Insights in the electronic structure and redox reaction energy in LiFePO{sub 4} battery material from an accurate Tran-Blaha modified Becke Johnson potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Araujo, Rafael B., E-mail: rafael.barros@physics.uu.se; Almeida, J. de S; Instituto de Física, Universidade Federal da Bahia, Salvador, Bahia

The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO{sub 4} and FePO{sub 4} which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, thatmore » the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO{sub 4} and FePO{sub 4}. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.« less

Abstract shapes of RNA.

PubMed

Giegerich, Robert; Voss, Björn; Rehmsmeier, Marc

2004-01-01

The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.

Analytic energy gradients for the coupled-cluster singles and doubles method with the density-fitting approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozkaya, Uğur, E-mail: ugur.bozkaya@hacettepe.edu.tr; Department of Chemistry, Atatürk University, Erzurum 25240; Sherrill, C. David

2016-05-07

An efficient implementation is presented for analytic gradients of the coupled-cluster singles and doubles (CCSD) method with the density-fitting approximation, denoted DF-CCSD. Frozen core terms are also included. When applied to a set of alkanes, the DF-CCSD analytic gradients are significantly accelerated compared to conventional CCSD for larger molecules. The efficiency of our DF-CCSD algorithm arises from the acceleration of several different terms, which are designated as the “gradient terms”: computation of particle density matrices (PDMs), generalized Fock-matrix (GFM), solution of the Z-vector equation, formation of the relaxed PDMs and GFM, back-transformation of PDMs and GFM to the atomic orbitalmore » (AO) basis, and evaluation of gradients in the AO basis. For the largest member of the alkane set (C{sub 10}H{sub 22}), the computational times for the gradient terms (with the cc-pVTZ basis set) are 2582.6 (CCSD) and 310.7 (DF-CCSD) min, respectively, a speed up of more than 8-folds. For gradient related terms, the DF approach avoids the usage of four-index electron repulsion integrals. Based on our previous study [U. Bozkaya, J. Chem. Phys. 141, 124108 (2014)], our formalism completely avoids construction or storage of the 4-index two-particle density matrix (TPDM), using instead 2- and 3-index TPDMs. The DF approach introduces negligible errors for equilibrium bond lengths and harmonic vibrational frequencies.« less

Secure and scalable deduplication of horizontally partitioned health data for privacy-preserving distributed statistical computation.

PubMed

Yigzaw, Kassaye Yitbarek; Michalas, Antonis; Bellika, Johan Gustav

2017-01-03

Techniques have been developed to compute statistics on distributed datasets without revealing private information except the statistical results. However, duplicate records in a distributed dataset may lead to incorrect statistical results. Therefore, to increase the accuracy of the statistical analysis of a distributed dataset, secure deduplication is an important preprocessing step. We designed a secure protocol for the deduplication of horizontally partitioned datasets with deterministic record linkage algorithms. We provided a formal security analysis of the protocol in the presence of semi-honest adversaries. The protocol was implemented and deployed across three microbiology laboratories located in Norway, and we ran experiments on the datasets in which the number of records for each laboratory varied. Experiments were also performed on simulated microbiology datasets and data custodians connected through a local area network. The security analysis demonstrated that the protocol protects the privacy of individuals and data custodians under a semi-honest adversarial model. More precisely, the protocol remains secure with the collusion of up to N - 2 corrupt data custodians. The total runtime for the protocol scales linearly with the addition of data custodians and records. One million simulated records distributed across 20 data custodians were deduplicated within 45 s. The experimental results showed that the protocol is more efficient and scalable than previous protocols for the same problem. The proposed deduplication protocol is efficient and scalable for practical uses while protecting the privacy of patients and data custodians.

Investigation on the use of optimization techniques for helicopter airframe vibrations design studies

NASA Technical Reports Server (NTRS)

Sreekanta Murthy, T.

1992-01-01

Results of the investigation of formal nonlinear programming-based numerical optimization techniques of helicopter airframe vibration reduction are summarized. The objective and constraint function and the sensitivity expressions used in the formulation of airframe vibration optimization problems are presented and discussed. Implementation of a new computational procedure based on MSC/NASTRAN and CONMIN in a computer program system called DYNOPT for optimizing airframes subject to strength, frequency, dynamic response, and dynamic stress constraints is described. An optimization methodology is proposed which is thought to provide a new way of applying formal optimization techniques during the various phases of the airframe design process. Numerical results obtained from the application of the DYNOPT optimization code to a helicopter airframe are discussed.

Increasing the Efficiency of the One Room School.

ERIC Educational Resources Information Center

Berg, Paul

The one room school is a challenging educational setting for both teacher and student. Isolation of the school, limited availability of educational resources, and the demanding role of the school as the only formal educational institution within the community are conditions which make classroom efficiency an important consideration for the…

Efficiency and formalism of quantum games

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, C.F.; Johnson, Neil F.

We show that quantum games are more efficient than classical games and provide a saturated upper bound for this efficiency. We also demonstrate that the set of finite classical games is a strict subset of the set of finite quantum games. Our analysis is based on a rigorous formulation of quantum games, from which quantum versions of the minimax theorem and the Nash equilibrium theorem can be deduced.

A Method of Synthesizing Large Bodies of Knowledge in the Social Sciences.

ERIC Educational Resources Information Center

Thiemann, Francis C.

Employing concepts of formal symbolic logic, the philosophy of science, computer technology, and the work of Hans Zetterberg, a format is suggested for synthesizing and increasing use of the rapidly expanding knowledge of the social sciences. Steps in the process include formulating basic propositions, utilizing computers to establish sets, and…

Young Children "Solve for X" Using the Approximate Number System

ERIC Educational Resources Information Center

Kibbe, Melissa M.; Feigenson, Lisa

2015-01-01

The Approximate Number System (ANS) supports basic arithmetic computation in early childhood, but it is unclear whether the ANS also supports the more complex computations introduced later in formal education. "Solving for x" in addend-unknown problems is notoriously difficult for children, who often struggle with these types of problems…

A Computer-Supported Method to Reveal and Assess Personal Professional Theories in Vocational Education

ERIC Educational Resources Information Center

van den Bogaart, Antoine C. M.; Bilderbeek, Richel J. C.; Schaap, Harmen; Hummel, Hans G. K.; Kirschner, Paul A.

2016-01-01

This article introduces a dedicated, computer-supported method to construct and formatively assess open, annotated concept maps of Personal Professional Theories (PPTs). These theories are internalised, personal bodies of formal and practical knowledge, values, norms and convictions that professionals use as a reference to interpret and acquire…

Epistemological Pluralism: Styles and Voices within the Computer Culture.

ERIC Educational Resources Information Center

Papert, Seymour; Turkle, Sherry

1992-01-01

Describes a study in which the computer has emerged as an important factor in revolution of concrete--privileged medium for the growth of alternative voices in addressing the world of formal systems. Focuses on a concrete way of knowing and concludes that recent technological developments in interfaces, programming philosophy, and artificial…

Computer-Aided Experiment Planning toward Causal Discovery in Neuroscience.

PubMed

Matiasz, Nicholas J; Wood, Justin; Wang, Wei; Silva, Alcino J; Hsu, William

2017-01-01

Computers help neuroscientists to analyze experimental results by automating the application of statistics; however, computer-aided experiment planning is far less common, due to a lack of similar quantitative formalisms for systematically assessing evidence and uncertainty. While ontologies and other Semantic Web resources help neuroscientists to assimilate required domain knowledge, experiment planning requires not only ontological but also epistemological (e.g., methodological) information regarding how knowledge was obtained. Here, we outline how epistemological principles and graphical representations of causality can be used to formalize experiment planning toward causal discovery. We outline two complementary approaches to experiment planning: one that quantifies evidence per the principles of convergence and consistency, and another that quantifies uncertainty using logical representations of constraints on causal structure. These approaches operationalize experiment planning as the search for an experiment that either maximizes evidence or minimizes uncertainty. Despite work in laboratory automation, humans must still plan experiments and will likely continue to do so for some time. There is thus a great need for experiment-planning frameworks that are not only amenable to machine computation but also useful as aids in human reasoning.

Formalization of Generalized Constraint Language: A Crucial Prelude to Computing With Words.

PubMed

Khorasani, Elham S; Rahimi, Shahram; Calvert, Wesley

2013-02-01

The generalized constraint language (GCL), introduced by Zadeh, serves as a basis for computing with words (CW). It provides an agenda to express the imprecise and fuzzy information embedded in natural language and allows reasoning with perceptions. Despite its fundamental role, the definition of GCL has remained informal since its introduction by Zadeh, and to our knowledge, no attempt has been made to formulate a rigorous theoretical framework for GCL. Such formalization is necessary for further theoretical and practical advancement of CW for two important reasons. First, it provides the underlying infrastructure for the development of useful inference patterns based on sound theories. Second, it determines the scope of GCL and hence facilitates the translation of natural language expressions into GCL. This paper is an attempt to step in this direction by providing a formal syntax together with a compositional semantics for GCL. A soundness theorem is defined, and Zadeh's deduction rules are proved to be valid in the defined semantics. Furthermore, a discussion is provided on how the proposed language may be used in practice.

Privatization of solid waste collection services: Lessons from Gaborone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolaane, Benjamin, E-mail: bolaaneb@mopipi.ub.bw; Isaac, Emmanuel, E-mail: eisaac300@gmail.com

Highlights: • We compared efficiency and effectiveness of waste collection by the public and private sector. • Public sector performs better than private sector in some areas and vice versa. • Outsourcing waste collection in developing countries is hindered by limited capacity on contractual issues. • Outsourcing collection in developing countries is hampered by inadequate waste information. • There is need to build capacity in the public sector of developing countries to support outsourcing. - Abstract: Formal privatization of solid waste collection activities has often been flagged as a suitable intervention for some of the challenges of solid waste managementmore » experienced by developing countries. Proponents of outsourcing collection to the private sector argue that in contrast to the public sector, it is more effective and efficient in delivering services. This essay is a comparative case study of efficiency and effectiveness attributes between the public and the formal private sector, in relation to the collection of commercial waste in Gaborone. The paper is based on analysis of secondary data and key informant interviews. It was found that while, the private sector performed comparatively well in most of the chosen indicators of efficiency and effectiveness, the public sector also had areas where it had a competitive advantage. For instance, the private sector used the collection crew more efficiently, while the public sector was found to have a more reliable workforce. The study recommends that, while formal private sector participation in waste collection has some positive effects in terms of quality of service rendered, in most developing countries, it has to be enhanced by building sufficient capacity within the public sector on information about services contracted out and evaluation of performance criteria within the contracting process.« less

Design of a modular digital computer system DRL 4 and 5. [design of airborne/spaceborne computer system

NASA Technical Reports Server (NTRS)

1973-01-01

Design and development efforts for a spaceborne modular computer system are reported. An initial baseline description is followed by an interface design that includes definition of the overall system response to all classes of failure. Final versions for the register level designs for all module types were completed. Packaging, support and control executive software, including memory utilization estimates and design verification plan, were formalized to insure a soundly integrated design of the digital computer system.

Computer literacy in nursing education. An overview.

PubMed

Newbern, V B

1985-09-01

Nursing educators are beginning to realize that computer literacy has become a survival skill for the profession. They understand that literacy must be at a level that assures the ability to manage and control the flood of available information and provides an openness and awareness of future technologic possibilities. The computer has been on college campuses for a number of years, used primarily for record storage and retrieval. However, early on a few nurse educators saw the potential for its use as a practice tool. Out of this foresight came both formal and nonformal educational offerings. The evolution of formal coursework in computer literacy has moved from learning about the computer to learning with the computer. Today the use of the computer is expanding geometrically as microcomputers become common. Graduate students and faculty use them for literature searches and data analysis. Undergraduates are routinely using computer-assisted instruction. Coursework in computer technology is fast becoming a given for nursing students and computer competency a requisite for faculty. However, inculcating computer competency in faculty and student repertoires is not an easy task. There are problems related to motivation, resources, and control. Territorial disputes between schools and colleges must be arbitrated. The interface with practice must be addressed. The paucity of adequate software is a real concern. But the potential is enormous, probably restricted only by human creativity. The possibilities for teaching and learning are profound, especially if geographical constraints can be effaced and scarce resources can be shared at minimal cost. Extremely sophisticated research designs and evaluation methodologies can be used routinely.(ABSTRACT TRUNCATED AT 250 WORDS)

Language-Agnostic Reproducible Data Analysis Using Literate Programming.

PubMed

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.

Language-Agnostic Reproducible Data Analysis Using Literate Programming

PubMed Central

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir. PMID:27711123

Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction.

PubMed

Boniolo, Giovanni; D'Agostino, Marcello; Di Fiore, Pier Paolo

2010-03-03

We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word zetaomegaeta, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical "deduction". Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction.

Toward a computational framework for cognitive biology: Unifying approaches from cognitive neuroscience and comparative cognition

NASA Astrophysics Data System (ADS)

Fitch, W. Tecumseh

2014-09-01

Progress in understanding cognition requires a quantitative, theoretical framework, grounded in the other natural sciences and able to bridge between implementational, algorithmic and computational levels of explanation. I review recent results in neuroscience and cognitive biology that, when combined, provide key components of such an improved conceptual framework for contemporary cognitive science. Starting at the neuronal level, I first discuss the contemporary realization that single neurons are powerful tree-shaped computers, which implies a reorientation of computational models of learning and plasticity to a lower, cellular, level. I then turn to predictive systems theory (predictive coding and prediction-based learning) which provides a powerful formal framework for understanding brain function at a more global level. Although most formal models concerning predictive coding are framed in associationist terms, I argue that modern data necessitate a reinterpretation of such models in cognitive terms: as model-based predictive systems. Finally, I review the role of the theory of computation and formal language theory in the recent explosion of comparative biological research attempting to isolate and explore how different species differ in their cognitive capacities. Experiments to date strongly suggest that there is an important difference between humans and most other species, best characterized cognitively as a propensity by our species to infer tree structures from sequential data. Computationally, this capacity entails generative capacities above the regular (finite-state) level; implementationally, it requires some neural equivalent of a push-down stack. I dub this unusual human propensity "dendrophilia", and make a number of concrete suggestions about how such a system may be implemented in the human brain, about how and why it evolved, and what this implies for models of language acquisition. I conclude that, although much remains to be done, a neurally-grounded framework for theoretical cognitive science is within reach that can move beyond polarized debates and provide a more adequate theoretical future for cognitive biology.

Toward a computational framework for cognitive biology: unifying approaches from cognitive neuroscience and comparative cognition.

PubMed

Fitch, W Tecumseh

2014-09-01

Progress in understanding cognition requires a quantitative, theoretical framework, grounded in the other natural sciences and able to bridge between implementational, algorithmic and computational levels of explanation. I review recent results in neuroscience and cognitive biology that, when combined, provide key components of such an improved conceptual framework for contemporary cognitive science. Starting at the neuronal level, I first discuss the contemporary realization that single neurons are powerful tree-shaped computers, which implies a reorientation of computational models of learning and plasticity to a lower, cellular, level. I then turn to predictive systems theory (predictive coding and prediction-based learning) which provides a powerful formal framework for understanding brain function at a more global level. Although most formal models concerning predictive coding are framed in associationist terms, I argue that modern data necessitate a reinterpretation of such models in cognitive terms: as model-based predictive systems. Finally, I review the role of the theory of computation and formal language theory in the recent explosion of comparative biological research attempting to isolate and explore how different species differ in their cognitive capacities. Experiments to date strongly suggest that there is an important difference between humans and most other species, best characterized cognitively as a propensity by our species to infer tree structures from sequential data. Computationally, this capacity entails generative capacities above the regular (finite-state) level; implementationally, it requires some neural equivalent of a push-down stack. I dub this unusual human propensity "dendrophilia", and make a number of concrete suggestions about how such a system may be implemented in the human brain, about how and why it evolved, and what this implies for models of language acquisition. I conclude that, although much remains to be done, a neurally-grounded framework for theoretical cognitive science is within reach that can move beyond polarized debates and provide a more adequate theoretical future for cognitive biology. Copyright © 2014. Published by Elsevier B.V.

Replicating the benefits of Deutschian closed timelike curves without breaking causality

NASA Astrophysics Data System (ADS)

Yuan, Xiao; Assad, Syed M.; Thompson, Jayne; Haw, Jing Yan; Vedral, Vlatko; Ralph, Timothy C.; Lam, Ping Koy; Weedbrook, Christian; Gu, Mile

2015-11-01

In general relativity, closed timelike curves can break causality with remarkable and unsettling consequences. At the classical level, they induce causal paradoxes disturbing enough to motivate conjectures that explicitly prevent their existence. At the quantum level such problems can be resolved through the Deutschian formalism, however this induces radical benefits—from cloning unknown quantum states to solving problems intractable to quantum computers. Instinctively, one expects these benefits to vanish if causality is respected. Here we show that in harnessing entanglement, we can efficiently solve NP-complete problems and clone arbitrary quantum states—even when all time-travelling systems are completely isolated from the past. Thus, the many defining benefits of Deutschian closed timelike curves can still be harnessed, even when causality is preserved. Our results unveil a subtle interplay between entanglement and general relativity, and significantly improve the potential of probing the radical effects that may exist at the interface between relativity and quantum theory.

Transversal Clifford gates on folded surface codes

DOE PAGES

Moussa, Jonathan E.

2016-10-12

Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surfacemore » codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.« less

Adapting GOMS to Model Human-Robot Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drury, Jill; Scholtz, Jean; Kieras, David

2007-03-09

Human-robot interaction (HRI) has been maturing in tandem with robots’ commercial success. In the last few years HRI researchers have been adopting—and sometimes adapting—human-computer interaction (HCI) evaluation techniques to assess the efficiency and intuitiveness of HRI designs. For example, Adams (2005) used Goal Directed Task Analysis to determine the interaction needs of officers from the Nashville Metro Police Bomb Squad. Scholtz et al. (2004) used Endsley’s (1988) Situation Awareness Global Assessment Technique to determine robotic vehicle supervisors’ awareness of when vehicles were in trouble and thus required closer monitoring or intervention. Yanco and Drury (2004) employed usability testing to determinemore » (among other things) how well a search-andrescue interface supported use by first responders. One set of HCI tools that has so far seen little exploration in the HRI domain, however, is the class of modeling and evaluation techniques known as formal methods.« less

Next-to-leading-logarithmic power corrections for N -jettiness subtraction in color-singlet production

NASA Astrophysics Data System (ADS)

Boughezal, Radja; Isgrò, Andrea; Petriello, Frank

2018-04-01

We present a detailed derivation of the power corrections to the factorization theorem for the 0-jettiness event shape variable T . Our calculation is performed directly in QCD without using the formalism of effective field theory. We analytically calculate the next-to-leading logarithmic power corrections for small T at next-to-leading order in the strong coupling constant, extending previous computations which obtained only the leading-logarithmic power corrections. We address a discrepancy in the literature between results for the leading-logarithmic power corrections to a particular definition of 0-jettiness. We present a numerical study of the power corrections in the context of their application to the N -jettiness subtraction method for higher-order calculations, using gluon-fusion Higgs production as an example. The inclusion of the next-to-leading-logarithmic power corrections further improves the numerical efficiency of the approach beyond the improvement obtained from the leading-logarithmic power corrections.

Stochastic Dynamics through Hierarchically Embedded Markov Chains

NASA Astrophysics Data System (ADS)

Vasconcelos, Vítor V.; Santos, Fernando P.; Santos, Francisco C.; Pacheco, Jorge M.

2017-02-01

Studying dynamical phenomena in finite populations often involves Markov processes of significant mathematical and/or computational complexity, which rapidly becomes prohibitive with increasing population size or an increasing number of individual configuration states. Here, we develop a framework that allows us to define a hierarchy of approximations to the stationary distribution of general systems that can be described as discrete Markov processes with time invariant transition probabilities and (possibly) a large number of states. This results in an efficient method for studying social and biological communities in the presence of stochastic effects—such as mutations in evolutionary dynamics and a random exploration of choices in social systems—including situations where the dynamics encompasses the existence of stable polymorphic configurations, thus overcoming the limitations of existing methods. The present formalism is shown to be general in scope, widely applicable, and of relevance to a variety of interdisciplinary problems.

DEEP-SaM - Energy-Efficient Provisioning Policies for Computing Environments

NASA Astrophysics Data System (ADS)

Bodenstein, Christian; Püschel, Tim; Hedwig, Markus; Neumann, Dirk

The cost of electricity for datacenters is a substantial operational cost that can and should be managed, not only for saving energy, but also due to the ecologic commitment inherent to power consumption. Often, pursuing this goal results in chronic underutilization of resources, a luxury most resource providers do not have in light of their corporate commitments. This work proposes, formalizes and numerically evaluates DEEP-Sam, for clearing provisioning markets, based on the maximization of welfare, subject to utility-level dependant energy costs and customer satisfaction levels. We focus specifically on linear power models, and the implications of the inherent fixed costs related to energy consumption of modern datacenters and cloud environments. We rigorously test the model by running multiple simulation scenarios and evaluate the results critically. We conclude with positive results and implications for long-term sustainable management of modern datacenters.

Framing a Knowledge Base for a Legal Expert System Dealing with Indeterminate Concepts.

PubMed

Araszkiewicz, Michał; Łopatkiewicz, Agata; Zienkiewicz, Adam; Zurek, Tomasz

2015-01-01

Despite decades of development of formal tools for modelling legal knowledge and reasoning, the creation of a fully fledged legal decision support system remains challenging. Among those challenges, such system requires an enormous amount of commonsense knowledge to derive legal expertise. This paper describes the development of a negotiation decision support system (the Parenting Plan Support System or PPSS) to support parents in drafting an agreement (the parenting plan) for the exercise of parental custody of minor children after a divorce is granted. The main objective here is to discuss problems of framing an intuitively appealing and computationally efficient knowledge base that can adequately represent the indeterminate legal concept of the well-being of the child in the context of continental legal culture and of Polish law in particular. In addition to commonsense reasoning, interpretation of such a concept demands both legal expertise and significant professional knowledge from other domains.

Framing a Knowledge Base for a Legal Expert System Dealing with Indeterminate Concepts

PubMed Central

Araszkiewicz, Michał; Łopatkiewicz, Agata; Zienkiewicz, Adam

2015-01-01

Despite decades of development of formal tools for modelling legal knowledge and reasoning, the creation of a fully fledged legal decision support system remains challenging. Among those challenges, such system requires an enormous amount of commonsense knowledge to derive legal expertise. This paper describes the development of a negotiation decision support system (the Parenting Plan Support System or PPSS) to support parents in drafting an agreement (the parenting plan) for the exercise of parental custody of minor children after a divorce is granted. The main objective here is to discuss problems of framing an intuitively appealing and computationally efficient knowledge base that can adequately represent the indeterminate legal concept of the well-being of the child in the context of continental legal culture and of Polish law in particular. In addition to commonsense reasoning, interpretation of such a concept demands both legal expertise and significant professional knowledge from other domains. PMID:26495435

Single electron dynamics in a Hall thruster electromagnetic field profile

NASA Astrophysics Data System (ADS)

Marini, Samuel; Pakter, Renato

2017-05-01

In this work, the single electron dynamics in a simplified three dimensional Hall thruster model is studied. Using Hamiltonian formalism and the concept of limiting curves, one is able to determine confinement conditions for the electron in the acceleration channel. It is shown that as a given parameter of the electromagnetic field is changed, the particle trajectory may transit from regular to chaotic without affecting the confinement, which allows one to make a detailed analysis of the role played by the chaos. The ionization volume is also computed, which measures the probability of an electron to ionize background gas atoms. It is found that there is a great correlation between chaos and increased effective ionization volume. This indicates that a complex dynamical behavior may improve the device efficiency by augmenting the ionization capability of each electron, requiring an overall lower electron current.

Quantum Steering Beyond Instrumental Causal Networks

NASA Astrophysics Data System (ADS)

Nery, R. V.; Taddei, M. M.; Chaves, R.; Aolita, L.

2018-04-01

We theoretically predict, and experimentally verify with entangled photons, that outcome communication is not enough for hidden-state models to reproduce quantum steering. Hidden-state models with outcome communication correspond, in turn, to the well-known instrumental processes of causal inference but in the one-sided device-independent scenario of one black-box measurement device and one well-characterized quantum apparatus. We introduce one-sided device-independent instrumental inequalities to test against these models, with the appealing feature of detecting entanglement even when communication of the black box's measurement outcome is allowed. We find that, remarkably, these inequalities can also be violated solely with steering, i.e., without outcome communication. In fact, an efficiently computable formal quantifier—the robustness of noninstrumentality—naturally arises, and we prove that steering alone is enough to maximize it. Our findings imply that quantum theory admits a stronger form of steering than known until now, with fundamental as well as practical potential implications.

Stochastic Dynamics through Hierarchically Embedded Markov Chains.

PubMed

Vasconcelos, Vítor V; Santos, Fernando P; Santos, Francisco C; Pacheco, Jorge M

2017-02-03

Studying dynamical phenomena in finite populations often involves Markov processes of significant mathematical and/or computational complexity, which rapidly becomes prohibitive with increasing population size or an increasing number of individual configuration states. Here, we develop a framework that allows us to define a hierarchy of approximations to the stationary distribution of general systems that can be described as discrete Markov processes with time invariant transition probabilities and (possibly) a large number of states. This results in an efficient method for studying social and biological communities in the presence of stochastic effects-such as mutations in evolutionary dynamics and a random exploration of choices in social systems-including situations where the dynamics encompasses the existence of stable polymorphic configurations, thus overcoming the limitations of existing methods. The present formalism is shown to be general in scope, widely applicable, and of relevance to a variety of interdisciplinary problems.

Random-Phase Approximation Methods

NASA Astrophysics Data System (ADS)

Chen, Guo P.; Voora, Vamsee K.; Agee, Matthew M.; Balasubramani, Sree Ganesh; Furche, Filipp

2017-05-01

Random-phase approximation (RPA) methods are rapidly emerging as cost-effective validation tools for semilocal density functional computations. We present the theoretical background of RPA in an intuitive rather than formal fashion, focusing on the physical picture of screening and simple diagrammatic analysis. A new decomposition of the RPA correlation energy into plasmonic modes leads to an appealing visualization of electron correlation in terms of charge density fluctuations. Recent developments in the areas of beyond-RPA methods, RPA correlation potentials, and efficient algorithms for RPA energy and property calculations are reviewed. The ability of RPA to approximately capture static correlation in molecules is quantified by an analysis of RPA natural occupation numbers. We illustrate the use of RPA methods in applications to small-gap systems such as open-shell d- and f-element compounds, radicals, and weakly bound complexes, where semilocal density functional results exhibit strong functional dependence.

High Fidelity CFD Analysis and Validation of Rotorcraft Gearbox Aerodynamics Under Operational and Oil-Out Conditions

NASA Technical Reports Server (NTRS)

Kunz, Robert F.

2014-01-01

This document represents the evolving formal documentation of the NPHASE-PSU computer code. Version 3.15 is being delivered along with the software to NASA in 2013.Significant upgrades to the NPHASE-PSU have been made since the first delivery of draft documentation to DARPA and USNRC in 2006. These include a much lighter, faster and memory efficient face based front end, support for arbitrary polyhedra in front end, flow-solver and back-end, a generalized homogeneous multiphase capability, and several two-fluid modelling and algorithmic elements. Specific capability installed for the NASA Gearbox Windage Aerodynamics NRA are included in this version: Hybrid Immersed Overset Boundary Method (HOIBM) [Noack et. al (2009)] Periodic boundary conditions for multiple frames of reference, Fully generalized immersed boundary method, Fully generalized conjugate heat transfer, Droplet deposition, bouncing, splashing models, and, Film transport and breakup.

A robust anonymous biometric-based authenticated key agreement scheme for multi-server environments

PubMed Central

Huang, Yuanfei; Ma, Fangchao

2017-01-01

In order to improve the security in remote authentication systems, numerous biometric-based authentication schemes using smart cards have been proposed. Recently, Moon et al. presented an authentication scheme to remedy the flaws of Lu et al.’s scheme, and claimed that their improved protocol supports the required security properties. Unfortunately, we found that Moon et al.’s scheme still has weaknesses. In this paper, we show that Moon et al.’s scheme is vulnerable to insider attack, server spoofing attack, user impersonation attack and guessing attack. Furthermore, we propose a robust anonymous multi-server authentication scheme using public key encryption to remove the aforementioned problems. From the subsequent formal and informal security analysis, we demonstrate that our proposed scheme provides strong mutual authentication and satisfies the desirable security requirements. The functional and performance analysis shows that the improved scheme has the best secure functionality and is computational efficient. PMID:29121050

A robust anonymous biometric-based authenticated key agreement scheme for multi-server environments.

PubMed

Guo, Hua; Wang, Pei; Zhang, Xiyong; Huang, Yuanfei; Ma, Fangchao

2017-01-01

In order to improve the security in remote authentication systems, numerous biometric-based authentication schemes using smart cards have been proposed. Recently, Moon et al. presented an authentication scheme to remedy the flaws of Lu et al.'s scheme, and claimed that their improved protocol supports the required security properties. Unfortunately, we found that Moon et al.'s scheme still has weaknesses. In this paper, we show that Moon et al.'s scheme is vulnerable to insider attack, server spoofing attack, user impersonation attack and guessing attack. Furthermore, we propose a robust anonymous multi-server authentication scheme using public key encryption to remove the aforementioned problems. From the subsequent formal and informal security analysis, we demonstrate that our proposed scheme provides strong mutual authentication and satisfies the desirable security requirements. The functional and performance analysis shows that the improved scheme has the best secure functionality and is computational efficient.

Extended phase graphs with anisotropic diffusion.

PubMed

Weigel, M; Schwenk, S; Kiselev, V G; Scheffler, K; Hennig, J

2010-08-01

The extended phase graph (EPG) calculus gives an elegant pictorial description of magnetization response in multi-pulse MR sequences. The use of the EPG calculus enables a high computational efficiency for the quantitation of echo intensities even for complex sequences with multiple refocusing pulses with arbitrary flip angles. In this work, the EPG concept dealing with RF pulses with arbitrary flip angles and phases is extended to account for anisotropic diffusion in the presence of arbitrary varying gradients. The diffusion effect can be expressed by specific diffusion weightings of individual magnetization pathways. This can be represented as an action of a linear operator on the magnetization state. The algorithm allows easy integration of diffusion anisotropy effects. The formalism is validated on known examples from literature and used to calculate the effective diffusion weighting in multi-echo sequences with arbitrary refocusing flip angles. Copyright 2010 Elsevier Inc. All rights reserved.

Combinational Reasoning of Quantitative Fuzzy Topological Relations for Simple Fuzzy Regions

PubMed Central

Liu, Bo; Li, Dajun; Xia, Yuanping; Ruan, Jian; Xu, Lili; Wu, Huanyi

2015-01-01

In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computational fuzzy topological space is applied to simple fuzzy regions to efficiently and more accurately solve fuzzy topological relations. Thus, extending the existing research and improving upon the previous work, this paper presents a new method to describe fuzzy topological relations between simple spatial regions in Geographic Information Sciences (GIS) and Artificial Intelligence (AI). Firstly, we propose a new definition for simple fuzzy line segments and simple fuzzy regions based on the computational fuzzy topology. And then, based on the new definitions, we also propose a new combinational reasoning method to compute the topological relations between simple fuzzy regions, moreover, this study has discovered that there are (1) 23 different topological relations between a simple crisp region and a simple fuzzy region; (2) 152 different topological relations between two simple fuzzy regions. In the end, we have discussed some examples to demonstrate the validity of the new method, through comparisons with existing fuzzy models, we showed that the proposed method can compute more than the existing models, as it is more expressive than the existing fuzzy models. PMID:25775452

A general mass term for bigravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cusin, Giulia; Durrer, Ruth; Guarato, Pietro

2016-04-01

We introduce a new formalism to study perturbations of Hassan-Rosen bigravity theory, around general backgrounds for the two dynamical metrics. In particular, we derive the general expression for the mass term of the perturbations and we explicitly compute it for cosmological settings. We study tensor perturbations in a specific branch of bigravity using this formalism. We show that the tensor sector is affected by a late-time instability, which sets in when the mass matrix is no longer positive definite.

Priority in Process Algebras

NASA Technical Reports Server (NTRS)

Cleaveland, Rance; Luettgen, Gerald; Natarajan, V.

1999-01-01

This paper surveys the semantic ramifications of extending traditional process algebras with notions of priority that allow for some transitions to be given precedence over others. These enriched formalisms allow one to model system features such as interrupts, prioritized choice, or real-time behavior. Approaches to priority in process algebras can be classified according to whether the induced notion of preemption on transitions is global or local and whether priorities are static or dynamic. Early work in the area concentrated on global pre-emption and static priorities and led to formalisms for modeling interrupts and aspects of real-time, such as maximal progress, in centralized computing environments. More recent research has investigated localized notions of pre-emption in which the distribution of systems is taken into account, as well as dynamic priority approaches, i.e., those where priority values may change as systems evolve. The latter allows one to model behavioral phenomena such as scheduling algorithms and also enables the efficient encoding of real-time semantics. Technically, this paper studies the different models of priorities by presenting extensions of Milner's Calculus of Communicating Systems (CCS) with static and dynamic priority as well as with notions of global and local pre- emption. In each case the operational semantics of CCS is modified appropriately, behavioral theories based on strong and weak bisimulation are given, and related approaches for different process-algebraic settings are discussed.

Elastic theory of origami-based metamaterials

NASA Astrophysics Data System (ADS)

Brunck, V.; Lechenault, F.; Reid, A.; Adda-Bedia, M.

2016-03-01

Origami offers the possibility for new metamaterials whose overall mechanical properties can be programed by acting locally on each crease. Starting from a thin plate and having knowledge about the properties of the material and the folding procedure, one would like to determine the shape taken by the structure at rest and its mechanical response. In this article, we introduce a vector deformation field acting on the imprinted network of creases that allows us to express the geometrical constraints of rigid origami structures in a simple and systematic way. This formalism is then used to write a general covariant expression of the elastic energy of n -creases meeting at a single vertex. Computations of the equilibrium states are then carried out explicitly in two special cases: the generalized waterbomb base and the Miura-Ori. For the waterbomb, we show a generic bistability for any number of creases. For the Miura folding, however, we uncover a phase transition from monostable to bistable states that explains the efficient deployability of this structure for a given range of geometrical and mechanical parameters. Moreover, the analysis shows that geometric frustration induces residual stresses in origami structures that should be taken into account in determining their mechanical response. This formalism can be extended to a general crease network, ordered or otherwise, and so opens new perspectives for the mechanics and the physics of origami-based metamaterials.

Modified subaperture tool influence functions of a flat-pitch polisher with reverse-calculated material removal rate.

PubMed

Dong, Zhichao; Cheng, Haobo; Tam, Hon-Yuen

2014-04-10

Numerical simulation of subaperture tool influence functions (TIF) is widely known as a critical procedure in computer-controlled optical surfacing. However, it may lack practicability in engineering because the emulation TIF (e-TIF) has some discrepancy with the practical TIF (p-TIF), and the removal rate could not be predicted by simulations. Prior to the polishing of a formal workpiece, opticians have to conduct TIF spot experiments on another sample to confirm the p-TIF with a quantitative removal rate, which is difficult and time-consuming for sequential polishing runs with different tools. This work is dedicated to applying these e-TIFs into practical engineering by making improvements from two aspects: (1) modifies the pressure distribution model of a flat-pitch polisher by finite element analysis and least square fitting methods to make the removal shape of e-TIFs closer to p-TIFs (less than 5% relative deviation validated by experiments); (2) predicts the removal rate of e-TIFs by reverse calculating the material removal volume of a pre-polishing run to the formal workpiece (relative deviations of peak and volume removal rate were validated to be less than 5%). This can omit TIF spot experiments for the particular flat-pitch tool employed and promote the direct usage of e-TIFs in the optimization of a dwell time map, which can largely save on cost and increase fabrication efficiency.

Water Planetary and Cometary Atmospheres: H2O/HDO Transmittance and Fluorescence Models

NASA Technical Reports Server (NTRS)

Villanueva, G. L.; Mumma, M. J.; Bonev, B. P.; Novak, R. E.; Barber, R. J.; DiSanti, M. A.

2012-01-01

We developed a modern methodology to retrieve water (H2O) and deuterated water (HDO) in planetary and cometary atmospheres, and constructed an accurate spectral database that combines theoretical and empirical results. Based on a greatly expanded set of spectroscopic parameters, we built a full non-resonance cascade fluorescence model and computed fluorescence efficiencies for H2O (500 million lines) and HDO (700 million lines). The new line list was also integrated into an advanced terrestrial radiative transfer code (LBLRTM) and adapted to the CO2 rich atmosphere of Mars, for which we adopted the complex Robert-Bonamy formalism for line shapes. We then retrieved water and D/H in the atmospheres of Mars, comet C/2007 WI, and Earth by applying the new formalism to spectra obtained with the high-resolution spectrograph NIRSPEC/Keck II atop Mauna Kea (Hawaii). The new model accurately describes the complex morphology of the water bands and greatly increases the accuracy of the retrieved abundances (and the D/H ratio in water) with respect to previously available models. The new model provides improved agreement of predicted and measured intensities for many H2O lines already identified in comets, and it identifies several unassigned cometary emission lines as new emission lines of H2O. The improved spectral accuracy permits retrieval of more accurate rotational temperatures and production rates for cometary water.

Massively parallel and linear-scaling algorithm for second-order Møller-Plesset perturbation theory applied to the study of supramolecular wires

NASA Astrophysics Data System (ADS)

Kjærgaard, Thomas; Baudin, Pablo; Bykov, Dmytro; Eriksen, Janus Juul; Ettenhuber, Patrick; Kristensen, Kasper; Larkin, Jeff; Liakh, Dmitry; Pawłowski, Filip; Vose, Aaron; Wang, Yang Min; Jørgensen, Poul

2017-03-01

We present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide-Expand-Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide-Expand-Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalability of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the "resolution of the identity second-order Møller-Plesset perturbation theory" (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.

A new and trustworthy formalism to compute entropy in quantum systems

NASA Astrophysics Data System (ADS)

Ansari, Mohammad

Entropy is nonlinear in density matrix and as such its evaluation in open quantum system has not been fully understood. Recently a quantum formalism was proposed by Ansari and Nazarov that evaluates entropy using parallel time evolutions of multiple worlds. We can use this formalism to evaluate entropy flow in a photovoltaic cells coupled to thermal reservoirs and cavity modes. Recently we studied the full counting statistics of energy transfers in such systems. This rigorously proves a nontrivial correspondence between energy exchanges and entropy changes in quantum systems, which only in systems without entanglement can be simplified to the textbook second law of thermodynamics. We evaluate the flow of entropy using this formalism. In the presence of entanglement, however, interestingly much less information is exchanged than what we expected. This increases the upper limit capacity for information transfer and its conversion to energy for next generation devices in mesoscopic physics.

Comparison of the iterated equation of motion approach and the density matrix formalism for the quantum Rabi model

NASA Astrophysics Data System (ADS)

Kalthoff, Mona; Keim, Frederik; Krull, Holger; Uhrig, Götz S.

2017-05-01

The density matrix formalism and the equation of motion approach are two semi-analytical methods that can be used to compute the non-equilibrium dynamics of correlated systems. While for a bilinear Hamiltonian both formalisms yield the exact result, for any non-bilinear Hamiltonian a truncation is necessary. Due to the fact that the commonly used truncation schemes differ for these two methods, the accuracy of the obtained results depends significantly on the chosen approach. In this paper, both formalisms are applied to the quantum Rabi model. This allows us to compare the approximate results and the exact dynamics of the system and enables us to discuss the accuracy of the approximations as well as the advantages and the disadvantages of both methods. It is shown to which extent the results fulfill physical requirements for the observables and which properties of the methods lead to unphysical results.

Bridging the gap between formal and experience-based knowledge for context-aware laparoscopy.

PubMed

Katić, Darko; Schuck, Jürgen; Wekerle, Anna-Laura; Kenngott, Hannes; Müller-Stich, Beat Peter; Dillmann, Rüdiger; Speidel, Stefanie

2016-06-01

Computer assistance is increasingly common in surgery. However, the amount of information is bound to overload processing abilities of surgeons. We propose methods to recognize the current phase of a surgery for context-aware information filtering. The purpose is to select the most suitable subset of information for surgical situations which require special assistance. We combine formal knowledge, represented by an ontology, and experience-based knowledge, represented by training samples, to recognize phases. For this purpose, we have developed two different methods. Firstly, we use formal knowledge about possible phase transitions to create a composition of random forests. Secondly, we propose a method based on cultural optimization to infer formal rules from experience to recognize phases. The proposed methods are compared with a purely formal knowledge-based approach using rules and a purely experience-based one using regular random forests. The comparative evaluation on laparoscopic pancreas resections and adrenalectomies employs a consistent set of quality criteria on clean and noisy input. The rule-based approaches proved best with noisefree data. The random forest-based ones were more robust in the presence of noise. Formal and experience-based knowledge can be successfully combined for robust phase recognition.

The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.

PubMed

Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; Heinecke, A; Bungartz, H-J; Lederer, H

2014-05-28

Obtaining the eigenvalues and eigenvectors of large matrices is a key problem in electronic structure theory and many other areas of computational science. The computational effort formally scales as O(N(3)) with the size of the investigated problem, N (e.g. the electron count in electronic structure theory), and thus often defines the system size limit that practical calculations cannot overcome. In many cases, more than just a small fraction of the possible eigenvalue/eigenvector pairs is needed, so that iterative solution strategies that focus only on a few eigenvalues become ineffective. Likewise, it is not always desirable or practical to circumvent the eigenvalue solution entirely. We here review some current developments regarding dense eigenvalue solvers and then focus on the Eigenvalue soLvers for Petascale Applications (ELPA) library, which facilitates the efficient algebraic solution of symmetric and Hermitian eigenvalue problems for dense matrices that have real-valued and complex-valued matrix entries, respectively, on parallel computer platforms. ELPA addresses standard as well as generalized eigenvalue problems, relying on the well documented matrix layout of the Scalable Linear Algebra PACKage (ScaLAPACK) library but replacing all actual parallel solution steps with subroutines of its own. For these steps, ELPA significantly outperforms the corresponding ScaLAPACK routines and proprietary libraries that implement the ScaLAPACK interface (e.g. Intel's MKL). The most time-critical step is the reduction of the matrix to tridiagonal form and the corresponding backtransformation of the eigenvectors. ELPA offers both a one-step tridiagonalization (successive Householder transformations) and a two-step transformation that is more efficient especially towards larger matrices and larger numbers of CPU cores. ELPA is based on the MPI standard, with an early hybrid MPI-OpenMPI implementation available as well. Scalability beyond 10,000 CPU cores for problem sizes arising in the field of electronic structure theory is demonstrated for current high-performance computer architectures such as Cray or Intel/Infiniband. For a matrix of dimension 260,000, scalability up to 295,000 CPU cores has been shown on BlueGene/P.

A call for formal telemedicine training during stroke fellowship

PubMed Central

Jia, Judy; Gildersleeve, Kasey; Ankrom, Christy; Cai, Chunyan; Rahbar, Mohammad; Savitz, Sean I.; Wu, Tzu-Ching

2016-01-01

During the 20 years since US Food and Drug Administration approval of IV tissue plasminogen activator for acute ischemic stroke, vascular neurology consultation via telemedicine has contributed to an increased frequency of IV tissue plasminogen activator administration and broadened geographic access to the drug. Nevertheless, a growing demand for acute stroke coverage persists, with the greatest disparity found in rural communities underserved by neurologists. To provide efficient and consistent acute care, formal training in telemedicine during neurovascular fellowship is warranted. Herein, we describe our experiences incorporating telestroke into the vascular neurology fellowship curriculum and propose recommendations on integrating formal telemedicine training into the Accreditation Council for Graduate Medical Education vascular neurology fellowship. PMID:27016522

A call for formal telemedicine training during stroke fellowship.

PubMed

Jagolino, Amanda L; Jia, Judy; Gildersleeve, Kasey; Ankrom, Christy; Cai, Chunyan; Rahbar, Mohammad; Savitz, Sean I; Wu, Tzu-Ching

2016-05-10

During the 20 years since US Food and Drug Administration approval of IV tissue plasminogen activator for acute ischemic stroke, vascular neurology consultation via telemedicine has contributed to an increased frequency of IV tissue plasminogen activator administration and broadened geographic access to the drug. Nevertheless, a growing demand for acute stroke coverage persists, with the greatest disparity found in rural communities underserved by neurologists. To provide efficient and consistent acute care, formal training in telemedicine during neurovascular fellowship is warranted. Herein, we describe our experiences incorporating telestroke into the vascular neurology fellowship curriculum and propose recommendations on integrating formal telemedicine training into the Accreditation Council for Graduate Medical Education vascular neurology fellowship. © 2016 American Academy of Neurology.

SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Yang; Sivalingam, Kantharuban; Neese, Frank, E-mail: Frank.Neese@cec.mpg.de

2016-03-07

Multi-reference (MR) electronic structure methods, such as MR configuration interaction or MR perturbation theory, can provide reliable energies and properties for many molecular phenomena like bond breaking, excited states, transition states or magnetic properties of transition metal complexes and clusters. However, owing to their inherent complexity, most MR methods are still too computationally expensive for large systems. Therefore the development of more computationally attractive MR approaches is necessary to enable routine application for large-scale chemical systems. Among the state-of-the-art MR methods, second-order N-electron valence state perturbation theory (NEVPT2) is an efficient, size-consistent, and intruder-state-free method. However, there are still twomore » important bottlenecks in practical applications of NEVPT2 to large systems: (a) the high computational cost of NEVPT2 for large molecules, even with moderate active spaces and (b) the prohibitive cost for treating large active spaces. In this work, we address problem (a) by developing a linear scaling “partially contracted” NEVPT2 method. This development uses the idea of domain-based local pair natural orbitals (DLPNOs) to form a highly efficient algorithm. As shown previously in the framework of single-reference methods, the DLPNO concept leads to an enormous reduction in computational effort while at the same time providing high accuracy (approaching 99.9% of the correlation energy), robustness, and black-box character. In the DLPNO approach, the virtual space is spanned by pair natural orbitals that are expanded in terms of projected atomic orbitals in large orbital domains, while the inactive space is spanned by localized orbitals. The active orbitals are left untouched. Our implementation features a highly efficient “electron pair prescreening” that skips the negligible inactive pairs. The surviving pairs are treated using the partially contracted NEVPT2 formalism. A detailed comparison between the partial and strong contraction schemes is made, with conclusions that discourage the strong contraction scheme as a basis for local correlation methods due to its non-invariance with respect to rotations in the inactive and external subspaces. A minimal set of conservatively chosen truncation thresholds controls the accuracy of the method. With the default thresholds, about 99.9% of the canonical partially contracted NEVPT2 correlation energy is recovered while the crossover of the computational cost with the already very efficient canonical method occurs reasonably early; in linear chain type compounds at a chain length of around 80 atoms. Calculations are reported for systems with more than 300 atoms and 5400 basis functions.« less

Finding the best resolution for the Kingman-Tajima coalescent: theory and applications.

PubMed

Sainudiin, Raazesh; Stadler, Tanja; Véber, Amandine

2015-05-01

Many summary statistics currently used in population genetics and in phylogenetics depend only on a rather coarse resolution of the underlying tree (the number of extant lineages, for example). Hence, for computational purposes, working directly on these resolutions appears to be much more efficient. However, this approach seems to have been overlooked in the past. In this paper, we describe six different resolutions of the Kingman-Tajima coalescent together with the corresponding Markov chains, which are essential for inference methods. Two of the resolutions are the well-known n-coalescent and the lineage death process due to Kingman. Two other resolutions were mentioned by Kingman and Tajima, but never explicitly formalized. Another two resolutions are novel, and complete the picture of a multi-resolution coalescent. For all of them, we provide the forward and backward transition probabilities, the probability of visiting a given state as well as the probability of a given realization of the full Markov chain. We also provide a description of the state-space that highlights the computational gain obtained by working with lower-resolution objects. Finally, we give several examples of summary statistics that depend on a coarser resolution of Kingman's coalescent, on which simulations are usually based.

Multipolar electrostatics.

PubMed

Cardamone, Salvatore; Hughes, Timothy J; Popelier, Paul L A

2014-06-14

Atomistic simulation of chemical systems is currently limited by the elementary description of electrostatics that atomic point-charges offer. Unfortunately, a model of one point-charge for each atom fails to capture the anisotropic nature of electronic features such as lone pairs or π-systems. Higher order electrostatic terms, such as those offered by a multipole moment expansion, naturally recover these important electronic features. The question remains as to why such a description has not yet been widely adopted by popular molecular mechanics force fields. There are two widely-held misconceptions about the more rigorous formalism of multipolar electrostatics: (1) Accuracy: the implementation of multipole moments, compared to point-charges, offers little to no advantage in terms of an accurate representation of a system's energetics, structure and dynamics. (2) Efficiency: atomistic simulation using multipole moments is computationally prohibitive compared to simulation using point-charges. Whilst the second of these may have found some basis when computational power was a limiting factor, the first has no theoretical grounding. In the current work, we disprove the two statements above and systematically demonstrate that multipole moments are not discredited by either. We hope that this perspective will help in catalysing the transition to more realistic electrostatic modelling, to be adopted by popular molecular simulation software.

Efficient Radiative Transfer for Dynamically Evolving Stratified Atmospheres

NASA Astrophysics Data System (ADS)

Judge, Philip G.

2017-12-01

We present a fast multi-level and multi-atom non-local thermodynamic equilibrium radiative transfer method for dynamically evolving stratified atmospheres, such as the solar atmosphere. The preconditioning method of Rybicki & Hummer (RH92) is adopted. But, pressed for the need of speed and stability, a “second-order escape probability” scheme is implemented within the framework of the RH92 method, in which frequency- and angle-integrals are carried out analytically. While minimizing the computational work needed, this comes at the expense of numerical accuracy. The iteration scheme is local, the formal solutions for the intensities are the only non-local component. At present the methods have been coded for vertical transport, applicable to atmospheres that are highly stratified. The probabilistic method seems adequately fast, stable, and sufficiently accurate for exploring dynamical interactions between the evolving MHD atmosphere and radiation using current computer hardware. Current 2D and 3D dynamics codes do not include this interaction as consistently as the current method does. The solutions generated may ultimately serve as initial conditions for dynamical calculations including full 3D radiative transfer. The National Center for Atmospheric Research is sponsored by the National Science Foundation.

Using Formal Grammars to Predict I/O Behaviors in HPC: The Omnisc'IO Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dorier, Matthieu; Ibrahim, Shadi; Antoniu, Gabriel

2016-08-01

The increasing gap between the computation performance of post-petascale machines and the performance of their I/O subsystem has motivated many I/O optimizations including prefetching, caching, and scheduling. In order to further improve these techniques, modeling and predicting spatial and temporal I/O patterns of HPC applications as they run has become crucial. In this paper we present Omnisc'IO, an approach that builds a grammar-based model of the I/O behavior of HPC applications and uses it to predict when future I/O operations will occur, and where and how much data will be accessed. To infer grammars, Omnisc'IO is based on StarSequitur, amore » novel algorithm extending Nevill-Manning's Sequitur algorithm. Omnisc'IO is transparently integrated into the POSIX and MPI I/O stacks and does not require any modification in applications or higher-level I/O libraries. It works without any prior knowledge of the application and converges to accurate predictions of any N future I/O operations within a couple of iterations. Its implementation is efficient in both computation time and memory footprint.« less

The next generation of similarity measures that fully explore the semantics in biomedical ontologies.

PubMed

Couto, Francisco M; Pinto, H Sofia

2013-10-01

There is a prominent trend to augment and improve the formality of biomedical ontologies. For example, this is shown by the current effort on adding description logic axioms, such as disjointness. One of the key ontology applications that can take advantage of this effort is the conceptual (functional) similarity measurement. The presence of description logic axioms in biomedical ontologies make the current structural or extensional approaches weaker and further away from providing sound semantics-based similarity measures. Although beneficial in small ontologies, the exploration of description logic axioms by semantics-based similarity measures is computational expensive. This limitation is critical for biomedical ontologies that normally contain thousands of concepts. Thus in the process of gaining their rightful place, biomedical functional similarity measures have to take the journey of finding how this rich and powerful knowledge can be fully explored while keeping feasible computational costs. This manuscript aims at promoting and guiding the development of compelling tools that deliver what the biomedical community will require in a near future: a next-generation of biomedical similarity measures that efficiently and fully explore the semantics present in biomedical ontologies.

Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

PubMed

Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

2015-05-08

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

Utilization of information technology in medical education: a questionnaire survey of students in a Malaysian institution.

PubMed

Nurjahan, M I; Lim, T A; Yeong, S W; Foong, A L S; Ware, J

2002-12-01

The objective of this survey was to obtain a self-reported assessment of the use of Information and Communication Technology (ICT) by medical students at the International Medical University, Malaysia. Students' perceived skills and extent of usage of ICT were evaluated using a questionnaire. Chi-square analysis were performed to ascertain the association between variables. Further statistical testing using Chi-square test for trend was done when one of the variables was ordered, and Spearman rank correlation when both variables were ordered. Overall, (98%) of students responded to the questionnaire. Twenty seven students (5.7%) did not use a computer either in the university or at home. Most students surveyed reported adequate skills at word processing (55%), e-mailing (78%) and surfing the internet (67%). The results suggests that in order to increase the level of computer literacy among medical students, positive steps would need to be taken, for example the formal inclusion of ICT instruction in the teaching of undergraduate medicine. This will enhance medical students' ability to acquire, appraise, and use information in order to solve clinical and other problems quickly and efficiently in the course of their studies, and more importantly when they graduate.

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

Level set immersed boundary method for gas-liquid-solid interactions with phase-change

NASA Astrophysics Data System (ADS)

Dhruv, Akash; Balaras, Elias; Riaz, Amir; Kim, Jungho

2017-11-01

We will discuss an approach to simulate the interaction between two-phase flows with phase changes and stationary/moving structures. In our formulation, the Navier-Stokes and heat advection-diffusion equations are solved on a block-structured grid using adaptive mesh refinement (AMR) along with sharp jump in pressure, velocity and temperature across the interface separating the different phases. The jumps are implemented using a modified Ghost Fluid Method (Lee et al., J. Comput. Physics, 344:381-418, 2017), and the interface is tracked with a level set approach. Phase transition is achieved by calculating mass flux near the interface and extrapolating it to the rest of the domain using a Hamilton-Jacobi equation. Stationary/moving structures are simulated with an immersed boundary formulation based on moving least squares (Vanella & Balaras, J. Comput. Physics, 228:6617-6628, 2009). A variety of canonical problems involving vaporization, film boiling and nucleate boiling is presented to validate the method and demonstrate the its formal accuracy. The robustness of the solver in complex problems, which are crucial in efficient design of heat transfer mechanisms for various applications, will also be demonstrated. Work supported by NASA, Grant NNX16AQ77G.

Empirically Understanding Can Make Problems Go Away: The Case of the Chinese Room

ERIC Educational Resources Information Center

Overskeid, Geir

2005-01-01

The many authors debating whether computers can understand often fail to clarify what understanding is, and no agreement exists on this important issue. In his Chinese room argument, Searle (1980) claims that computers running formal programs can never understand. I discuss Searle's claim based on a definition of understanding that is empirical,…

Computation-Friendly Shape Grammars with Application to Determining the Interior Layout of Buildings from Image Data

ERIC Educational Resources Information Center

Yue, Kui

2009-01-01

A shape grammar is a formalism that has been widely applied, in many different fields, to analyzing designs. Computer implementation of a shape grammar interpreter is vital to both research and application. However, implementing a shape grammar interpreter is hard, especially for parametric shapes defined by open terms. This dissertation…

A State Cyber Hub Operations Framework

DTIC Science & Technology

2016-06-01

to communicate and sense or interact with their internal states or the external environment. Machine Learning: A type of artificial intelligence that... artificial intelligence , and computational linguistics concerned with the interactions between computers and human (natural) languages. Patching: A piece...formalizing a proof of concept for cyber initiatives and developed frameworks for operationalizing the data and intelligence produced across state

Development of a Formal Theory of Agent-Based Computing for System Evaluation and System-Design Guidance

DTIC Science & Technology

2004-06-01

Department of EE and Computer Science University of Michigan Ann Arbor, MI 48109, USA pollackm@eecs.umich.edu Sujata Banerjeez Info. Sci. & Telecom. Dept...University of Pittsburgh Pittsburgh, PA 15260, USA sujata @tele.pitt.edu Abstract An important aspect of Business to Business E- Commerce is the agile

The Impact of Computer Supported Collaborative Learning on Internship Outcomes of Pharmacy Students

ERIC Educational Resources Information Center

Timmers, S.; Valcke, M.; de Mil, K.; Baeyens, W. R. G.

2008-01-01

This article focuses on an evaluation of the impact of an innovative instructional design of internships in view of a new integrated pharmaceutical curriculum. A key innovative element was the implementation of a computer-supported collaborative learning environment. Students were, as part of their formal curriculum, expected to work in a…

Using Rule-Based Computer Programming to Unify Communication Rules Research.

ERIC Educational Resources Information Center

Sanford, David L.; Roach, J. W.

This paper proposes the use of a rule-based computer programming language as a standard for the expression of rules, arguing that the adoption of a standard would enable researchers to communicate about rules in a consistent and significant way. Focusing on the formal equivalence of artificial intelligence (AI) programming to different types of…

Young Children's Skill in Using a Mouse to Control a Graphical Computer Interface.

ERIC Educational Resources Information Center

Crook, Charles

1992-01-01

Describes a study that investigated the performance of preschoolers and children in the first three years of formal education on tasks that involved skills using a mouse-based control of a graphical computer interface. The children's performance is compared with that of novice adult users and expert users. (five references) (LRW)

Type Theory, Computation and Interactive Theorem Proving

DTIC Science & Technology

2015-09-01

postdoc Cody Roux, to develop new methods of verifying real-valued inequalities automatically. They developed a prototype implementation in Python [8] (an...he has developed new heuristic, geometric methods of verifying real-valued inequalities. A python -based implementation has performed surprisingly...express complex mathematical and computational assertions. In this project, Avigad and Harper developed type-theoretic algorithms and formalisms that

The Roles of Internal Representation and Processing in Problem Solving Involving Insight: A Computational Complexity Perspective

ERIC Educational Resources Information Center

Wareham, Todd

2017-01-01

In human problem solving, there is a wide variation between individuals in problem solution time and success rate, regardless of whether or not this problem solving involves insight. In this paper, we apply computational and parameterized analysis to a plausible formalization of extended representation change theory (eRCT), an integration of…

Counterfactuals and Causal Models: Introduction to the Special Issue

ERIC Educational Resources Information Center

Sloman, Steven A.

2013-01-01

Judea Pearl won the 2010 Rumelhart Prize in computational cognitive science due to his seminal contributions to the development of Bayes nets and causal Bayes nets, frameworks that are central to multiple domains of the computational study of mind. At the heart of the causal Bayes nets formalism is the notion of a counterfactual, a representation…

Efficient Time Propagation Technique for MAS NMR Simulation: Application to Quadrupolar Nuclei.

PubMed

Charpentier; Fermon; Virlet

1998-06-01

The quantum mechanical Floquet theory is investigated in order to derive an efficient way of performing numerical calculations of the dynamics of nuclear spin systems in MAS NMR experiments. Here, we take advantage of time domain integration of the quantum evolution over one period as proposed by Eden et al. (1). But a full investigation of the propagator U(t, t0), and especially its dependence with respect to t and t0 within a formalized approach, leads to further simplifications and to a substantial reduction in computation time when performing powder averaging for any complex sequence. Such an approximation is suitable for quadrupolar nuclei (I > 1/2) and can be applied to the simulation of the RIACT (rotational induced adiabatic coherence transfer) phenomenon that occurs under special experimental conditions in spin locking experiments (2-4). The present method is also compared to the usual infinite dimensional Floquet space approach (5, 6), which is shown to be rather inefficient. As far as we know, it has never been reported for quadrupolar nuclei with I >/= 3/2 in spin locking experiments. The method can also be easily extended to other areas of spectroscopy. Copyright 1998 Academic Press.

Improving Biometric-Based Authentication Schemes with Smart Card Revocation/Reissue for Wireless Sensor Networks.

PubMed

Moon, Jongho; Lee, Donghoon; Lee, Youngsook; Won, Dongho

2017-04-25

User authentication in wireless sensor networks is more difficult than in traditional networks owing to sensor network characteristics such as unreliable communication, limited resources, and unattended operation. For these reasons, various authentication schemes have been proposed to provide secure and efficient communication. In 2016, Park et al. proposed a secure biometric-based authentication scheme with smart card revocation/reissue for wireless sensor networks. However, we found that their scheme was still insecure against impersonation attack, and had a problem in the smart card revocation/reissue phase. In this paper, we show how an adversary can impersonate a legitimate user or sensor node, illegal smart card revocation/reissue and prove that Park et al.'s scheme fails to provide revocation/reissue. In addition, we propose an enhanced scheme that provides efficiency, as well as anonymity and security. Finally, we provide security and performance analysis between previous schemes and the proposed scheme, and provide formal analysis based on the random oracle model. The results prove that the proposed scheme can solve the weaknesses of impersonation attack and other security flaws in the security analysis section. Furthermore, performance analysis shows that the computational cost is lower than the previous scheme.

Improving Biometric-Based Authentication Schemes with Smart Card Revocation/Reissue for Wireless Sensor Networks

PubMed Central

Moon, Jongho; Lee, Donghoon; Lee, Youngsook; Won, Dongho

2017-01-01

User authentication in wireless sensor networks is more difficult than in traditional networks owing to sensor network characteristics such as unreliable communication, limited resources, and unattended operation. For these reasons, various authentication schemes have been proposed to provide secure and efficient communication. In 2016, Park et al. proposed a secure biometric-based authentication scheme with smart card revocation/reissue for wireless sensor networks. However, we found that their scheme was still insecure against impersonation attack, and had a problem in the smart card revocation/reissue phase. In this paper, we show how an adversary can impersonate a legitimate user or sensor node, illegal smart card revocation/reissue and prove that Park et al.’s scheme fails to provide revocation/reissue. In addition, we propose an enhanced scheme that provides efficiency, as well as anonymity and security. Finally, we provide security and performance analysis between previous schemes and the proposed scheme, and provide formal analysis based on the random oracle model. The results prove that the proposed scheme can solve the weaknesses of impersonation attack and other security flaws in the security analysis section. Furthermore, performance analysis shows that the computational cost is lower than the previous scheme. PMID:28441331

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chevalier, Michael W., E-mail: Michael.Chevalier@ucsf.edu; El-Samad, Hana, E-mail: Hana.El-Samad@ucsf.edu

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation timesmore » of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.« less